A Three-Pound Monkey Brain

PhyloPic Is Back!

2012-01-26T12:30:00.000-08:00

Last year, I launched a project called PhyloPic. The goal of this project was to create an open database of freely reuseable silhouette images of organisms. Furthermore, it featured a phylogenetic taxonomy so that, if a taxon wasn't illustrated, an approximation could be found.

Pleurosiga minima

This image is in the public domain.

I launched it as a "public alpha", meaning that it wasn't complete and still had some bugs. The year turned out to be very busy for me: an awful thing happened, and a wonderful thing happened. And I didn't really have time to push PhyloPic to the next level.

Unfortunately, I hadn't built it well enough in the first place. The architecture was not optimized, and the site became extremely slow and buggy. I took it offline, hoping to release a new version in short order, but it turned out to need a lot more work than I first thought.

Happily, it is now ready again!

PHYLOPIC
public alpha 2.0

What's Changed?

Aside from general optimization, here's a summary of major changes:

Vector files (SVG) are now supported! Unlike raster bitmaps, vector images can be scaled to any size without loss of resolution. Most silhouettes are still only available as raster bitmaps (PNG format), but a few can also be downloaded as SVG files.
The submission process was completely rewritten. It now only uses Flash for opening and preparing the files; everything else is HTML/Ajax. (And I'll probably phase out the Flash component in the future, once HTML5 matures enough that it can reliably take that task over.)

A major new feature in the submission process is Social Network Login. You can now log in via Facebook, Google, Twitter, and Yahoo! This lowers the barrier to submission and will hopefully encourage more people to submit silhouettes.

Taxon and search pages load progressively. The first time anyone goes to a taxon page or performs a new search, PhyloPic grabs the appropriate data from uBio. (Subsequently the data is cached.) This can take a really long time, if there is a lot of data. (In fact, this was the main reason I shut the site down before.) Now the page will load instantaneously then try to update the data, if necessary. And taxon pages will show status updates as data is pulled.
Image search is enhanced. Now you can search for related taxa in addition to supertaxa and subtaxa.
There are no developer APIs. (What, you thought all the changes were positive?) I have been working on updated APIs, but it's not quite ready for primetime yet. I didn't want it to delay the relaunch, so it'll hopefully be bundled into public alpha 2.1.
URLs are different. (And a bit uglier, to be honest, but it's for the best in the long run.) Don't expect all the old ones to work, but do expect the new ones to work from here on out.

Triadobatrachus massinoti
Image by Nobu Tamura.

What's Ahead?

I have a lot of plans for the future of PhyloPic. You can keep abreast of the latest plans here. (Now we'll see if I have the time to finish them....)

In Anticipation: The Evolution of the Raven, in Silhouettes

2012-01-16T11:24:00.000-08:00

Any day now there will be a relaunch of a certain project I launched last year. (Just working through some technical details.) In anticipation of that, here's the evolutionary history of the Common Raven (Corvus corax), illustrated with silhouettes:

click to enlarge

A Proposal to Amend the PhyloCode

2012-01-16T10:29:00.000-08:00

The draft PhyloCode has been in a pretty stable form for a while. But recently, there has been a proposal to drastically change how it handles species. You can read the proposal here:

Proposal for Changes to the PhyloCode, with Respect to Species

The first paragraph:

The overarching goal of this proposal is to remove all mention of "species" from the PhyloCode. Detailed justifications for this goal are given in a supporting paper (Cellinese, Baum, and Mishler, in review); here we present a summary of the main arguments, along with specific proposals for change.

Before I weigh in on this, I'm curious as to what other people think. Please comment below, or send comments to David Marjanović, the Secretary of the Committee on Phylogenetic Nomenclature.

UPDATE:
If anyone would like a Microsoft Word version of this document, just ask.

Season's Greetings

2011-12-19T12:26:00.000-08:00

If you look at last year's Yule greeting, you'll note that we have lost a few at the Keesey-Havens household. The mighty Monstro now swims alone in his aquarium, his fellow goldfish Cousteau and his pet minnow Fido having passed away. Young Half-Pint died rather unexpectedly, leaving his chinchilla family in mourning (father Bernard, mother Lillian, sister Hyzenthlay). (I might be posting on him again, though....)

The family tree, as of Yuletide 2010.

But, in brighter news, we have a new addition! Lucy, the little human pictured above with our Christmas tree. And so it comes time to sadly trim but joyfully decorate our household's phylogenetic tree:

Updated for 2011.

EDIT: Whoops, misspelled "silvestris" in the 2011 version.

Guest Post: Looks, Personality, and Attraction

2011-12-04T22:45:00.001-08:00

Apropos of my recently having managed to pass on my genes to a new generation, here is a guest post by Elaine Hirsch on the topic of sexual selection. See also one of my favorite Onion articles ever, "That Female Looks Capable of Passing on my Genetic Material".

Looks, Personality, and Attraction

For centuries people have pondered the mystery of attraction. Countless people have stared at happy couples and wondered, "What in the world does she see in him?" or, "Why would he stay with her?" Obviously the factors that contribute to attraction, love, and commitment are complex and often make no sense to those outside a relationship. Somehow, people still manage to get by without a master's degree in romantic strategy.

Over the years researchers have attempted to figure out scientifically and biologically why people fall in love, what features attract men, what features attract women, and how those factors all work together to proliferate the human race. Through various studies, scientists are learning a little more all the time about the biological factors that contribute to the attraction between men and women.

Oh mama!
Image by Nancy Ellis

Some scientific studies indicate the way men are attracted to women is tied to evolutionary urges to reproduce with women who are most fertile. Fertile women's physical traits subconsciously indicate to men that those woman will give their offspring the best chances of survival. Scientists use this theory to explain why men are typically attracted to the classic "hourglass" shape of the female body.

Additionally, men tend to find feminine facial features extremely important in choosing mates. Scientists have discovered that women with the most feminine faces have the highest estrogen levels, implying they will be the most fertile.

Sexy!
Image unattributed

While men are more visually driven in attraction, women seem to consider many other factors in addition to the physical. Personality, ambition, and intelligence have been found to be significant factors in female preferences. A particular leaning is evidenced toward men who demonstrate ability to be good fathers and provide long-term stability and protection.

Economic and social compatibility are also factors men and women both consider for long-term relationships. Scientists have also found altruistic women more frequently pair with altruistic men. Scientists theorize altruism evolved as human children developed longer periods of neediness in their development. Men and women who are more altruistic are more likely to support and care for their offspring and their mates during this long period.

HAWT.
Image from first edition
of Harper's Bazaar

Complicating the question further, many of our opinions of beauty and attractiveness can be culturally influenced by family and society. Consider the medieval Chinese preference for tiny feet or the 19th-century wasp waist styles with huge bustles. In modern times, such fads seem ridiculous, but in their own times and places these standards of beauty were taken as true measures of attractiveness.

Despite all the science of brain chemistry and evolutionary development, much of attraction and what people consider beauty still remains a mystery. Purely scientific research may never explain the biological basis of long-term love and commitment, even as our understanding of the adaptive drives behind our behavior improves.

What Is and Is Not a Stem Group

2011-11-16T14:12:00.001-08:00

In recent years, I've noticed a trend: the prefix "stem-" is becoming more and more popular for stem groups. For those who don't know what a "stem group" is:

A crown group is the last common ancestor or two or more extant taxa, and all descendants thereof.
A total group is the first ancestor of a crown group that is not also ancestral to any other extant taxa, and all descendants thereof.
A stem group is a total group minus its crown group. (Which means, of course, that a total group is a crown group plus its stem group.)

Or, to put it more simply, an extinct organism is a stem-X if it does not belong to X, but it shares more ancestry with X than with any extant organisms outside of X. Real-life examples:

Velociraptor mongoliensis, a stem-avian.
Illustration by myself (Mike Keesey).

Stem-mammals: Dimetrodon, Moschops, Cynognathus, Castorocauda.
Stem-avians: Marasuchus, Psittacosaurus, Plateosaurus, Tyrannosaurus, Velociraptor, Archaeopteryx, Hesperornis.
Stem-humans: Ardipithecus(?), Australopithecus, Paranthropus, Homo habilis, Homo erectus.
Stem-cetaceans: Ambulocetus, Pakicetus, Maiacetus, Basilosaurus.
Stem-felines: Proailurus, Smilodon.
~~Stem-~~~~pterygotes~~ Stem-neopterans: Dictyoneura, Lithomantis.

This is a great convention. It's consistently useful in every area of the Tree of Life. It's concise. It communicates instantly the general area we're talking about, and sets us up to make proper phylogenetic inferences (when the fossil data is lacking).

So I'm glad this trend is becoming more popular. Unfortunately, I've also noticed another trend: rampant misuse!

Case in point:

CABREIRA & al. (2011). New stem-sauropodomorph (Dinosauria, Saurischia) from the Triassic of Brazil. Naturwissenschaften (online early). doi:10.1007/s00114-011-0858-0

This looks to be an excellent paper on a very interesting find, so it's unfortunate that there's a glaring error in the title, but there it is: "stem-sauropodomorph". There is no such thing, because Sauropodomorpha is not a crown group. It doesn't even include a crown group (sadly—it'd be very cool if it did). Rather, all sauropodomorphs are part of the avian stem group.

Panphagia protos, a stem-avian
(not a "stem-sauropodomorph").
Photo by Eva K.
Used under the GFDL.

I see a lot of people making this mistake. I think what's happening is that they're using the basic concept of a stem group, but replacing "total group" with "some large clade" and "crown group" with "an interesting subclade". In this case, Sauropodomorpha is "some large clade" and Sauropoda is "an interesting subclade". (And in that case, the usage is even wronger, because it should at least be "stem-sauropod".)

This misuse is unfortunate because it is subjective, while the proper usage is objective. One could make the argument that the real "interesting subclade" of Sauropodomorpha is Titanosauria, or Neosauropoda, or whatever, and then the terminology would mean something very different. By contrast, e.g., "stem-crocodylian" very clearly indicates a particular paraphyletic group.

So, please, people, use the "stem-" prefix, but use it correctly!

Lucy Gwyn Havens

2011-11-04T11:47:00.000-07:00

Last Saturday our first child was born: a daughter, Lucy Gwyn Havens.

We've made our own contribution to the phylogenetic tree!

Lucy.—There are many famous Lucys. Here's one relevant to the blog:

And of course, that one is named after this one:

Lucy in the Sky with Diamonds
by Julian Lennon

Gwyn.—Gwyn is an old Welsh family name on my side. More recently it was spelled "Guinn", but we decided to use the older spelling.

Havens.—You'll notice her surname is from her mother, not me. We decided early on that boys would be Keeseys and girls would be Havenses. If this becomes a tradition, it would link patrilineal names to the Y chromosome (something the dominant English system already does) and matrilineal names to the mitochondrial chromosome (a feature sorely lacking in the English system).

We love you, li'l Lulu!

Human Clades: A Look at a Complex Phylogeny

2011-10-11T07:49:00.000-07:00

Most methods of phylogenetic analysis deal with simple trees. In these phylogenies, every taxonomic unit has a single direct ancestor (or "parent"). But we know that phylogeny is often more complex than this. Our own species is an excellent example—while we are all primarily descended from one population in Africa, different peoples around the globe have inherited smaller percentages of ancestry from preexisting populations.

A new study by Reich & al. looks in some detail at peoples who have inherited DNA from the Denisovans, a fossil group known from Siberia. Ancient DNA has been retrieved from these fossils, although unfortunately the fossils are otherwise too scant to tell us much about what Denisovans looked like (other than "humanlike").

Reich & al. posit a complex phylogeny wherein populations are often descended from multiple ancestral populations. Lets take a look at the clades posited in this study.

Operational Taxonomic Units

Reich & al. used the following nine populations, seven extant and two extinct, as operational taxonomic units.

Yoruba.—An ethnicity from West Africa (Nigeria, Benin, Ghana, etc.)
(Photo by Marc Trip.)

Han.—The most populous Chinese ethnicity.
(Photo by Brian Yap.)

Mamanwa.—One of the "Lumad" ("indigenous") ethnicities of the southern Philippines.
(Photo by Richard Parker.)

Jehai.—One of the Orang Asli ("original people") groups of Malaysia.
Note: this photo is of a woman from a different Orang Asli tribe, the Batik.
(Photo by Wazari Wazir.)

Onge.—A group of Andaman Islanders, from the Bay of Bengal.
(Photo from The Andamanese, by George Weber.)

Australians.—The indigenous ("aboriginal") peoples of Australia.
(Photo by Rusty Stewart.)

Papuans.—The indigenous peoples of the New Guinean highlands.
(Photo owned by the Center for International Forestry Research.)

Neandertals.—An extinct group of robust near-human peoples from West Eurasia.
(Photo by myself, of a sculpture by John Gurche.)

Denisovans.—An extinct group of near-human peoples known from Siberia but thought to have had a wider range.
Note: The photo is of a sculpture of Homo heidelbergensis, thought to be the common ancestor of humans, Neandertals, and Denisovans. Denisovans may not have looked exactly like this.
(Photo by myself, of a sculpture by John Gurche.)

Phylogeny

Reich & al. postulated the simplest phylogeny that could possibly explain their data. (Note that the actuality is likely more complex than this, but it's a good starting point.) More recent groups are to the right, and the thickness of the lines indicates the percentage of DNA contributed from population to population.

My diagram, not theirs. Any inaccuracies are my own.
Free for reuse under Public Domain.

I've added a line for the Denisovans' mitochondrial (motherline) ancestor, even though it's not part of the paper's phylogeny. More on that as we start looking through the various clades.

For looking at the clades I'll use a different diagram that does not reflect percentage of ancestry, but simply shows direct descent as unweighted arcs connecting parent and child taxonomic units.

Phylogeny of human and near-human populations according to Reich & al. 2011.
Created using Names on Nodes.
Free for reuse under Public Domain.

Clades

Technically, every terminal node is itself a clade, at least in the context of the phylogeny. So the first nine clades are the nine operational taxonomic units, each consisting of an ancestor (the taxonomic unit) and all of its descendants (vacuous, as there are none). Now on to the larger clades, starting with the largest.

Mitochondrial DNA Crown Group.—Although most Denisovan DNA shows shared ancestry with Neandertals, exclusive of humans, the mitochondrial DNA tells a different story. Denisovan mtDNA diverged from human-Neandertal mtDNA a very long time ago, perhaps around a million years ago. So we begin with this, the oldest clade of the human total group wherein mtDNA is known for all direct sub-branches.

From the timing, the ancestor of this clade might be Homo antecessor or a similar contemporary. There are two main branches that we know of: one which produced Neandertals, humans, and the nuclear component of Densiovan ancestry, and the other of which produced the mitochondrial component of Denisovan ancestry. Perhaps as Denisovans migrated eastward over Asia they mated with the females of another lineage.

Nuclear DNA Crown Group.—This is the oldest clade represented by nuclear DNA, roughly 400 millennia old. The ancestors of this clade would probably be classified as Homo heidelbergensis. Two major subclades are known: one leading to humans and the other to "archaic" Eurasians (Neandertals and Denisovans).

Strictly speaking, there is an even older nuclear ancestor, since another study indicates that some South and Central Africans inherited some nuclear DNA from an ancestor that split off around 700 millennia ago. But those populations aren't covered by this phylogenetic hypothesis.

Eurasians.—This clade originates from an ancestor around 350 millennia ago. The two major subclades are Neadertals and Denisovans, but it also includes non-African humans, which are partly descended from Neandertals (and, in some cases, Denisovans as well).

Humans.—Humans (in the strict sense) are a crown group that originated in Africa roughly around 200 millennia ago. Some, such as the Yoruba, are descendants of those who stayed in Africa. Those who left Africa, into Eurasia, mixed with the "archaics" already living there.

"Neanderthaloids".—This clade includes Neandertals and their (partial) descendants, the Eurasian humans. (There's no existing name for it so I just made one up.)

Eurasian Humans.—Eurasian humans are mostly descended from early African humans, but have inherited 1–4% of their DNA from Neandertals.

"Denisovoids".—This clade includes Denisovans and their (partial) descendants, the indigenous peoples of Oceania. (As with "Neanderthaloids", there's no existing name for the clade so I just made one up.)

"Denisovoid" Oceanian.—The indigenous peoples of Oceania, not the later Austronesians, Chinese, Europeans, etc. (except insofar as they overlap, e.g., in the Mamanwa). This includes the indigenous peoples of Australinea (Australia + New Guinea), the Philippines (Lumad peoples—Mamanwa, Monobo, etc.), the Lesser Sunda Islands (Alor, Flores, Roti, Timor, etc.), Melanesians (Fijians, etc.), and Polynesians.

All of these peoples are part of other, overlapping human clades as well, but all of them have some percentage of Denisovan ancestry. The highest percentage (~5%) is found in Australinea. Reich & al. postulate that the original admixture level was even higher (~7%), but was diluted by later waves of Australoid and Mongoloid peoples, the former contributing to the ancestry of Australineans and the latter contributing to the ancestry of Lumad Filipinos (such as the Mamanwa).

Australoids.—Australineans share an ancestral component with West Negritos such as Andaman Islanders (including the Onge) and Orang Asli of Malaysia (including the Jehai and Batik). This corresponds fairly well to the old idea of an Australoid race, although the Andamanese are actually a purer representation than Australians, who are roughly half "Denisovoid" Oceanian, so "Andamanoid" would be a better term (oh well). Orang Asli peoples are also part Mongoloid (see below).

Australineans.—This clade originated with the first settlers of New Guinea and Australia, which were joined as one landmass at the time, due to low sea levels. This landmass is variously called Australinea, Meganesia, or Sahul. These peoples are roughly equal parts "Denisovoid" Oceanian and Australoid.

West Negritos.—"Negrito" is general term for the dark-skinned, often diminutive peoples of Southeast Asia and Oceania. They do not really form one group, but the West Negritos, as represented by the Orang Asli (Jehai, Batik, etc.) and the Onge, share an ancestral Australoid component.

Mongoloids.—These peoples originated in East Asia. Reich & al. find two major subclades. One includes the Orang Asli peoples of Malaysia (such as the Jehai and Batik), who are also part Australoid. The other leads to Chinese and Filipino peoples.

"Sinoids".—Traditionally "Sinoid" is a synonym of "Mongoloid", but here I am using it for the subclade of Mongoloids including Chinese and Filipinos. Indigenous Filipinos (Lumad peoples, such as the Mamanwa) are also part "Denisovoid" Oceanian.

Clades with Multi-Unit Cladogens.—This is a clade. One of its possible definitions is branch-based: the clade stemming from the initial ancestor of Australians and Han Chinese which was not also ancestral to [late Siberian] Denisovans. But if you look closely, there's something odd about this clade (my apologies that it's not a bit easier to see). Namely, the "ancestor" of this clade is two taxonomic units! One is the "Neanderthaloid" ancestor and the other is the human ancestor.

But isn't a clade supposed to be "an ancestor and all of its descendants"? Well, as I discussed in my 2007 paper and more recently on Names on Nodes, we need to define exactly what we mean by "ancestor". I define a clade ancestor, or cladogen, as a union of one or more taxonomic units wherein 1) none of the units are ancestral to each other, and 2) there exists at least one other unit which is descended from (or equal to, in case the cladogen is a single unit) all of the units in the cladogen. The union of the ancestral populations of "Neanderthaloids" and humans, respectively, satisfies these conditions. They can be seen as part of a population that does not include the Denisovans, since they share descendants that do not have Denisovan ancestry (including, e.g., the Han, West Negritos, ... and myself!) So, even though they consist of two units in this study, they still comprise a population and can be used as a clade ancestor.

Many Parents, Not One

Studies like this one may seem to some to test the usefulness of phylogenetic nomenclature, since it features clades that overlap. In fact, phylogenetic nomenclature has always allowed for overlapping clades. It is phylogenetic analyses that routinely assume no overlap. In many cases this is useful, but I tend to wonder if it doesn't obscure our vision in a lot of cases. Studies like this one are encouraging to me, since they move toward embracing the fact that Life is not a simple tree.

Soft Tissue Characters Supporting the Great Ape Clades

2011-09-15T13:23:00.000-07:00

In my last post, I took a look at some morphological cladistic analyses of hominoids (apes) and tried to compile list of characters that supported the major clades: great apes, African great apes, and mangani (chimpanzees + humans). Unfortunately the studies I looked at only considered skeletal characters (and one of them only craniodental characters). Fortunately, a reader (Dartian) suggested some studies that look at soft tissue characters. I've just skimmed this paper:

GIBBS, S., COLLARD, M. & WOOD, B. (2002). Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis. Journal of Anatomy 200:3–49. doi:10.1046/j.0021-8782.2001.00001.x

The authors compiled a matrix of 171 soft tissue characters and found strong support for the topology produced by earlier molecular studies (gibbons, (orangutans, (gorillas, (humans, chimpanzees)))). Below, I've compiled lists of character states that unambiguously support the major clades:

Great ape synapomorphies (orangutans and African great apes):

Apical lingual gland present in at least some specimens
Most common pattern of insertion of extensor indicis does not involve digit IV (digit II and possibly III only)
Origin of gluteus minimus is discontinuous or variably continuous
Rectus femoris has two heads in at least some specimens
Articularis genus present in at least some specimens
Ratio of nipple position to horizontal height index of nipple position between 1.0 and 1.8

African great ape synapomorphies (gorillas and mangani):

Conical ﬁliform predominate over cylindrical ﬁliform
Radial head of ﬂexor pollicis brevis originates from ﬂexor retinaculum and trapezium only
Humeroulnar head of ﬂexor digitorum superﬁcialis takes origin from intermuscular septum
Palmaris longus not present in all specimens
Orientation of pronator quadratus moderately or weakly oblique
Flexor pollicis longus originates from anterior radius and interosseous membrane
Slips from extensor digitorum tendon for digit IV to digits III and V
Coracobrachialis origination from intermuscular septum in at least some specimens
Anterior extension of insertion of coracobrachialis present in most specimens
Extensor pollicis brevis origination from ulna and interosseous membrane
Most common pattern of insertion of extensor indicis does not involve digit III (digit II only)
Teres minor insertion extends onto shaft below greater tubercle
Subclavius takes origin on ﬁrst rib only
Extent of clavicular origin of pectoralis major: 1/3 to 1/2 (less than 2/3)
Origin of psoas major does not extend to S1 in all specimens
Piriformis normally fused with gluteus medius
Quadratus femoris not split at insertion or variable
Adductor magnus insertion into inferior border of quadratus femoris insertion
Peroneus brevis may insert onto ﬁrst and second phalanges of digit V
Soleus often has tibial origin
Cephalic vein sometimes limited to forearm
Origin of radialis indicus may include ﬁrst palmar metacarpal artery
Point at which radial artery enters palm: dorsum of ﬁrst interosseous space
Superior ulnar collateral artery may originate from brachial artery
Lateral thoracic artery normally an independent branch of axillary artery
Superior thoracic artery
Most common form of branches from aortic arch is E (Keith, 1895)
Lateral plantar artery dominant in at least some specimens
Normally 3.5 digits supplied by median nerve
Psoas minor innervated by femoral nerve
Muscular branches of tibial nerve includes ﬂexor digitorum longus
Average body hair density moderate to low
Sternal glands
Axillary organ
Transverse rugae of vagina

Mangani synapomorphies (humans and chimpanzees):

Extensor digitorum originates from antebrachial fascia
Lateral head of triceps brachii originates from lateral intermuscular septum
Extension of extensor carpi ulnaris to ﬁrst phalanx of digit V in some specimens
Teres minor shares origin from intermuscular septum with teres major
Latissimus dorsi may originate from inferior scapular angle
Extent of clavicular origin of pectoralis major: 1/2
Tensor fascia latae normally fused proximally with gluteus maximus
Origin of short head of biceps femoris: posterolateral femur and lateral intermuscular septum*
Extensor digitorum longus originates from crural fascia
Peroneus longus does not originate from lateral tibial condyle*
Plantaris often present
Extensor digitorum brevis tendon to digit V not normally present*
Slip from abductor hallucis into base of MI
Abductor hallucis may insert onto medial cuneiform
Medial and lateral heads of ﬂexor hallucis brevis not separated by septum*
First dorsal interosseous originates from MI and MII
Flexor digitorum brevis originates from plantar aponeurosis
Origin of posterior interosseous artery: common interosseus (not brachial artery)
Dorsalis indicis and dorsal metacarpal branches of ulnar artery absent*
Superﬁcial palmar artery may pass over thenar muscles
Dorsalis pollicis
Profunda brachii may originate from brachial artery*
No perforating branch of peroneal artery anastomoses with anterior lateral malleolar artery*
Inferior medial and inferior lateral genicular branches of popliteal artery*
Medial femoral circumﬂex artery may originate from profunda femori
Muscular branches of profunda femoris for hamstrings
Gangliform enlargement at junction of radial and posterior interosseous nerves
Axillary nerve does not innervate subscapularis*
Muscular branches of obturator nerve may include pectineus
Superﬁcial peroneal nerve supplies medial side of digit II
Average body hair density low
Scrotum normally postpenial
Scrotum semidependent or dependent (never nondependent)
Relative testes size (ratio of observed/predicted body testes size) greater than 0.4

* also in gibbons

I'll be honest, I barely know what most of these are. But I intend to find out!

Characters that Support the Great Ape Clades

2011-08-31T10:13:00.000-07:00

Anyone familiar with the current state of great ape phylogeny knows that the following structure is well-supported:

Great apes are a clade.

Orangutans are a subclade of great apes.
African great apes are a subclade of great apes.

Gorillas are a subclade of African great apes.
Mangani are a subclade of African great apes.

Humans are a subclade of mangani.
Chimpanzees are a subclade of mangani.

And most such people probably know that the primary evidence for this structure is molecular. But there has to be morphological data to back this up, right?

Great Apes

I've been trying to hunt down such morphological data, but it's been a bit hard. There really aren't that many morphology-based cladistic studies of primates, and the few that exist either exclude humans or focus on stem-humans more than living great apes.

An example of a study that looks at a wide array of fossil and living primates, but fails to include humans:

Rossie & Seiffert (2006). Continental paleobiogeography as phylogenetic evidence. Pages 469–522 in Lehman & Fleagle (eds.) Primate Biogeography: Progress and Prospects. Springer, New York. 546pp. isbn:0387298711

An example of a study that includes some living great apes, but focuses on stem-humans:

Strait & al. (1997). A reappraisal of early hominid phylogeny. Journal of Human Evolution 32(1):17–82. pmid:9034954

I've compiled some shared character lists from these:

CHARACTERS SHARED BY CHIMPANZEES AND HUMANS, BUT NOT GORILLAS (Strait & al. 1997):

Inferior orbital margin never rounded laterally
Sagittal crest not present in males*
Postorbital constriction moderate or slight
Narrow supraglenoid gutter width
External auditory meatus positioned medially (not laterally)
Consistently small mandibular cross-section area at M₁
Narrow mandibular extramolar sulcus
Very small premolar crown area
Very small molar crown area

* Fossils show this to be a convergence.

CHARACTERS SHARED BY CHIMPANZEES AND GORILLAS, BUT NOT ORANGUTANS OR GIBBONS (Rossie & Seiffert 2006):

Upper premolar cusp heteromorphy reduced
P₃ MD length narrow
M₁-M₂ waisting present
M₁-M₂ crown tapering distal
Talon size large relative to trigon
Radial head outline smaller ﬂat area
Dorsal ridge on radius present
Os centrale fused*
Metacarpal dorsal ridges present
Hamate hamulus distally projecting
Posterior calcaneoastragular joint faces dorsally
Supraorbital region strong inflated tori
Frontal sinus present*

* I've verified that these are present in humans, too. I'm sure most or all of the others are as well, but I haven't had time to check.

CHARACTERS SHARED BY CHIMPANZEES, GORILLAS, AND ORANGUTANS, BUT NOT GIBBONS (Rossie & Seiffert 2006):

I₂ cingulum present
P₄ crown shape sub-ovoid
P₄ MD length narrow
p₃ mesiolingual beak present
p₃ sectoriality poor
p₄ length very broad
m₁-m₃ distal fovea wide
Transverse process inclination dorsally and caudally inclined
Transverse processes on pedicle
Four lumbar vertebrae
Deltoid insertion on distal half
Radial styloid process reduced
Trapezium-MC1 joint sellar
MC1 prox articulation lateral extension
Hamate distolateral edge interrupted by ligament pit
Tibial condylar facets medial larger
Femoral condyles medial larger
Talar head width greater than height
Anterior calcaneal length less than one third
Heel tubercle present
Infraorbital surface of maxilla slopes anteroinferiorly
Snout length protruding
Palate shape parallel to tooth rows
Orbit inferior margin ﬂush with cheek
Orbit position high
Nasal shape narrow superiorly
Horizontal palatine process narrow

What I'd like to do eventually is synthesize these into easily-readable lists of characters supporting the major great ape clades (great apes, African great apes, mangani). The lists are in pretty sloppy form right now, though. Things left to do:

Double-check against the character matrices.
Find the human state for the relevant characters in Rossie & Seiffert 2006.
Weed out the symplesiomorphies and homoplasies.
Translate these into less technical language, insofar as possible.

Guest Post: Similarities Between Macaque and Human Brains

2011-08-30T17:09:00.000-07:00

Despite the title of this blog, I've rarely if ever actually discussed simian brains. (The title refers to my own brain, or more generally the brain of any human that's ever thought about their place in the universe.) Reader Allison Gamble has kindly volunteered to rectify this situation with A Three-Pound Monkey Brain's first-ever guest post. Enjoy!

Similarities Between Macaque and Human Brains

by Allison Gamble

Rhesus macaque
mother and child
by David Lewis

Evolutionary scientists believe that humans and Old World monkeys, such macaques, evolved from a common ancestor. At some point in the past our paths diverged. As different as we may look on the outside, humans and macaques share many common behavioral traits, all of which have a basis hidden deep within our brains.

Rhesus macaques and other Old World monkeys are often used in scientific and medical experimentation. They make ideal research subjects because in many ways, human brains and Old World monkey brains are very similar. The more we learn about the similarities and differences between human and Old World monkey brains, the better the picture we can get of the two groups’ evolutionary paths since diverging from that common ancestor about 30 million years ago. What's more, these Rhesus macaques’ brains may hold keys to understanding the neurological and cognitive bases of prejudice, racial discrimination, and associated violent behaviors that could be massive boons to forensic psychology and other disciplines we humans use to better understand ourselves.

Size Matters

Scans of Rhesus macaque brains
by Ellery Chen

What is the primary difference between Old World monkey brains and human brains? Size and shape are the most obvious. The average adult human brain weighs between 1,300 and 1,400 grams, and even an average newborn human baby's brain is about 350 to 400 grams. An average Rhesus macaque's brain is approximately 90 to 97 grams. Humans have the largest brain-to-body ratio of any primate.

A Single Gene Makes a Huge Difference

Skeleton of 'Able',
a Rhesus macaque sent into space.
From the Otis Historical Archives,
National Museum of
Health & Medicine.

According to a recent study conducted at Emory University, Rhesus macaques demonstrated a trait previously thought to belong solely to humans: recalling past images and applying them to a current situation. Why is this important? The ability to learn from past actions is the basis for imagination and planning for the future, the key to complex societies and survivability of the species. A Yale University study found the primary difference between Old World monkey brains and human brains may be the activation of a single gene, NDE1, which controls the growth of the cerebral cortex.

The cerebral cortex covers both hemispheres of the brain. While parts of it control basic physiological functions like sensory input and limb or eye movement, other areas are responsible for advanced functions like memory, abstract thinking, language, creativity, emotion, judgment and attention. While initially it may seem like these are solely human abilities, studies and research have shown that this idea is false.

Macaques Have Self-Doubt

As an example, one study found that macaques have the capacity to doubt themselves in a manner similar to humans. The professors conducting the study, Michael Beran from Georgia State University and John David Smith from State University of New York, trained macaques to play a computer game that asked the macaques questions. The macaques were given a treat when they answered the questions correctly. Over time, the macaques learned to avoid the difficult questions. When they were unsure of their answer, they could pass on the question. New World monkeys were also tested, but did not show the same awareness of their own thought. Since New World monkeys are not as similar to us as Old World monkeys this was to be expected. The significance of the study, according to Dr. Smith, is that self-awareness is a crucial part of human development, and the presence of it in Old World monkeys could help provide a sense of how it evolved.

Macaques Have Mirror Neurons

Both humans and macaques have what are known as 'mirror neurons.' These brain cells fire when we observe someone else performing the same action as us. What is the significance of mirror neurons? They're crucial to the capacity for behaviors such as empathy, emotional contagion (for example, when others laugh and you can't help but start laughing as well), and even developmental disorders like autism.

Instincts in Humans

Rhesus macaque
by Vincent van Dam

Some scientists don't like to use the word 'instincts' in association with humans. They prefer terms like 'natural predisposition.' While this may simply be a semantic difference, it is the cause of much controversy and debate in scientific circles.

Do humans have an instinct for violence? If so, where did that instinct come from? The answer isn't simple, as the nature vs. nurture debate has been raging for ages. One study indicated that Rhesus macaques recognize other Rhesus macaques as either belonging to the group or as outsiders. They also appeared to associate the outsiders with things that were frightening or dangerous, leading the researcher to conclude that the macaques had instincts for prejudice and even racism. By extension, humans may also have a disposition towards racism and prejudice, two behaviors that have certainly inspired a fair share of violence over the years.

By continuing to study our Old World cousins, we can discover much about our own behavior, including how we learn, how we view others and, how we view ourselves. However, despite the striking similarities between human and Old World monkey cognition and behavior, a crucial difference in humans remains that once we are aware of how we behave, we can self-correct. In this way we separate ourselves from the monkeys, and perhaps it is this ability that more than anything else defines our humanity.

Silence

2011-05-27T09:20:00.000-07:00

So I was busily and excitedly writing about my new site, PhyloPic, back in February and early March, and then this blog went silent. What happened?

Something terrible.

—

My father, Timothy Alan Keesey, passed away on March 10th. He had gone into the hospital the previous day. He didn't last the night.

Dad was known as a "gentle giant"—a towering, athletic man of great patience. He was a pleasant man, very well-liked.

He instilled an appreciation of nature in his children, my sister and me. Our most common family pastime was hiking. We frequented the Billy Goat Trail, between the Potomac River and the C&O Canal, where he showed me how to catch reptiles, and how to tell a broad-headed skink from a five-lined skink. He'd been a biology major, and I owe my interest in biology in large part to him (by both genetic and memetic transmission).

I also owe my interest in programming to him. Not that he was a programmer (apart from taking one course back in the punch-card days), but he bought the family a TI-99/4A back during a time when it was pretty rare to have a home computer. We never got any software for it, so the only way to use it was to learn BASIC. I became pretty much the sole user, teaching myself how to program from the BASIC manual. No other single act has contributed so much to my ultimate career.

Dad's obituary is here. It doesn't tell much about him as a person—his quiet demeanor, his keen intellect, his skill with cars, sports, and animals.

Goodbye, Dad, and thanks.

—

But this year has not been entirely without good news.

I'm comforted by the fact that, before he passed away, Dad knew he'd be getting another grandchild. (My sister already has a daughter.) My wife, Susan, is expecting our first child.

My dad was a wonderful father. I have both a good model to follow and a high standard to live up to.

By strange coincidence, our daughter's due date is October 14th—Dad's birthday.

To Flash or not to Flash

2011-03-08T14:56:00.000-08:00

I love building stuff with Flash technologies. I think ActionScript 3.0 is an excellent language and Flex 4 is a very good framework. I'm not particularly enamored of the alternatives. I find JavaScript to be a mediocre language (albeit with some excellent libraries). I don't like wrangling CSS more than I have to (although Less makes it much nicer). I find HTML 5 to be a pretty immature technology so far. SilverLight's days are probably numbered. (I haven't yet delved into mobile operating systems, like Android and iOS, so I can't speak for those. And those aren't complete alternatives, anyway.)

Because I love Flash, I have a tendency to want to build everything in it. But over the years I've learned that this tendency must be curbed whenever possible. There are definite downsides to Flash, and especially to doing entire websites in Flash. (The now-defunct March of Man website and some abandoned versions of the Dinosauricon are testaments to this.)

For PhyloPic, it was pretty clear to me that there would be no significant advantage to building it in Flash. Load times would be increased without any functionality enhancement. I wouldn't be able to use it on my iPhone. And all the functionality I needed was easily available in plain old HTML/JavaScript/CSS.

With one exception.

The Submission Tool is built as a Flex app. There is one primary reason for this: image processing. Processing the silhouettes on the server side was an option, but one that could have potentially bogged the server down. (It's already starting to buckle a bit as is, pending some optimizations.) But, by using Flash's BitmapData class, I can do that bit of work on the client side before the silhouettes are shipped off to the database.

Of course there are some other benefits as well. In descending order of importance:

Flash allows for a more unified experience for the submitter. No page reloads and no cross-browser differences.
SPAM bots are much more capable of cracking HTML forms than cracking custom AMF web services. SWF files are generally opaque to them.
It was easier for me to build and test.

Had it just been those three reasons, there might still have been a good argument to do it as HTML/AJAX. The image processing requirement is what really tipped the scales. One hundred submitters contrasting, cropping, and rescaling bitmaps is much nicer if they're doing it on their own machines than if they're all doing it on the server. (Okay, I've barely had even two simultaneous submitters so far, but I can dream....)

There may be other Flash tools in PhyloPic's future. For example, I think it is the best technology for the Cladogram Generator. But for the rest of the site, plain old HTML/JavaScript/CSS is certainly sufficient—better, even.

UPDATE (2012 Jan 26): The Submission Page still uses Flash but is not a Flex app.

PhyloPic Week 2: Lineages, Browsing, and API

2011-03-05T22:42:00.000-08:00

Another good week for PhyloPic. There are now well over 200 silhouettes in the database. I also rolled out some new features and enhancements.

Redesigned Lineage Pages

Lineage pages now provide taxonomic and license information for each image. As a visual touch, figures now fade as they go deeper and deeper into the past. Here's a few of my favorite lineage pages so far:

Anhanguera santanae (pterosaur)
Catocala nupta (moth)
Corvus corax (avian theropod dinosaur)
Damon johnstonii (whip spider)
Giraffatitan brancai (sauropod dinosaur)
Homo sapiens sapiens (primate)
Pantodon buccholzi (butterflyfish)
Therizinosaurus cheloniformis (theropod dinosaur)

Yes, they're all bilaterian animals. There's a definite bias.

Image Browser

Now you can peruse the entire gallery much more easily, with the Image Browser. Use the arrow(s) on the side to navigate through pages of silhouettes.

Developer API

For any developers out there who want to use the PhyloPic database to create their own apps, now you can. I've provided an initial API, available both as a JSON service and an AMF service for Flex apps.

Also of news to developers: I've opened up the code base for viewing and cloning. (Still need to add the licenses, though.) It's a Django app, written in Python. Feel free to poke around.

Thanks

I'd like to thank everyone who's submitted images so far, especially FunkMonk, Scott Hartman, Matt Martyniuk and Maija Karala for their many contributions. (Each of them has submitted at least a dozen.) Thanks also to Steven Coombs, Craig Dylke, Mo Hassan, Neil Kelley, Dann Pigdon, Ville-Veikko Sinkkonen, Patrick Strutzenberger, Reka Szabo, David Tana, Michael P. Taylor, and Emily Willoughby!

The First Week of PhyloPic

2011-02-28T09:59:00.000-08:00

I announced PhyloPic last week and the response has been great. I launched with ~95 images and we are already up to 170! (Possibly more by the time you read this.) Some of the lineages are becoming pretty complete. Some of the better ones:

For the last one, I made a special collage:

(Click on it and check out the Flickr page to find an extremely high-resolution version.)

Of course, other areas of the Tree of Life are not quite so fleshed out. For example, if you look up a plant you'll usually get this. (Or even less if you didn't happen to pick a tracheophyte.) So there is plenty of illustrating left to do.

There is also plenty of programming left to do. You can see a list of major remaining tasks on PhyloPic's BitBucket page. Here are a few, with links to their pages:

If any of these interest you, I encourage you to vote for them by clicking the "Bump!" button:

And if you have any ideas, you can also suggest features.

At least one blog has created its own PhyloPic feature. Traumador at Art Evolved put together an excellent tutorial on creating silhouettes using Photoshop. (They also posted about PhyloPic here.) Blogger David Tana of Superoceras also awarded PhyloPic his Interweb Science of the Week award.

In summary, the project's going very well and I'm pretty excited about it. I can't wait to see what the rest of the year holds for PhyloPic!

Introducing PhyloPic: An Open Database of Reusable Silhouettes

2011-02-21T23:43:00.000-08:00

Ever had this problem? "Boy, I could sure use a silhouette of [some kind of organism] for this diagram I'm working on. But I can't find anything on the web! Well, except for a few images which are copyrighted...."

What if there were a website with an open database of reusable images, available under Creative Commons licenses? What if you could do phylogenetic searches, so that, even if there weren't a silhouette for the taxon in question, you could at least find something close? What if you could build images like this...

Evolution of the Aardvark

...without having to look all over the web for figures?

Well, now you can! I've launched a new site called:

PHYLOPIC

It's currently in public alpha, which means it's not quite done. So, I have some caveats:

I'm pulling most taxonomic data from uBio. It's great because it's really comprehensive. But it's also a huge mess because it stores multiple classifications, many of which are outdated and disagree with each other. (This isn't uBio's fault, as its goal is to store all these classifications, not to offer one nice, neat classification.) So you may (will) find some errata in the phylogenetic system. I'm working on cleaning it up, but there are a lot of taxonomic names out there....
It's still early on, so there are only about a hundred images in the database. It will grow over time, but don't be surprised if the closest image it has for your favorite invertebrate is some kind of indiscriminate worm.
There are some known bugs (and I don't mean Hemiptera). The Issues Page is open to all, though, so you can read the known issues and report new ones. (Please do!)

It's a work in progress, but I think it has enormous potential. And I think it's reached a state where it's ready for public use and feedback. So have a look, see what you think, and let me know! (And, if you're artistically inclined, please consider submitting some silhouettes of your own.)

Hybridizing Stem-Humans: Or, Is Everyone Right?

2011-01-04T14:22:00.000-08:00

Analysis of mitochondrial DNA shows that the human matrilineage split from the Denisovan matrilineage around a million years ago. The nuclear genome shows a more recent split of humans (Homo sapiens) from both Denisovans (Homo sp. indet.) and Neandertals (Homo neanderthalensis) around 270–440 millennia ago. And yet some modern humans (Melanesians) appear to have inherited a small portion (4–6%) of nuclear DNA from Denisovans. This means that hominin populations can recombine even after being split for hundreds of thousands of years.

A "wholphin" (Tursiops truncatus × Pseudorca crassidens).
Photo by Mark Interrante.

Properly considered, this is not shocking at all. In other placental species, populations that have been split for far longer periods of time can hybridize. Look at "wholphins", hybrids between bottlenose dolphins (Tursiops truncatus) and false killer whales (Pseudorca crassidens). Those parent species have been split for around seven million years, longer even than the split between humans and chimpanzees!

Of course, humans can't (or at least don't) interbreed with chimpanzees, so the length of the split is not a perfect predictor of whether lineages can recombine. But it's interesting to consider how much lineage recombination might have occurred in stem-humans. The most divergent known lineages from our own are probably late Paranthropus (P. robustus and P. boisei). Our common ancestor with them is generally thought to be something like Australopithecus africanus, or perhaps Praeanthropus afarensis. Even opting for the older choice, this would make the length of their split from our putative contemporaneous ancestor, Homo habilis, only around a million years (roughly). That's not a terribly long split.

Did Homo habilis have multiple ancestors?
(Photo by Charles Roffey)

What this says to me is that there is no a priori reason to suppose that any two contemporary populations of hominin could not have interbred. Maybe Paranthropus aethiopicus interbred with early Homo—could this explain Australopithecus garhi? Maybe the Denisovans themselves are Homo erectus × neanderthalensis. Maybe Homo floresiensis are pinheaded, pygmy descendants of Homo erectus and an unknown, pre-Homo lineage! (I'm not saying I necessarily support any of these ideas; I'm just throwing them out there.)

Also consider the debates over human ancestry in the field of paleoanthropology. It's a common observation that whenever someone finds a new stem-human (or stem-mangani) species, they declare it a human ancestor, while their rival colleagues pooh-pooh the finding and maintain that their own specimens are the true ancestors. (There are notable exceptions to this, of course, but it does seem to happen again and again.) But what if everyone is right? What if most of these fossil species are ancestral to us, but in varying proportions? I can't see any reason why this would be unimaginable.

A human with partial
Neandertal ancestry
(blog's author).

Again, this is not an uncommon phenomenon in other placental species. Consider coyotes (Canis latrans)—the eastern populations have partial ancestry from wolves (Canis lupus). Eastern lowland gorillas (Gorilla beringei graueri) may have partial ancestry from western gorillas (Gorilla gorilla). Our species is not unique in being partially hybridized.

So when people argue whether we are descended from Praeanthropus afarensis vs. Australopithecus africanus vs. Orrorin tugenensis vs. Kenyanthropus platyops—maybe everyone is right! At the very least, it seems to me that future discovery depends on allowing for significant amounts of admixture, and not blindly assuming simple bifurcation.

References

Ackermann & Bishop (2009). Morphological and molecular evidence reveals recent hybridization between gorilla taxa. Evolution 64(1):271–290. doi:10.1111/j.1558-5646.2009.00858.x
Green & al. (2010). A draft sequence of the Neandertal genome. Science 328:710–722. doi:10.1126/science.1188021
Kays & al. (2009). Rapid adaptive evolution of northeastern coyotes via hybridization with wolves. Biol. Lett. 6:89–93. doi:10.1098/rsbl.2009.0575
Kim & al. (2009). Evolutionary charactterization of a highly repetitive sequence identified from the false killer whale (Pseudorca crassidens). Genes Genet. Sys. 84:185–189. doi:10.1266/ggs.84.18
Reich & al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060 doi:10.1038/nature09710
Xiong & al. (2009). Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evol. Biol. 9. doi:10.1186/1471-2148-9-20

What is a human?

2010-12-23T00:31:00.000-08:00

Find the human! Pretty easy, right? RIGHT??

It is obvious what is "human" and what is not if we just look at living organisms. There's a clear gap between us and our closest living relatives, the chimpanzees. No danger of mistaking one for the other.

But this clarity vanishes as soon as we look at the fossil record. There's a gradient of forms between us and things that are not clearly closer to us or chimpanzees (Ardipithecus, Orrorin, Sahelanthropus). Which ones are "human" and which are not? Is Praeanthropus afarensis human? What about Homo habilis? Homo ergaster? Neandertals? Homo sapiens idaltu?

Find the human! Or is there more than one?
Or are they all human?

This issue crops up for all kinds of taxa. Much time has been spent arguing what is and is not e.g., avian, or mammalian. The issue is more common within vertebrates than many other taxa, since vertebrates have an especially good and well-studied fossil record. But it applies, in theory or practice, to every extant taxon.

I subscribe to the school of thought that names born from neontology (the study of extant organisms) are best restricted to the crown group (that is, to the living forms, their final common ancestor, and all descendants of that ancestor). Arguments for restricting common names to crown groups were first laid out by de Queiroz and Gauthier (1992). The primary reason for doing this is that it prevents unjustified inferences about stem groups (that is, the extinct taxa which are not part of the crown group, but are closer to it than to anything else extant). For example, we currently have no way of knowing whether the statement, "Within all mammalian species, mothers produce milk," is true if we include things like Docodon as mammals (or, as a few have done, even earlier things like Dimetrodon). However, if we restrict Mammalia to the last common ancestor of monotremes and therians (marsupials and placentals) and all descendants of that ancestor, then the statement unambiguously holds.

This system also gives us a very easy way to refer to any stem group: just add the prefix "stem-". Some examples:

stem-avians: Pterodactylus, Iguanodon, Diplodocus, Eoraptor, Coelophysis, Tyrannosaurus, Oviraptor, Velociraptor, Archaeopteryx, Ichthyornis
stem-mammals: Casea, Dimetrodon, Moschops, Cynognathus, Docodon
stem-whales: Indohyus, Ambulocetus, Pakicetus, Basilosaurus, Dorudon
stem-humans: Ardipithecus(?), Praeanthropus, Australopithecus, Homo habilis, Homo ergaster

stem-humans

This is a nice, neat system. However, for humans, it gets a little sloppy the closer we get to the crown group.

For a long time, there was a debate in paleoanthropology as to how our species originated. We are distributed across the globe, so it's not immediately obvious where we are from. As the hominin fossil record gradually came to light during the 20th century, it became clearer that the earliest roots of the human total group were in Africa, since that's where the oldest remains are found. Everything before two million years ago is African, and only after that time period do we start to see remains in Eurasia, all of them belonging to the genus Homo. Remains in Australia and America don't occur until very late, and only modern humans appear in those regions.

But this leaves open the question of our own species' origin. Homo had spread all over the Old World by the time modern humans appeared, so we could have come from anywhere in Africa or Eurasia. Two major hypotheses were formed. The Out of Africa Hypothesis suggested that the ancestors of humans originated in Africa and then spread out over the globe, displacing all other populations of Homo: the Neandertals in West Eurasia, Peking Man in Asia, Java Man in Malaya, etc. The Multiregional Hypothesis, on the other hand, suggested that modern human races evolved more or less in their current areas: Negroids were descended from Rhodesian Man, Caucasoids from Neandertal Man, and Mongoloids from Peking Man.

These hypotheses competed with each other until the advent of genetic analysis. When scientists were finally able to study the mitochondrial genome, which is copied from mother to child, they found that all living humans shared a relatively recent matrilineal ancestor, much more recent than the splits between Rhodesian, Neandertal, and Peking fossils. Furthermore, the matrilineal family tree strongly points to an ancestor in Africa, where the most divergence is found. Study of the Y chromosome, which is copied from father to son, indicated an even more recent patrilineal ancestor, also African. The case seemed closed. Out of Africa had won.

The case seemed further bolstered when the Neandertal mitochondrial genome was recovered. It revealed a signature which clearly placed it outside the modern human group (Teschler-Nicola & al. 2006). Earlier this year, mitochondrial DNA was also retrieved from an indeterminate fossil from Denisova, Siberia, indicating that it represented a matrilineage even further out, preceding the human-Neandertal split (Krause & al. 2010).

This would give us a pretty nice, clean series of splits. And it would mean that Neandertals, Denisovans, etc. are stem-humans.

But there is more to ancestry than just the matrilineage and the patrilineage. Most of our ancestral lineages include members of both sexes (think of your mother's father and your father's mother). The matrilineage and patrilineage are the only ones that can be studied with clarity, since all other chromosomes undergo a shuffling process. But those other lineages exist nonetheless.

Only very recently has evidence come to light which challenges Out of Africa, at least in its strong form. Earlier this year, a study suggested that all humans except for Sub-Saharan Africans have inherited 1–4% of their DNA from Neandertal ancestors (Green & al. 2010). And just yesterday, a new analysis of Denisovan nuclear DNA showed that Melanesians have inherited 4–6% of their DNA from Denisovans. This nuclear DNA seems to originate from an ancestor close to the human-Neandertal split, but somewhat on the Neandertal side.

Long story short, the picture has gotten a lot more complicated. It's no longer, "Out of Africa, yes, Multiregional, no." Now it's, "Out of Africa, mostly; Multiregional, somewhat."

So what does this mean for the term "human"? Are Neandertals and Denisovans human? After all, they seem to be ancestral to some, but not all, modern human populations.

Well, they can only belong to the crown clade if they are the final common ancestor of all living humans, or descended from it. Neither of these criteria appear to hold. So, for now, I would still say that they are not human, only very close to human. (Note that this does not mean that people descended, in part, from Neandertals and/or Denisovans are somehow "less human" than those with pure African ancestry. The African ancestors are also not humans but stem-humans under this usage. This usage is discrete; you're either human or you aren't.)

Still, at this level of resolution, we start to see a problem with the crown clade usage. What is the final common ancestor? Many would assume it to be the last-occurring common ancestor, but this is problematic, and not just because that ancestor probably lived within recorded history (making, e.g., the Sumerians inhuman!). When I say "final" I'm really referring to something a bit more complex—the maximal members of a predecessor union. (More discussion here.) But determining what that is, exactly, requires better datasets than we have.

I still think it's a good convention, and if its application is a bit vague, so be it—our knowledge is a bit vague. For now I would say that humans are a clade of large, gracile hominins with high-vaulted crania that emerged roughly 150,000 years ago in Africa, and then spread out. They are descended from not one but at least three major populations of stem-human. One of these, the African population (idaltu, helmei, etc.), forms the majority of the ancestry, up to 100% in some populations. The others, Neandertals and Denisovans, only form a small part of the ancestry of some humans.

I feel this convention is useful because it prevent unjustified inferences. For example, we know that all living human populations have languages with highly complex grammar. We really don't know whether Neandertals and Denisovans had such languages, or whether the immediate African predecessors of humans did, for that matter. So it's good to be able to categorize them as stem-humans, because it reminds us that we don't have as much data available on them as we do for the crown group. We have to be more clever in figuring these things out.

And if we ever cloned a Neandertal? Well, ask me again once that happens.

References

de Queiroz & Gauthier (1992). Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23:449–480. [PDF]
Green & al. (2010). A draft sequence of the Neandertal genome. Science 328:710–722. doi:10.1126/science.1188021
Krause & al. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464(7290):894–897. doi:10.1038/nature08976
Reich & al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060 doi:10.1038/nature09710
Teschler-Nicola & al. (2006). No evidence of Neandertal mtDNA contribution to early modern humans. Pages 491–503 in Early Modern Humans at the Moravian Gate. Springer Vienna. doi:10.1007/978-3-211-49294-9_17

The Purpose of Generic Names: Or, Everyone's a Homo

2010-12-21T13:32:00.000-08:00

Vrſvs Lotor Linn.

It can be surprising for a modern-day biology student to look at 18th-century texts and see how broad the genera are. Consider Linnaeus: he named raccoons as a species of bear (Ursus lotor, the "washer bear"—still called "tvättbjörn" ["washbear"] in Swedish). Nowadays raccoons aren't even placed in the same family as bears, and bears are split into anywhere from roughly three to seven extant genera. Or consider bats, nowadays comprising about 60 extant genera, while Linnaeus classified them as just one (Vespertilio). These aren't even the craziest examples.

Was Linnaeus nuts? Of course not. He saw that the task of creating a unique name for every species would be extremely difficult, so he decided it would be okay to reuse the same names if they were prefaced by the name of a more general category—a genus. Thus, for example, he was able to call the house mouse Mus musculus and the blue whale Balaena musculus (now either Balaenoptera or Sibbaldus). Although they have the same specific epithet, those epithets are unique within their general category. As long as homonymy is avoided, there's no nomenclatural need to restrict genera, so why not make them broad?

In this way, genera function as what we in the computer science world call namespaces. Different things are allowed to have the same local name as long as they are within different namespaces. The qualified name, which combines a namespace identifier with the local name, is globally unique, even if the local name is not.

Biological Nomenclature

generic name + specific epithet = species name

Computer Science

namespace identifier + local name = qualified name

Recently, this got me to thinking—why have we restricted our genera so much, when this was their original purpose? If we just want to be sure that each species has a globally unique name, we could have much larger genera—in some cases, even larger than Linnaeus'.

Consider our own genus, Homo. It has exactly one extant species, Homo sapiens, and that species has an epithet that is already, as far as I know, globally unique. How is that useful? Even Linnaeus thought this was rather silly—he would have included humans in his anthropoid genus, Simia, except he feared backlash. (Even including us in the same order as other primates was controversial at the time.)

How far could we extend our genus and retain its usefulness as a namespace? How far out can we go without having duplicate local names? Within Homo we already have local names like sapiens, erectus, habilis, etc. We actually do have at least one duplicate name, Homo capensis, but it's universally considered a junior synonym. (Although this case is a bit complicated.) If we only consider valid, non-synonymous names, how far can we push our genus?

If we include all stem-humans there's no problem. We add things like Homo afarensis and Homo robustus.

Left to right: Homo sapiens, gorilla, troglodytes, lar, & pygmaeus.

If we push it out to the crown clade of African apes there's still no problem. We get things like Homo gorilla (western gorillas) and Homo troglodytes (common chimpanzees). (Admittedly Homo troglodytes was already named by Linnaeus, but it's a nomen oblitum without any specimens or certainty as to what, exactly, it was supposed to indicate.)

Still no problem if we push it out to the great ape crown clade, adding things like Homo pygmaeus (Bornean orangutans) and Homo indicus (otherwise Sivapithecus).

Pushing it out to the ape crown clade still works, as we add things like Homo lar (lar gibbons) and Homo syndactylus (siamangs). (Interestingly enough, Homo lar is Linnaeus' original name for the species. Only later was it given a new genus, Hylobates, by Illiger, where it resides to this day. I'm not quite sure why Linnaeus classified it this way, but my guess is he wasn't that familiar with the animal in question, as was often the case.)

But if we go beyond that, we hit a duplicate: Homo africanus (Hopwood 1933, originally Proconsul) and Homo africanus (Dart 1925, originally Australopithecus). (We actually already hit Meganthropus africanus Weinert, 1950 a while ago, but that's universally considered a synonym.)

So there we go, Homo could be used as the generic name for all crown-group apes without any problem. (I'm willing to bet I missed something, though, and I'm looking forward to some commenter correcting me.) We have restricted our genera far more than they need to be restricted in order for species names to be unique.

Are we nuts? Of course not. A genus is much more than just a namespace. We also use genera on their own, as groups in their own right. Expanding Homo to embrace all extant apes would ruin its utility as a name for a certain subclade of the human total group, and make it redundant with a name that we already have (Hominoidea). (In computer science namespaces are also often narrower than they technically could be.)

Then again, maybe it is a bit nuts to have one thing performing two jobs. Why not allow other, larger taxa to be used as namespaces? Well, under the PhyloCode, that will actually be a possibility. We can refer to Hominoidea syndactylus and Hominoidea sapiens if we want. In fact, I think you could use Synapsida syndactylus (avoiding homonymy with Bleda syndactylus, the red-tailed bristlebill) and Biota sapiens (this epithet being globally unique already, as previously mentioned). These particular examples will probably never be popular and I wouldn't use them myself, but I think it's neat that the possibility exists.

pymathema, a Python tool for evaluating MathML

2010-12-14T11:35:00.000-08:00

Lately I've been learning the programming language Python, and I've really been enjoying it. In particular, as a dynamic language (i.e., having loose types), it's really well-suited for mathematical tools. (Having sets and tuples as native types doesn't hurt, either.)

I started creating a MathML-Content evaluator in Python, with an extension for Names on Nodes which implements phyloreferencing expressions. As part of this I am working on Version 2.0 of the Names on Nodes MathML Definitions, which will expand upon the current ones.

Basic functionality is pretty much complete, although there are some niceties to add. If you'd like to check it out and maybe collaborate, have a look here: PYMATHEMA.

What I Do For A Living: TRONiverse

2010-10-12T17:26:00.000-07:00

We recently launched a Flash app for the upcoming film TRON: Legacy:

TRONiverse

It pulls posts from Twitter, Facebook, and Flickr and displays them orbiting a 3D globe. You can click on the globe to find posts near that area. Post about TRON and your post might appear, too!

Also, we added a neat little Easter egg: click on the globe and then hold down the "M", "C", and "P" keys. (People who've seen the original film might have an idea what to expect....)

An Example of Why We Need the PhyloCode

2010-08-17T16:51:00.000-07:00

I just ran Radish on Zea mays (maize, a.k.a. corn). Look what the combined taxonomies from uBio look like:

What a mess! Keep in mind that the multiplicity of paths is not due to differing phylogenies (they all seem to agree on that), but to differing nomenclature. Even if uBio were to add some of the more obvious synonymies (e.g., Embryophyta and "Embryophytes"), it'd still be pretty wild.

Eventually I plan to have Radish work with automatically-generated taxonomies, made by placing PhyloCode names (from RegNum) onto TreeBase phylogenies using Names on Nodes algorithms, but until then I guess this is the best option.

And Zea mays is just a particularly egregious example. In contrast, here's a nice, neat "radish" for Scarabaeus sacer:

Apart from the one errant use of Animalia, pretty nice!

Radish: Pulling Up Taxonomic Hierarchies From Leaf to Root

2010-08-17T10:32:00.000-07:00

I've just released a small open-source Java library called Radish. It contains tools for interfacing with uBio (and hopefully other services in the future), with the purpose of looking up a taxon's hierarchy. It does this by synthesizing multiple taxonomies into a single graph. Here, for example, is the graph produced by looking up Homo sapiens Linnaeus 1758 (click the image to enlarge):

This is a synthesis of several taxonomies. Some have more ranks than others, but they all converge on a single chain, with the exception of the taxa above the "phylum level", where at least two of them use different schemes. (Although it may be tempting to synonymize Biota and "Cellular life", or Animalia and Metazoa, these are not objective synonymies, and arguably the former is a bad idea anyway.) Ideally the library would be able to figure out that "Cellular life" includes Biota (if the latter is a crown clade), and that Animalia either includes or is a synonym of Metazoa, but it can only work with the data it's given.

Why the name "Radish"? From the project's wiki:

The English word "radish" is derived from Latin "radicem" (nominative: "radix"), meaning "root". (This is also where the word "radical" comes from.) The idea of the Radish library is that by "grabbing a leaf" (i.e., selecting a smaller taxon), you can "pull up the root" (i.e., extract that taxon's hierarchy of supertaxa, up to the root of all life).

Radish is part of a larger project I am working on ... I should have more to say about that in the near future....

Phun Phylogenies

2010-08-02T12:10:00.000-07:00

Pete Buchholz recently started compiling a phylogeny of edible plants, based on the APG III system. I ran it through Names on Nodes and produced a diagram:

(Unfortunately, this version strips out the clade labels—I'll try and rectify that at some point.)

When I saw this, I though, what a fantastic way to learn plant phylogeny! It's something I don't know much about (apart from basics, like the differerence between gymnosperms and angiosperms), and so I found it fascinating to see the ways the foods I eat are related to each other.

It's such a good idea, I couldn't resist doing another version for edible animals and fungi:

And this reminded me of another project I'd been meaning to start for a while, so I finally took a stab at it. A phylogeny of cartoon animals!

(That's right, there's a stuffed tiger clade.)

Yet Another 3D Visualization of Mangani Fossils

2010-07-27T13:47:00.000-07:00

This one's better'n the last one, I think:

Click here to view the app.

Same dataset, different way of viewing it.

3D Visualization of the Fossil Distribution of the Human-Chimpanzee Total Clade

2010-07-26T11:36:00.000-07:00

What it says.

Click on the image to open the visualization.

I've been compiling data on "pan-mangani" fossils. This is my first March of Man toolshop post in a while: a 3D visualization of that data, where the horizontal axis is longitude, the vertical axis is latitude, and depth (the z-axis) is age. The "blobs" each represent a fossilized individual, and you can mouse over them to see what their taxon is.

Some data is missing, notably a lot of entries for our own species. Other data needs to be refined—some of the better-known species (ahem, Neandertals) are big clouds that need to be tied down to specific sites. Also, I obviously need to do more work on that present-day distribution map. But it's a decent start.

Fun things to do:

See if you can find the oldest individual (the lone specimen of Sahelanthropus tchadensis).
Try to find its Chadian compatriots.
Find the earliest non-African individuals (hint: East Europe and the Malayan Archipelago).
Wonder what the heck that thing in India is.
Look for the single cluster of extinct chimpanzees (Pan sp.).
Find the three subspecies of Homo sapiens other than our own. (Note: these may not be distinct from each other—I just prefer to err on the side of splitting for projects like these. Easier to revise later.)
Marvel at how easy it is to become sympathetic to multiregionalism when you just view the distribution data without any morphological context and ignore the fact that not all regions are good for preservation.
Wonder how people can possibly believe in baraminology in the face of such ample evidence. (Adding morphological data to this would help a lot—there really aren't any good "cutoff" points for our lineage.)

UPDATE:

Better version here.

A Plea to Providers of Open Webservices

2010-07-06T19:36:00.000-07:00

Let's suppose you have a webservice, and you have decided, out of the goodness of your heart, to make it "open". Anyone can browse it, search it, and utilize the data it provides. This is something you want—for anyone to be able to utilize the data and present it in new, creative ways.

I'm willing to bet you missed a step.

Consider my Flash application, Names on Nodes. Right now it's a standalone program—it can import and export files locally from your system. But it doesn't read data from any webservice. There are many places in the program where it would be extremely useful to do so. For example, instead of having to enter LSIDs manually, it could search for them in uBio. Instead of having to open NexML files locally, it could pull them from TreeBase. Wouldn't that be nice? Why haven't I done that?

Well, fact is, I can't.

The Flash Player has a security mechanism whereby it will not load data across different domains. If my SWF resides on namesonnodes.org, then that is the only place it can load data from. Of course, there are ways around this: a good way, a less good way, and a really stupid way.

The Good Way

If your domain has a file called crossdomain.xml in its root, then the Flash Player will read that to see if cross-domain permission has been allowed. Here's an example of a crossdomain.xml file that allows maximum access across all domains:

<?xml version="1.0"?>
<!DOCTYPE cross-domain-policy SYSTEM "http://www.adobe.com/xml/dtds/cross-domain-policy.dtd">
<cross-domain-policy>
   <site-control permitted-cross-domain-policies="all"/>
   <allow-access-from domain="*" secure="false"/>
   <allow-http-request-headers-from domain="*" headers="*" secure="false"/>
</cross-domain-policy>

(Or, download it here.)

For more information, see the Cross-Domain Policy File Specification.

(Note that the folks at TreeBase are looking into this. I'm on tenterhooks.)

The Less Good Way

I could also make Names on Nodes as an AIR application. This is less good because it means the user would have to install it as an application on their local system, and they couldn't just access it online. But it would allow for more possibilities—not just the ability to load data from anywhere regardless of policy files, but also drag-and-drop from other applications, etc. I am actually planning to create an AIR version someday, but it's not my top priority right now.

The Really Stupid Way

Of course, I could also make a little server-side component on my domain and simply have it pull data from your domain before feeding it to the Flash application. This is really stupid because it greatly increases traffic on my webserver while still causing just as much traffic on your webserver as it would if you had just allowed cross-domain access with a policy file.

In Summary

It takes a matter of seconds to place a cross-domain policy file in your server's root directory (assuming you have access), there are no drawbacks if your service is intended to be open anyway, and there are huge benefits for us Flash developers who want to use your service. I mean, really, why not?

Wrapping Up In Portland

2010-07-02T00:14:00.000-07:00

Yesterday was the last day of the iEvoBio Conference, and tonight is my last night in Portland. The conference was quite illuminating and I would definitely like to return for another one.

I've had some time tonight to address a few issues I would like to have tended to before the conference. For one, I hadn't updated the Names on Nodes website to link to the application! This has been remedied. In the process, I removed links to the NEXUS demo application, since it's a bit old and out of sync with the rest by now. I'll probably add it back after adding support for the NEXUS format to Names on Nodes.

I also made a few simple additions to Names on Nodes, including:

Fullscreen mode
Ability to specify which characters in a matrix you wish to import

The latter in particular should prove useful—some people were finding it impossible to open NexML files with character matrices. Since Names on Nodes only uses characters as part of apomorphy-based definitions, it's usually a big waste of time and memory to import entire matrices when only a few nomenclaturally-relevant characters (if any) are needed.

Once again I'd like to encourage people to check out the application and make feature requests and report issues on the BitBucket page.

Names on Nodes is finally online.

2010-06-26T04:45:00.000-07:00

A month ago I got notice that my abstract had been accepted, and that I would be demoing Names on Nodes at the iEvoBio conference's Software Bazaar on June 29. This is the first time Names on Nodes has ever truly had a hard deadline. Since it's a personal project, until now I have had the luxury of languidly rebuilding and polishing and rebuilding and polishing. But now I have to get something up. So it's up.

Names on Nodes

There's still a lot left to do, but this will have to do for now. You can load NexML and Newick files (not NEXUS for now, sorry—although, really, you should be sorry for still using it when NexML is available). You can save as MathML and export PNG image files. You can create phylogenies and phylogenetic definitions on the fly using a visual interface that emphasizes drag-and-drop. Or you can type them in (as Newick and MathML, respectively), should you prefer that.

There are still a lot of bugs, and a lot of unimplemented features. If you come across issues or if you have feature requests, please feel free to submit an issue. And if you want to look at the code, it's open source (MIT license) and available on BitBucket.

gautengensis in the sediba phylogeny

2010-05-28T15:29:00.000-07:00

Here's the phylogeny/taxonomy from the Australopithecus sediba paper overlaid with the taxonomy from the Homo gautengensis paper:

(click to enlarge)

I've highlighted the taxonomic units that Curnoe referred to Homo gautengensis. Note that, by Berger & al.'s phylogeny, Homo gautengensis is polyphyletic. Each of those units represents a single specimen, so this could potentially be explained by individual variation, age differences, sexual dimorphism, etc. Or the new species is overextended—I'm not really qualified to judge.

Note also that Homo is polyphyletic in this phylogeny. One way to fix this is to move sediba into Homo.

A Homo gautengensis by any other name...

2010-05-28T10:38:00.000-07:00

A new species of our genus, Homo, was recently published:

Curnoe (2010). A review of early Homo in southern Africa focusing on cranial, mandibular and dental remains, with the description of a new species (Homo gautengensis sp. nov.). HOMO Journal of Comparative Human Biology (online early). doi:10.1016/j.jchb.2010.04.002

Here's the abstract:

The southern African sample of early Homo is playing an increasingly important role in understanding the origins, diversity and adaptations of the human genus. Yet, the affinities and classification of these remains continue to be in a state of flux. The southern African sample derives from five karstic palaeocave localities and represents more than one-third of the total African sample for this group; sampling an even wider range of anatomical regions than the eastern African collection. Morphological and phenetic comparisons of southern African specimens covering dental, mandibular and cranial remains demonstrate this sample to contain a species distinct from known early Homo taxa. The new species Homo gautengensis sp. nov. is described herein: type specimen Stw 53; Paratypes SE 255, SE 1508, Stw 19b/33, Stw 75–79, Stw 80, Stw 84, Stw 151, SK 15, SK 27, SK 45, SK 847, SKX 257/258, SKX 267/268, SKX 339, SKX 610, SKW 3114 and DNH 70. H. gautengensis is identified from fossils recovered at three palaeocave localities with current best ages spanning ~2.0 to 1.26–0.82 million years BP. Thus, H. gautengensisis probably the earliest recognised species in the human genus and its longevity is apparently well in excess of H. habilis.

The holotype, Stw 53, has previously been referred to either Homo habilis Leakey & al. 1964 or Australopithecus africanus Dart 1923. Interestingly, though, one of the paratypes, SK 15, is already the holotype of Telanthropus capensis Robinson 1949! So Homo gautengensis would appear to be a junior subjective synonym.

It gets even more interesting (for us nomenclature buffs, anyway): if Telanthropus capensis were to be transferred to Homo, then it would be a junior homonym of Homo capensis Broom 1918 (a.k.a. "Boskop Man"), which itself is a junior subjective synonym of Homo sapiens (the type specimen probably representing an early Khoisan individual).

I'm not sure if any of this is discussed by Curnoe, because I don't have access to the paper. If anyone has a PDF, feel free to e-mail to keesey [at] gmail [dot] com.

UPDATE: I have the paper now and will be looking it over.

ANOTHER UPDATE: Telanthropus is mentioned in passing, but the synonymy is not discussed.

Upcoming Names on Nodes Presentation

2010-05-27T15:29:00.000-07:00

I'll also be presenting Names on Nodes at iEvoBio, at the Software Bazaar on June 29. Here's the abstract:

Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
Names on Nodes¹ is an open-source² Flex application which utilizes a mathematical approach to automate the application of phylogenetically-defined names to phylogenetic hypotheses. Phylogenetic hypotheses are modeled as directed, acyclic graphs, and may be read from bioinformatics or graph files (Nexus, NexML, Newick, and GraphML) or created de novo. Hypotheses may also be merged from multiple sources. Names on Nodes stores hypotheses as MathML, an XML-based language for representing mathematical content and presentation. Phylogenetic definitions may be constructed using a visual editor and exported in MathML. Thus, it is possible to create a dictionary of defined names and automatically apply them to phylogenetic hypotheses. In the current version of the application, such dictionaries exist only as MathML files, but in future versions definitions may also be loaded from databases (e.g., RegNum).
Additional functionality in Names on Nodes includes the ability to coarsen a phylogenetic graph (thereby simplifying it while still reflecting the overall structure) or to export it as an image file (raster or vector, potentially with semantic annotations).
Source code available at: http://bitbucket.org/keesey/namesonnodes-sa/
MIT license

I have my work cut out for me....

Upcoming Talk: Toward a Complete Phyloreferencing Language

2010-05-26T12:36:00.000-07:00

I'll be giving a “Lightning Talk” (five minutes) at the iEvoBio Conference in Portland, Oregon. Here's the abstract:

Toward a Complete Phyloreferencing Language
A phyloreference is a statement indicating a taxon within a phylogenetic context. A common use for phyloreferences is in phylogenetic definitions, which tie taxonomic names to taxa via such statements. Several conventions for writing phyloreferences have been proposed, but most only cover a few “standard” forms (node-, branch-, and perhaps apomorphy-based clades) without the capacity to represent more “exotic” forms (e.g., ancestor-based clades and qualified/modified references). In order to build a complete phyloreferencing language, the mathematical underpinnings of phylogenetic contexts must be clarified. A phylogenetic context may be modeled as a directed, acyclic graph, wherein nodes model taxonomic units and directed edges model immediate descent. Higher taxa are modeled as unions of nodes. A phyloreferencing language must minimally allow for certain classes of entity: Boolean values, sets (including taxa, relations, and the empty set), and lists (including graphs and functions). It must also minimally allow for basic operations related to logic, set theory, and graph theory. Higher structures such as declarations and piecewise constructs must also be possible. With these as a basis, functions related to phylogeny can be defined: maximal, minimal, predecessor union/intersection, successor union/intersection, exclusive predecessors, synapomorphic predecessors, clade, crown clade, and total clade. I show how such a language may be used to represent various types of phyloreference, both “standard” and “exotic”.

Now to figure out how to condense that into a five-minute talk....

Names on Nodes Issue Tracker

2010-05-21T15:42:00.000-07:00

Yesterday I transferred the list of remaining Names on Nodes issues from my whiteboard to the bitbucket issue tracker. My goal is to get through most of these by the end of June. (Some "nice-to-haves", like DOT or HTML 5 exporting, may have to wait.)

Essential features left to implement, complete or fix:

FILES AND FORMATS

Certain formats for import, especially NexML and NEXUS. (Currently only Newick can be imported. MathML files can be loaded as well.)
Certain formats for export, especially NexML. (Currently only PNG can be exported. MathML files can be saved as well.)
Ability to save just the definitions or just the phylogeny to a MathML file.
Ability to import definitions from a MathML file.
MathML tweaks. (Use csymbol instead of ci for taxa. Normalize presentation.)
Ability to write in Newick strings directly.

DISPLAY

Skin various components (sliders, steppers, checkboxes, etc.).
Fix line breaks in MathML formulas.
Various scrollbar issues.
Special character issues.

NAMES

Rich editor for taxon labels, including ability to edit taxon URIs.

NODES

Arc bisection tool.
Fix node merging (i.e., synonymization).
Add ability to select definition type when creating a name.
Node Pane Control Bar revisions. (Change Resolution Slider to a stepper. Add Zoom Slider.)

DEFINITIONS

Definition Editor tweaks/fixes. (Some actions are blocked that should be possible. Textual Editor does not always update. Various layout issues.)

OTHER

About/Help Panel.

Why HTML 5 Canvas Will Not Be Replacing Flash That Soon

2010-05-12T19:23:00.000-07:00

Previously I mentioned a tool, PhyloPainter, which uses the HTML 5 <canvas> element to draw a phylogenetic graph. Here's what it looks like on my iPhone:

Not only are the arrowheads missing (as they are on Safari on all platforms, not just the iPhone), but the labels have bizarrely been placed outside the canvas, flipped upside-down! The tool works fine on Firefox and Chrome. (Internet Explorer has not implemented <canvas> yet, and I haven't played enough with the interim solution, ExplorerCanvas, to get it working.)

I think the <canvas> element is a cool idea, and I'll continue to play with it. But it has a long way to go to compete with a cross-platform tool like Flash. HTML 5 may be "open"—but it also needs to "work".

PhyloPainter: Happy Little Trees

2010-05-06T10:30:00.000-07:00

The whole Flash/Apple fracas has been rather distasteful to me. But I'm not going to dwell on that right now. Instead, I am trying to keep an open mind by trying out some of the technologies that are competing with my favored development tools. First up: HTML 5.

I'll probably write more on the topic later, but suffice to say for now that working HTML 5 feels like I've traveled in time back to 2001, the days of ActionScript 1.0. JavaScript is a poor language for anything complicated. Canvas has covered the basics of vector drawing well, but little else. That said, I see potential and I'm pretty certain the tools will improve.

For my first HTML 5 app, I ported some basic functionality from Names on Nodes, namely, the ability to read Newick tree strings and the ability to draw graphs. I give you:

PhyloPainter

It's a bit rough right now. For one thing, it doesn't work in Internet Explorer (despite the inclusion of a workaround JavaScript tool—the current version of IE doesn't support HTML 5 Canvas). But it's a start.

Give it a try—paint some happy little trees!

Biota: Another Example of Coarse vs. Fine Phylogenies

2010-04-09T13:36:00.000-07:00

Yesterday I posted an example of how graph-coarsening algorithms can be used to make the high-level patterns of a phylogeny more immediately visible. That example used a phylogenetic hypothesis about placental mammals. The hypothesis involves a lot of nodes (i.e., taxonomic units), but not much branching complexity. By which I mean each node has only a single parent.

So here's an example where nodes may have multiple parents. This is a phylogeny of Biota, i.e., Life:

Eukaryotes (organisms with cellular nuclei, i.e., plants [Embryophyta, etc.], animals [Metazoa], fungi [Eumycota], and "protists") have been highlighted in yellow. Some nodes have multiple parents due to one of two phenomena:

Lateral transfer. Many organisms (especially bacteria) are capable of acquiring genetic material from unrelated organisms.
Endosymbiosis. Some organisms have evolved into organelles within the cells of other organisms, notably mitochondria (descended from proteobacteria related to those that cause rickets) and plastids (photosynthesizing organelles in plants, descended from cyanobacteria). In these cases, the organelle often retains its own DNA, although much of it may have leapt over to the "host's" nuclear DNA. In some cases, all of it may have leapt over (as with mitochondria descendants like mitosomes).

Both lateral transfer and endosymbiosis are considered valid forms of descent in this hypothesis.

Here's the graph coarsened one step:

We can see the general patterns more clearly here. Eukaryotes share a relationship with archaeans, but also have descent from proteobacteria (via mitochondria). One clade of eukaryotes (Plastida) is also descended from a basal form of cyanobacteria (via plastids). A few cases of lateral transfer are visible, but not in detail. We can also see there there is a lot of bacterial diversity, although the details are not spelled out.

Here's the graph coarsened another step:

The endosymbiosis is made even clearer, although most other relationships are obscured.

Disclaimer: This hypothesis was cobbled together from a number of sources and does not represent any rigorous research on my part. I suspect parts of it are outdated, but this area of the Tree of Life is not my bailiwick. I just wanted to throw something together for a demonstration.

Australopithecus sediba and its place among stem-humans

2010-04-08T19:26:00.000-07:00

A new stem-human species, Australopithecus sediba Berger et al. 2010, has just been announced. The paper's supplementary information contains the results of a cladistic analysis of stem-humans. For fun, I thought I'd plug the most parsimonious tree into the in-development version of Names on Nodes:

Stw 53 and SK 847 are specimens that are not readily assignable to named species. (SK 847 might be Homo ergaster). Our own species, sapiens, is presumably descended from the SK 847-erectus node.

The analysis finds sediba as a sister taxon to Homo (which includes habilis, rudolfensis, SK 847, and erectus), and possibly ancestral to it. Which begs the question, why not place it in Homo? If this hypothesis is correct, it shares more ancestry with the type species of Homo (sapiens) than it does with the type species of Australopithecus (africanus). Even Stw 53, which is here placed outside the sediba-Homo clade, has been attributed to Homo in the past.

Viewing Phylogenies at Different Graph Resolution

2010-04-08T16:31:00.000-07:00

Although I've been primarily reining in features on the next version of Names on Nodes, there was a new feature I couldn't resist adding. I think it's coming along pretty well.

A common problem with working with phylogenies is that many of them are gigantic, far too big to view all at once. As an example, consider Figure 1 from Beck et al. (2006). It models a hypothesis about placental mammal phylogeny, at an arbitrary resolution ("family-level"). Here's how the current version of Names on Nodes renders it:

When you look at it "zoomed out", it's almost impossible to know what's going on. When you look at it full size, you can see various local areas, but you lose a sense of what's going on with the larger image. Note that I've highlighted our own species' twig on the tree (Hominidae, the great ape clade) in yellow.

Earlier I used the term "resolution" to refer to the size of the graph's nodes. We can refer to a graph with very small nodes (e.g., each node representing an individual organism) as being "fine" and a graph with very large nodes (e.g., "class-level") as being "coarse". Thinking about the problem from this angle, I had the idea to create a control for coarsening or refining the viewed graph.

I implemented a simple graph-coarsening algorithm*, and then created an algorithm for picking the best name for the new, coarser graph's nodes. And here is the phylogeny at near-maximum coarseness:

This is placental phylogeny boiled down to its basics: rodents, laurasiatheres, and a bunch of other junk (including us). The node labelled "Placentalia*" contains the placental ancestor but not all descendants—it lacks an unnamed clade included most non-afrothere placentals. The unnamed greenish node includes all members of that unnamed clade except for rodents and laurasiatheres. (This happens to include Hominidae, which is why it has that greenish color.)

Let's refine it one step:

We're starting to get a better idea of the hypothesis. Finer:

Now we can see the basal split between afrotheres and other placentals, as well as developing complexity in Rodentia and Laurasiatheria. Finer:

Getting a little bit on the big side, now, but we can see more details. There are a lot of unnamed clades within Hystricoidea and Chiroptera—we can see that those clades are diverse, although we can't see details. Finer:

This has about 2/5 as many nodes as the base graph. It's a bit large, but still much easier to view than the base graph. Many important details are visible (e.g., the platyrrhine-catarrhine split), while others are just suggested (e.g., lots of diversity in Caviomorpha).

Obviously this works best if lots of clades have been named. I think it'll be a useful for boiling a phylogeny down to an appropriate level: coarser for quick overviews, finer for in-depth discussion.

* Basic summary of the coarsening algorithm:

Look through all nodes that have children, and find the ones whose children are all terminal (sinks).
Merge each of those nodes with their children to create a "supernode".
Merge all overlapping supernodes. (This is important for graphs where nodes may have multiple ancestors, although it doesn't come into play in this example.)
Remove the supernodes from the graph and repeat from step 1. Keep going until no nodes are left.
Add the supernodes to a new graph. A supernode is ancestral to another supernode if any of its subnodes are ancestral to any of the other supernode's subnodes.

Sketch of a Phylogenetic Query Language

2010-04-05T16:03:00.000-07:00

Names on Nodes uses MathML for two primary purposes:

Delineating phylogenetic hypotheses (as directed, acyclic graphs).
Associating identifiers with definitions.

In some ways this works out to be a bit like a query language. You can use it to set up data constructs, and then search them for groups of interest. For example, suppose you wanted a list of all stem-humans from Kenya. Assuming that your dataset included 1) a taxonomic unit called Homo sapiens, 2) a group called extant for all extant taxonomic units, and 3) a group called Kenya for all Kenyan taxonomic units, that query might look like this:

<apply xmlns="http://www.w3.org/1998/Math/MathML">
   <intersect/>
   <ci>Kenya</ci>
   <apply>
      <setdiff/>
      <apply>
         <csymbol definitionURL="http://namesonnodes.org/ns/math/2009#def-Total"/>
         <ci>Homo sapiens</ci>
         <ci>extant</ci>
      </apply>
      <ci>Homo sapiens</ci>
   </apply>
</apply>

MathML is great for being flexible and extensible enough to cover concepts like this. But ... it's also really verbose. This is fine for my purposes so far, but it may be cumbersome for other purposes. So I've been playing around with a more succinct way to write these expressions. Today I tossed up some rough ideas here:

Phylogenetic Query Script (Rough Draft)

This is a plain-text format loosely inspired by mathematical notation, the C language, etc. Using it, the above query becomes:

"Kenya" & (total("Homo sapiens", "extant") - "Homo sapiens")

...which is quite a bit shorter.

This is still in very early stages, so I thought I'd post it to get some feedback.

Here are a few of the simpler clade definition examples:

"Aves"       := clade("Struthio camelus" | "Tetrao major" |
                      "Vultur gryphus").

"Saurischia" := clade("Megalosaurus bucklandii" <-
                      "Iguanodon bernissartensis").

"Avialae"    := clade("wings used for powered flight" @
                      "Vultur gryphus").

Names on Nodes: MathML Definitions (Version 1.2)

2010-04-02T09:16:00.000-07:00

After the epiphany that Names on Nodes did not have to be associated with a database, I set to work creating a "standalone" version of the application. Progress has been pretty good, and if you are interested in the details (or collaborating), you can check the project out at its new home on Bitbucket (which also houses the related project, ASMathema).

I've just updated the Names on Nodes website based on these revisions to the project, most notably the MathML Definitions document. Most of the changes have actually been removals: no more mentions of rank-based taxonomy (which may be covered in future versions but not in this one), qualified names as taxonomic identifiers (no longer a necessary feature), etc. So if you didn't read it before because it was too long and dense ... well, it's still pretty long and dense, actually. But less so!

I've also added an example MathML document as a supplement. This document:

Defines a phylogenetic context (the same one used in the MathML Definitions examples), arranging taxonomic units as vertices in a directed, acyclic graph.
Defines sets based on characters ("wings used for powered flight" and "extant")
Refers a specimen (YPM-VP 1450) to a taxonomic unit (Ichthyornis).
Equates several species names as synonyms.
Defines some hybrid formulas as referring to specific taxonomic units.
Defines a number of clade names.

This file can be opened with Names on Nodes: Standalone Version, which I am currently developing and hope to release this year.

Sneak Peek

2010-03-28T16:58:00.000-07:00

(Click to view larger version.)

Names on Nodes: Cutting Out the Fat

2010-03-05T18:43:00.000-08:00

While pondering the headaches of homonymy recently, I started to ask myself, What am I doing with my life? Why am I worrying about this?

Seriously, though. I've been working on Names on Nodes on and off for about three years, and I still haven't launched it. And it's because I've been so focused on getting things like this right. (Well, that and having a day job.)

But things like this aren't part of the core functionality. The core functionality is the automated evaluation of phylogenetic definitions (encoded as MathML) within the context of phylogenetic hypotheses (modeled as directed, acyclic graphs). That part of it's been done for quite a while. So why am I wasting time on the rest?

By cutting out the entire database portion of the project, I could actually have something launched this year. Sure, it'd be nice to have a repository of taxonomic names, definitions, authorities, etc. But it's not necessary. It's phase II, not phase I. In fact, by the time I'm ready for a phase II, there will almost certainly be other services out there that already perform those things.

So, here on out, I'm going to be focusing on getting a lean, mean version of Names on Nodes up. Here's a quick summary of what you'll be able to do with it:

Open bioinformatics files (NEXUS to start with, other formats like nexml going forward).
View the phylogenies in a pretty graphical interface.
Merge phylogenies.
Tweak phylogenies (adding or removing parent-child relations, adding or removing taxonomic units, equating taxonomic units, etc.).
Formulate phylogenetic definitions using a spiffy interface.
Apply these definitions to the phylogeny.
Save your work as MathML files.

And that should be manageable (although there is still much work to be done, especially for the user interface). Once that's launched and working, then I'll look into connecting to other services and/or launching an associated database.

The Great PhyloCode Land Run

2010-03-01T12:22:00.000-08:00

Sometime in the near future, the PhyloCode will be enacted. For this to happen, two things need to happen concurrently:

1. The registration database (called "RegNum") must be completed and opened to the public. This is necessary because the PhyloCode requires all names to be registered electronically.

2. Phylonyms: a Companion to the PhyloCode must be published. This is a multi-authored volume that will include the earliest definitions under the PhyloCode.

Which names will be defined in Phylonyms? The original goal was to cover the most historically important names (what Alain Dubois calls "sozonyms"). However, proponents of phylogenetic nomenclature tend to be clustered in several fields (most notably vascular plant botany and vertebrate zoology—note that the code's authorship reflects this). This means certain parts of the Tree of Life (e.g., entomology) will unfortunately be underrepresented, due to lack of interest in those fields. (The alternative, having non-specialists define such names in Phylonyms, does not bear consideration.) So Phylonyms will be less about providing coverage and more about providing sturdy, well-reasoned definitions that can serve as examples.

What about all the names that it omits? What will happen to those once the PhyloCode is enacted? That will be interesting to see.

One thing I could envision is a sort of "land run". I picture it working this way. Let's consider a field, say, anthropology, where phylogenetic nomenclature has not taken much of a hold. Currently there is debate about how to use some taxonomic names related to the field. Some workers like to use the familial name "Hominidae" to refer to a large taxon, including humans and great apes. Others prefer to restrict it to the human total clade (i.e., humans and everything closer to them than to other extant taxa). Similarly, some workers use the generic name "Homo" in a broad sense to include short, small-brained species like Homo habilis, while others prefer to restrict it to the tall, large-brained clade (relegating H. habilis to another genus, e.g., Australopithecus).

Let's say there's a researcher out there named Dr. Statler, who prefers a strict usage for "Hominidae" and a broad use for "Homo". But his colleague, Dr. Waldorf, prefers a broad usage for "Hominidae". Dr. Waldorf isn't really that interested in phylogenetic nomenclature, but when he notes that "Hominidae" is not in the registration database, he sees an opportunity. He writes a quick paper defining "Hominidae" as a node-based clade: "The clade originating with the last common ancestor of humans (Homo sapiens Linnaeus 1758), Bornean orangutans (Pongo pygmaeus Linnaeus 1760), common chimpanzees (Pan troglodytes Oken 1816, originally Simia troglodytes Blumenbach 1775), and western gorillas (Gorilla gorilla Geoffroy 1852, originally Troglodytes gorilla Savage 1847)."

Dr. Statler is, of course, outraged. Not that he cares that much about phylogenetic nomenclature, but what if anthropologists do start using it? What if someone ruins another taxonomic name? His colleagues Drs. Honeydew and Beaker prefer a strict definition of "Homo"—what if they author a paper cementing that definition under the PhyloCode?

This cannot come to pass! Dr. Statler does some reading on the code and decides that a branch-based definition would work nicely for his broader usage. He defines "Homo" as, "The clade consisting of Homo sapiens Linnaeus 1758 and all organisms that share a more recent common ancestor with H. sapiens than with Australopithecus africanus Dart 1925, Paranthropus robustus Broom 1938, Zinjanthropus boisei Leakey 1959, or Australopithecus afarensis Johanson & White 1978." This sets off another anthropologist, and soon all sorts of anthropological/primatological names are being defined under the PhyloCode, as workers struggle to assert their usages.

This is not an ideal situation. It would be much nicer if a group of anthropologists were to come together, discuss the matters rationally, and arrive at an agreement which they then publish together. But it's still not a horrible situation—at least people are defining phylogenetic names and at least interest in phylogenetic nomenclature is being spread. I can't predict the future, but I feel like this sort of "land run" is bound to occur at least in some fields—and maybe that's okay.

One Name, One Taxon -- For One Rank Group

2010-02-27T13:36:00.000-08:00

How Many Taxa Per Name?

A while back I pondered a seeming contradiction between the way zoological nomenclature is practiced and what the ICZN actually says. To illustrate, let's consider the case of Columbina Illiger 1811 and Columbina Spix 1825. The former is a subtribe, typified by Genus Columba, and the latter is a genus. It's possible for Columbina Illiger 1811 to include Columbina Spix 1825, although, as I understand it, they would generally be considered disjoint taxa, with Columbina Spix 1825 in another subtribe.

In several places, it seems as though the ICZN would not allow one name to refer to different taxa. The Preamble states that one of its objectives is "to ensure that the name of each taxon is unique and distinct", and Art. 52.1 states that, "When two or more taxa are distinguished from each other they must not be denoted by the same name." Logically, it would seem that Columbina Spix 1825 should be considered invalid, and that Columbina Illiger 1811 should have priority.

But this is not how the code is interpreted. There is an understanding that homonymy only occurs within rank groups (family group, genus group, species group). Since Columbina Spix 1825 is a genus-group name and Columbina Illiger 1811 is a family-group name, they can't be homonyms. (Elsewhere, a term has been coined for such apparent homonyms: "hemihomonyms".)

This understanding is implicit. Nowhere does the ICZN explicitly lay it out. The closest it gets is in Article 53, which discusses the particulars of how homonymy works. It discusses homonymy within the family group, homonymy within the genus group, and homonymy within the species group. Nowhere does it discuss homonymy between rank groups. Only by this omission does the code hint at the idea that homonymy only occurs within rank groups.

I've communicated with several taxonomists, including people involved with the ICZN, and they all seem to agree that this is the code's intent and that the wordings in the Preamble and Art. 52.1 are confusing. Hopefully a future version of the code will clarify this.

When a Code Is Not a Namespace

So, with that more or less settled, now I'm back to my original problem. In Names on Nodes, authorities (such as nomenclatural codes) are treated as namespaces, i.e., sets of distinct names. So far as I know, there is no problem in treating the other codes (including the PhyloCode) in this manner, but apparently the ICZN does not work this way. Suppose I refer to the ICZN using a URI based on its ISBN number: urn:isbn:0853010064. What would the qualified name urn:isbn:0853010064::Columbina refer to?

Here are a few ideas I've come up with.

One Code, Three Namespaces

So the ICZN doesn't function as a namespace—but it does function as three namespaces, one for each rank group. I could use each zoological rank group as a namespace. The only problem with this is that there is no standard URI to refer to each group. At least, I don't know of any—if there is one, speak up! (I suppose I could use the draft BICI standard to refer to the particular page in the code where it defines the rank group in question, but that's a bit awkward.)

Orthographic Differences

Note that Columbina Illiger 1811 is in normal font and Columbina Spix 1825 is italicized. I could use this to distinguish the names from each other, e.g., urn:isbn:0853010064::Columbina (the subtribe) vs. urn:isbn:0853010064::_Columbina_ (the genus). For consistency, this would have to be done to species names as well, e.g., urn:isbn:0853010064::_Columbina+passerina_

This isn't the only way to do it, though. The ICZN makes a further distinction, putting family group names in all-capital letters, e.g., COLUMBINA Illiger 1811. (Although it never states this as a rule, and most publications don't follow this convention.) I could follow this convention in the qualified names, e.g., urn:isbn:0853010064::COLUMBINA (the subtribe) vs. urn:isbn:0853010064::Columbina (the genus). No change would be require for qualified species names, e.g., urn:isbn:0853010064::Columbina+passerina.

Augmented Local Names

Another possibility is to consider the rank group to be an essential part of the name itself. This could be reflected in a qualified name by augmenting the name with a prefix, e.g., urn:isbn:0853010064::fam:Columbina (the subtribe) vs. urn:isbn:0853010064::gen:Columbina (the genus). To be consistent, this would have to be applied to species names as well, e.g., urn:isbn:0853010064::sp:Columbina+passerina.

What About Other Names?

The ICZN has few rules to do with names above the level of the family group, and overall it doesn't govern much about them. Thus there are all kinds of examples of homonymous taxa above the rank of family group. For example, Pterodactyloidea Plieninger 1901 is a suborder which includes Pterodactyloidea Meyer 1830, a superfamily. "Decapoda" is the name of an order-group taxon in two different phyla, Arthropoda and Mollusca. Etc., etc.

I had wanted to be able to use qualified names for all zoological names, but I'm having trouble seeing how that will be possible for those ranked above the family group. I'll probably have to use the coining publications themselves as authorities, or a URI (e.g., an LSID) for each name. Rather inconvenient.

Defining Rank-Based Taxa Mathematically

2010-02-27T11:22:00.000-08:00

Let U be the set of all individuals.

Let ranks be represented by a contiguous series of natural numbers (ℕ). Let 1 represent the lowest (finest) rank and let some natural number n represent the highest (coarsest) rank.

Let T be a sequence of n sets of type individuals (i.e., individuals represented by type specimens). Let each set in the sequence (other than the last set) be a superset of the next set, i.e., T₁ ⊇ T₂ ⊇ … T_n.

Let d be a metric function measuring some distance between any two individuals: d(x, y) ∈ ℝ₀⁺ (the set of nonnegative real numbers). Note that, because it is a metric, d(x, x) = 0 and d(x, y) = d(y, x).

For each rank level r, let p_r be a function mapping each member, t, of T_r to a taxon (set of individuals): p_r(t) := {x ∈ U | for all s ∈ T_r, d(x, t) ≤ d(x, s)}. Let P_r be the image of p_r. Then P_r is the taxonomy of rank level r.

Note that some individuals may be placed in multiple taxa of the same rank if they are equidistant between type individuals. These individuals may be considered unclassifiable for that rank. Let U′ be the set of all individuals except for those which are unclassifiable for some rank. Similarly, let P′_r be P_r but with all unclassifiable individuals removed from each member taxon. P′_r is a partition on U′. For any two rank levels q and r, if q < r, then P′_q is a refinement of (or equal to) P′_r.

Tricksy Definitions Expressed Mathematically

2010-02-25T18:23:00.000-08:00

Just for fun, here are a few definitions of nonstandard type to go along with those in the previous post. As any practitioner of phylogenetic nomenclature knows, most definitions are node-, branch-, or apomorphy-based, but there have been a few that don't fall into these categories.

Here are Wagner's (2004) definitions of Panbiota and Biota:

   Panbiota := (Clade ∘ prc_∩)(Homo sapiens).

   Biota := Crown(Panbiota, "extant as of or after 2004").

This is one of the few cases where it makes more sense to define the crown clade based on the total clade rather than vice versa. (Maybe the only case? Not sure.) Technically, Wagner's wording for the definition of Panbiota might be better translated as (suc_∪ ∘ min ∘ prc_∩)(Homo sapiens), but it works out to the same thing.

And here's Clarke's (2004) definition of Ichthyornis:

   Let M := "apomorphy 2" ∩ "apomorphy 5" ∩ "apomorphy 6" ∩ "apomorphy 7" ∩ "apomorphy 8".
   (These refer to apomorphies in Clarke's Ichthyornis dispar Diagnosis.)

   Ichthyornithes := Clade(YPM 1450 ← Struthio camelus ∪ Tinamus major ∪ Vultur gryphus).
   ("YPM" refers to the Yale Peabody Museum's Vertebrate Paleontology collection. YPM 1450 is the Ichthyornis dispar holotype specimen.)

   Ichthyornis := Clade((M @ YPM 1450) ∩ Ichthyornithes).

Names on Nodes: MathML Definitions (Version 1.1)

2010-02-25T11:44:00.000-08:00

After posting Version 1.0 earlier this week, I had a revelation: the cladogen functions are completely unnecessary, and everything would work a lot nicer if I just tossed them. I also realized that there really was no reason I couldn't include the various relations (precedence, immediate precedence, proper precedence, etc.), just in case anyone wanted to do some seriously non-standard definitions. After some significant revisions, I present Version 1.1.

Some examples of the updated notation, using humans (Homo sapiens), platypuses (Ornithorhynchus anatinus), and Dimetrodon grandis, a stem-mammal:

Union. Homo sapiens ∪ Ornithorhynchus anatinus = all humans and all platypuses (polyphyletic taxon, also monothetic)

Exclusive Predecessors. Homo sapiens ← Ornithorhynchus anatinus = humans and all of their ancestors, except for the ancestors shared with platypuses (lineage)

Synapomorphic Predecessors. "milk glands" @ Homo sapiens = humans and all human ancestors to possess milk glands synapomorphic with those in humans (lineage)

Node-Based Clade. Clade(Homo sapiens ∪ Ornithorhynchus anatinus) = Mammalia

Branch-Based Clade (simple). Clade(Homo sapiens ← Ornithorhynchus anatinus) = "Pan-Theria"

Branch-Based Clade (multiple external specifiers). Clade(Homo sapiens ← Ornithorhynchus anatinus ∪ Dimetrodon grandis) = "Pan-Theria"

Branch-Based Clade (multiple internal specifiers). Clade(Homo sapiens ∪ Ornithorhynchus anatinus ← Dimetrodon grandis) = (unnamed clade comprised mostly of Therapsida)

Null Branch-Based Definition (multiple internal specifiers). Clade(Homo sapiens ∪ Dimetrodon grandis ← Ornithorhynchus anatinus) = ∅

Apomorphy-Based Clade. Clade("milk glands" @ Homo sapiens) = "Apo-Mammalia"

Node-Modified Crown Clade. Crown(Homo sapiens ∪ Dimetrodon grandis, "extant as of or after 2010") = Mammalia

Branch-Modified Crown Clade. Crown(Homo sapiens ← Ornithorhynchus anatinus, "extant as of or after 2010") = Theria

Apomorphy-Modified Crown Clade. Crown("milk glands" @ Homo sapiens, "extant as of or after 2010") = Mammalia

Total Clade. Total(Mammalia, "extant as of or after 2010") = Synapsida (or "Pan-Mammalia")

Image showing a node-based clade (Mammalia) under a given phylogenetic hypothesis. Click to enlarge. More here.

Names on Nodes: MathML Definitions (Version 1.0)

2010-02-21T22:08:00.000-08:00

I've just posted version 1.0 of the MathML definition for Names on Nodes. This document provides the foundation for the mathematical entities and operations in Names on Nodes. Previously I had posted an incomplete draft version—this is the first complete version, and also the first version with illustrations. It won't be the last version, but it (or a slightly edited version) will be associated with the first release of Names on Nodes.

This document refines and rectifies concepts laid out in my 2007 paper. It's an important milestone to completing Names on Nodes, a project I've been working on for almost six years.

One of the illustrations, showing how the Clade function works.

Mangani Individual Chart Update

2010-01-15T12:56:00.000-08:00

First things first: want to contribute to Haitian relief? Here's a guide to the appropriate charities.

Second things second: I just posted an update to my diagram showing all known mangani individuals.

Previous version here.

I'm trying a different value scheme to differentiate the vertices and the text. I also revised the earliest species (kadabba, ramidus, and anamensis) based on a rigorous review of the primary literature, and added one early species that had been overlooked (praegens, which may be a nomen dubium but is certainly a mangani or stem-mangani). The later species were revised a bit as well, but not as rigorously.

I really wish there were some place that just listed every known locality with its number of specimens and least possible number of individuals. I've been slowly compiling my own as a Google spreadsheet, but I'd like a better way to catalogue it. Hmmm, perhaps it's time to return to another project of mine.

The Mangani Holotypes, Entry I: Carl Linnaeus (Uppsala domkyrka)

2010-01-04T00:00:00.000-08:00

I, Human

Humans are an egotistic species. Ancient writers considered humans to be created in the image of the gods, destined to rule all other entities. We humans have not one, but two major fields of study devoted to ourselves and named accordingly (anthropology and the humanities). Pick up a book at random and its main topic is likely to be humans (or at least anthropomorphized non-humans).

Yet we are also an outward-looking species. Alone among the life forms of Earth, we regard the skies, the deep, the land. We observe what is, fashion tests to determine how it came to be, and speculate on where things are going. We are self-centered, but our curiosity about things other than ourselves is boundless.

One of the best examples of this apparent paradox lies with systematics, the naming and organizing of life. And no one person illustrates it better than the founder of systematics, Swedish botanist Carl Linnaeus.

Out of Chaos, Order

Carl Linnaeus lived during the 18th century, a time when science, in its modern meaning, was still emerging from what had been called "natural philosophy". The term "biology" had not even been invented yet. Microbes and cells had been discovered, but things like evolution, germ theory, genetics, biochemistry, etc. were a long way off. The study of life was largely a chaotic mess.

Carl Linnaeus as a young adventurer, dressed in Sámi clothing, painted by Martin Hoffman.

Enter the organizer: Linnaeus observed natural entities and saw order, not chaos. He began to arrange animals, plants, and minerals into hierarchical groups, first in his notes, then in pamphlets, and finally as a series of volumes, Systema Naturae. He was not the only naturalist of his time to do this, but he went further than most, and enjoyed more success. Unlike many scholars, his brilliance was recognized in his own time.

Perhaps nobody recognized it more than Linnaeus himself. True to his species, he had a healthy ego. "Deus creavit, Linnaeus disposuit," he was fond of saying: God created, Linnaeus organized. He thought enough of himself to slave over his autobiography almost as much as his systematic work. And he thought enough of his species to give it the name Homo sapiens—"wise human"—and place it in an order called Primates—"primary ones".

But religious leaders of the day took a different view of Primates. To them, the idea that humans could possibly be grouped alongside such lowly creations as lemurs, apes, and monkeys (and bats, originally included in Primates but long since removed) was sacrilege. (Compounding this, "primate" is a religious title as well.) The Roman Catholic Papa Clement XIII banned Linnaeus's books outright in 1758 (although in 1774 Papa Clement XIV actually fired his Professor of Botany for deficient knowledge of Linnaeus's system!) (Soulsby 1993:39). Even Linnaeus's own religious leader, the Lutheran Bishop of Uppsala, considered him impious (Aczel 2007), although this was no bar to Linnaeus being ennobled later on, whereafter he was known as Carl von Linné.

Carl von Linné in 1775, painted by Alexander Roslin

Privately, Linnaeus confessed that he would have liked to go even further in arranging humans with other members of Order Primates. He saw no anatomical reason not to include apes, monkeys, and humans in the same genus (which was a much broader category as he used it than as we use it today), let alone the same order. The only reason he did not name us Simia sapiens was because he feared theological backlash. (Linnaeus 1747)

So here we have a man who saw his species as "wise" and "primary", but recognized that it did not stand apart from other species. Subsequent biological research has upheld our connection to other living things. Ethologists have found that other species use tools, communicate vocally, and even domesticate other life forms. Geneticists have discovered that our DNA is little different from that of a chimpanzee. Paleontologists have found series of extinct species showing that we evolved from ancestors that we share with other animals. Phylogenetically, his inclination was correct—we are one of many kinds of monkey.

Today we struggle to find things that make humans unique. There are still a few—for one thing, no other terrestrial species has attempted to catalogue its fellow life forms. Ironically, this effort, which brings us into the fold with other life forms, also sets us apart.

Naming the Animals

"And Yahweh [of the El Gods] sculpted from the ground every living thing of the field and every flier of the sky-waters. And he brought the Human in to see how he would call them. And whatever the Human called it, that was that living animal's name. And the Human called names to all the beasts, to the fliers of the sky-waters, and to every living thing of the field."

—Anonymous Yahudi, Bereshith 2:19–20a (my translation)

Modern zoological nomenclature, as governed by the International Commission on Zoological Nomenclature according to the International Code of Zoological Nomenclature (ICZN), descends directly from Linnaeus's Systema Naturae. Many of his groupings seem quaint or even laughable today, but, on the other hand, many don't, and a large number of the names he coined are still in use (albeit often for somewhat different groups). The tenth edition of Systema Naturae, published in 1758, is considered one of the founding works of zoological nomenclature (along with Carl Alexander Clerck's lesser-known 1757 work, Aranei Suecici ["Swedish Spiders"]). By the ICZN's rules, these are the earliest works to contain valid zoological names.

The ICZN's way of doing things is a bit different from that of Linnaeus and other early systematists. In some respects this may be regrettable (e.g., the tying of names to ranks has led to much nomenclatural instability—in Linnaeus's time names were free to be ranked however the systematist saw fit, without any spelling change required [de Queiroz 2005]). In other ways, there has been improvement. One notable improvement is the mandating of type specimens.

In Linnaeus's works, names are paired with diagnoses—descriptions of the entities which the name signifies. But diagnoses are an unstable way to define biological groups. They may be too general, bringing unrelated forms into the same group. They may be too specific, excluding forms which should rightly belong. Sometimes they are flat-out wrong. Whatever the case, they are constantly revised in the literature.

What biological nomenclature needed was a way of anchoring definitions. Thus, the ICZN (as well as other nomenclatural codes) uses the concept of a type, one entity which "sets the standard" for the entire group. One specimen (a specimen being some object that has been catalogued within a collection) is selected as the standard-bearer for each species name. There are various types of types in zoological nomenclature, but the most important one is the holotype, the one specimen that anchors the name. Other individuals may be included or excluded as the systematist sees fit, but the one represented by the holotype must remain. (Note that, as practiced, this is different from the Platonic concept of an archetype, in that the holotype need not be a "typical" specimen. That concept is too subjective to be useful in science.)

The Human Holotype

The requirement that zoological names must have a holotype was not grandfathered in, or too many old names would have been invalidated. Instead, provisions were made such that subsequent authors could select a holotype if the original author did not. There are certain restrictions on this, set up to guarantee that the holotype is something that the original author would have included.

When Linnaeus named Homo sapiens, he diagnosed it much more succinctly than usual. "Homo, nosce te ipse," "HOMO nosce Te ipsum," he wrote: "HUMAN know yourself." Nothing further needed, at least at the time.

In 1959, in honor of the tenth edition of Systema Naturae's 200^th anniversary, W. T. Stearn wrote a commemorative article that, among other topics, addressed the lack of a holotype specimen for Homo sapiens:

"Since for nomenclatorial purposes the specimen most carefully studied and recorded by the author is to be accepted as the type, clearly Linnaeus himself, who was much addicted to autobiography, must stand as the type of his Homo sapiens!"

Although stated jokingly, this meets the ICZN's requirements for the designation of a type specimen. Linnaeus's remains, interred at the Uppsala Dome-Church, are the standard-bearer for the species Homo sapiens (and, by proxy, Genus Homo, Family Hominidae, etc.). A fitting tribute to his brilliance ... and his ego.

The Mangani Holotypes

Like any good human, I am fascinated by my own species. I spend much of my spare time studying our origins. It's tough going at times, because many people are fascinated by the same topic, and so there is a huge wealth of hypotheses, ranging from crackpot to well-substantiated. On one hand, the wealth of material is great, but, on the other hand, it's hard to sort out the solid ideas from the less solid. In short, it's a chaotic mess.

I am no Linnaeus (and I'm sure he would agree), but I like to organize my thoughts. So this is the first post in a series where I will take a look at what anchors we do have in this sea of confusion. One by one, I intend to look at each holotype specimen within the human-chimpanzee group, which I informally call "mangani", as explained in an earlier post.

I haven't decided on a particular order, but in many ways it seems that the most apt way to begin is with the first species to be named.

Carl Linnaeus (Uppsala domkyrka)

Collection	Uppsala domkyrka, Uppsala, Sweden (Sverige), Europe
Name	Carl Linnaeus
Other Names	Carolus Linnaeus (Latin) Carl von Linné (after ennoblement) Carolus von Linné (Latin, after ennoblement) L. (standard abbreviation in botanical literature)
Remains	interred corpse
Geography	born in Älmhult, Småland, Sweden (Sverige), Europe died in Uppsala, Sweden (Sverige), Europe
Chronology	born 1707 CE May 23 died 1778 CE January 10
Sex	male
Age	71 years
Height	~1.8m? ~1.6–1.7m?
Typified Taxa Names	Species Homo sapiens Linnaeus 1758 [holotype] Superspecies Homo (sapiens) Linnaeus 1758 [holotype] Subspecies Homo sapiens sapiens Linnaeus 1758 [holotype] Homo sapiens typifies: Genus Homo Linnaeus 1758 Subgenus Homo (Homo) Linnaeus 1758 Homo typifies: Superfamily Hominoidea Gray 1825 Family Hominidae Gray 1825 Subfamily Homininae Gray 1825 Tribe Hominini Gray 1825 Subtribe Hominina Gray 1825
Taxonomy	Although most of the higher taxa have varying usages, the species Homo sapiens is used fairly stably nowadays to include all living humans and their ancestors for approximately the past 200,000 years. More inclusive usages in the past included forms now generally placed in other species, such as Homo neanderthalensis and Homo heidelbergensis. (Genetic data has supported this for H. neanderthalensis [Krings & al. 1997].) Early specimens are similar to Homo heidelbergensis and Homo rhodesiensis, and are often placed in subspecies other than Homo sapiens sapiens (to be detailed in later entries). Of the higher taxa, the most stable is Hominoidea, which is generally used for the clade of tailless primates (gibbons and great apes, the latter including humans).
Comments	Many things about the designation of this specimen as the holotype are odd, not the least of which is that the individual represented by the specimen founded biological nomenclature. Apart from that, this specimen is not "typical" of its species in several ways. Notably, although Homo sapiens originated in Africa, this specimen is from a boreal peninsula of Europe, where members of the species exhibit some aberrant local adaptations, notably marked depigmentation. Even so, the individual still bears the distinctive hallmarks of the species: extremely high, vaulted cranium with high capacity, large body size coupled with gracile build, extremely flat face and small brow ridges, etc. Designation of this specimen as a holotype is problematic in that it is not available for study, on religious and cultural grounds. However, the individual is otherwise well-documented, both in writings and paintings, and was physically normal. Additionally, he has dozens of living descendants, via two of his daughters.

Carl von Linné's gravestone, at Uppsala domkyrka. Photo by Wrote.

Biotechnologist Martin Nervall with a painting of his great great great great great great grandfather, Carl Linnaeus. Photo by Teddy Thörnlund, appearing on Uppsala Universitet's page here.

References

Aczel, A. D. (2007). The Jesuit and the Skull: Teilhard de Chardin, Evolution, and the Search for Peking Man. Riverhead Books. isbn:1594489564
Clerck, C. A. (1757). Aranei suecici, descriptionibus et figuris oeneis illustrati, ad genera subalterna redacti speciebus ultra LX determinati. Svenska spindlar, uti sina hufvud-slagter indelte samt. Stockholmiae.
de Queiroz, K. (2005). Linnaean, rank-based, and phylogenetic nomenclature: restoring primacy to the link between names and taxa. Symb. Bot. Ups. 33(3):127–140. Available online at http://si-pddr.si.edu/dspace/bitstream/10088/4506/1/VZ_2005deQueirozSymBotUps.pdf
International Commission on Zoological Nomenclature (ICZN) (1999). International Code of Zoological Nomenclature, 4^th Ed.
London: International Trust for Zoological Nomenclature.
Krings, M., A. Stone, R. Schmitz, H. Krainitzki, M. Stoneking & S. Pääbo (1997). Neandertal DNA sequences and the origin of modern humans. Cell 90(1):19-30. doi:10.1016/S0092-8674(00)80310-4
Linnaeus, C. (1747). [Letter to J. G. Gmelin]. Available via The Linnaean Correspondence, http://linnaeus.c18.net, letter L0783 (consulted 2009 Jan 31).
Linnaeus, C. (1758). Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. ed. X, tom. I–II. Holmiae: Impensis L. Salvii.
Soulsby, B. H. (1933). A Catalogue of the Works of Linnaeus in the British Museum (2^nd Ed.). British Museum. Available online in partim at http://www.nhm.ac.uk/resources-rx/files/xi-zoological-works-23636.pdf
Stearn, W. T. (1959). The background of Linnaeus's contributions to the nomenclature and methods of systematic biology. Systematic Zoology 8:4–22.

3D March of Man

2009-12-01T19:52:00.000-08:00

A while back I started the March of Man project. The goal is to create a massive illustration of human evolution using hundreds of figures. My first attempt involved drawing them by hand on a big piece of paper. I think that lasted about a week.

My second attempt involved a rich web application, where people could submit image files according to certain specifications, and these would be incorporated into a big collage. This got a bit further, but went stagnant for a few reasons: 1) the application is a bit buggy and unwieldy (it was my first big Flex project), 2) drawing each figure still takes a while, and 3) I overestimated the amount of public interest there would be in contributing to this project. (Thanks to Steve O'Connor, though, for being the only other contributor!)

It's been a couple of years since I launched that site, and now I've started on a new method. Will it go anywhere? We'll see. It does solve some problems of the previous approaches.

This time, I'm doing it in 3D. The plan: 1) create a poseable model of an Ardipithecus ramidus female; 2) create morph targets for various other species, ages, and for males; 3) use this to create images for significant localities; 4) combine these into one vast mural.

So far I'm almost done with step #1. Here she is:

(Also posted on my sketch blog, Dragabok.)

Still have to tweak the hair a bit and make her poseable. After that, I've got my work cut out for me....

The Mangani Clade

2009-12-01T12:49:00.000-08:00

As I've mentioned earlier, the formal nomenclature for apes (including humans) is a huge mess. One person's "hominin" is another's "hominid" and my "hominine" might be your "homininan". And in this situation I honestly think the vernacular terms (adjusted in some cases to include humans) serve us better:

apes: gibbons, great apes

gibbons (or lesser apes): Hoolock, Hylobates, Nomascus, Symphalangus

great apes: African apes, Pongo

African apes: Gorilla, Homo, Pan

There, that covers all the major crown groups—with one important exception. There is no vernacular term I know of for the Homo-Pan clade. We are left with having to use unwieldy hyphenates like "the human-chimpanzee clade" or silly portmanteaux like "chuman" or "humanzee" (which refer more to the last common ancestor or theoretical hybrids than to the clade as a whole).

There is one possible vernacular term I've seen for this clade, and it comes from an unexpected source.

Tarzan is one of the most popular and enduring fictional creations of the 20th century. Everyone knows he was raised by apes—but what kind of apes? In various films they are depicted as gorilla-like (e.g., Disney's Tarzan) or chimpanzee-like (e.g., Greystoke: The Legend of Tarzan, Lord of the Apes). What were they in the novels?

The author, Edgar Rice Burroughs, never attempted to identify them scientifically. In the novels they have a primitive, guttural language, and they call themselves mangani. They are not gorillas, because they have another word for those (bolgani). Chimpanzees are never mentioned in the novels.

Interestingly, the mangani also use the word mangani for humans. For example, black people are gomangani and white people are tarmangani. So, in their own self-taxonomy, there is a group that includes themselves and humans, but excludes gorillas. Sound familiar?

The mangani can't be chimpanzees, because they are much larger (although less massive than gorillas). Like chimpanzees, they are fairly arboreal, but, unlike them, they do not use tools (apart from logs as drums, perhaps), do speak a language, and do not hunt cooperatively. Still, considering that chimpanzee behavior in the wild was virtually unknown when Burroughs was writing, and that chimpanzees were not thought to be closer to humans than to gorillas, perhaps he can be given some leeway here, since his prescience is otherwise impressive. (Especially given the recent discovery of a possible population of giant chimpanzees in the Bili Forest of the Congo.)

I'd love to learn of a good vernacular term for the human-chimpanzee crown clade, but until such a time as I do (or the formal nomenclature becomes actually useable), I like the idea of referring to humans, common chimpanzees, bonobos, Ardipithecus, "Lucy", Australopithecus, Floresian "hobbits", Homo erectus, Neandertals, etc. as "mangani".

More Human Evolution Diagrams

2009-11-20T12:30:00.000-08:00

I'm nearing the end of work on a review of the case for human evolution. I've uploaded some of the diagrams to my Flickr account before. Some of these were just updated and some new ones were added: see The Case for Human Evolution (Flickr set).

This is probably my favorite of the lot, showing the congruence between morphological/paleontological data (including radiometric dates) and genetic data (including molecular clocks):

(Click to see full size.)

Can you spot the single discrepancy? (No fair reading the caption on Flickr first.)

UPDATE: Revised some of the images, temporarily removed one.

What I Do For a Living, Part 312: Dr. Facilier's Parlour

2009-11-20T10:30:00.000-08:00

I recently completed a new application. This one is a collection of three games associated with Disney's upcoming animated film, The Princess and the Frog. This one requires a Facebook account: Dr. Facilier's Parlour. (Dr. Facilier is the villain of the movie.)

This is my first completed project using certain technologies:

Also see the Shadow Shakedown game therein for an example of how DisplacementMapFilter can be useful. (I also got to do a tiny bit of character animation there.)

I have to say I was very pleased with all of these new technologies. In particular, the Spark component set is a huge improvement over the previous Halo components. Skinning components is so easy now it's hard to imagine that it was ever difficult. Adobe has acted on the "Favor composition to inheritance" maxim, and it has paid off. Also, props to Code Igniter, with its flexible tools and strong emphasis on the MVC pattern, for making PHP development (something I had all but sworn off) actually kind of fun.

Enjoy!

Glimpses of Stuff I've Been Working On

2009-09-07T10:24:00.000-07:00

Two long-term projects of mine should see the light of day soon. Here are some previews (click to see full size):

(Why does everything I do lately involve directed, acyclic graphs?)

Online NEXUS File Viewer

2009-08-24T14:45:00.001-07:00

It's been a month since my last post, but I have a very good reason for the hiatus. Namely, I was busy getting married to this woman (at the Los Angeles County Museum of Natural History) and going on our honeymoon (in Sydney, Australia).

Now that I'm back in California, time to get back to work on Names on Nodes! I've just put together a small demo of two key parts of its functionality: the reading of NEXUS files and the displaying of phylogenetic networks. Click here to see the NEXUS Viewer demo. This application opens NEXUS files and displays the trees in them as a combined phylogenetic network.

Things you need to know:

You must have a NEXUS file stored locally on your computer to use this.
That file should have a TREES section. (If not, the viewer should just display a list of operational taxonomic units.)
This could get messy for NEXUS files with lots of trees. (Although it's kind of neat-looking.)
You can move the nodes around by clicking on them, or click anywhere else to move the entire diagram.
I would dearly love to know if, for some reason, it does not work for a given file.

Enjoy!

Two "Names on Nodes"-Related Launches

2009-07-23T13:24:00.001-07:00

I'm still a clear way away from launching the beta application, but I've just made a couple of launches related to my long-time work-in-progress, Names on Nodes.

First up, and probably of more interest to most people, I've begun the documentation for the MathML definitions used by Names on Nodes. The document includes general reviews of relevant mathematical and biological concepts, a quick review of MathML and the technologies it's based on, some comments on correlating mathematical and biological concepts, and definitions for all entities (including operations) used by Names on Nodes. Note that this covers a lot of the same ground as in my 2007 paper, with a few minor changes in the symbols and terminology (e.g., I now call the ancestor of a clade a "cladogen" rather than a "cladogenetic set").

Secondly, I've made the project open-source, by moving it to Google Code. If you are a developer interested in checking this out, go here. It's incomplete, so I don't know if anyone will have any real interest in looking at it yet. (Honestly, I mostly posted so that, on the off chance that I unexpectedly kick the bucket, my magnum opus won't be lost forever.)

This information is also on the new Names on Nodes home page.

"The Case for Human Evolution" - Illustrations

2009-07-22T14:28:00.000-07:00

I have been working on an essay entitled The Case for Human Evolution for a while. I've just posted some illustrations I've been working on:

The Case for Human Evolution (Flickr Set)

Enjoy!

New Useless Utility: Text Tree Maker

2009-06-30T19:49:00.000-07:00

I finally got around to launching something at namesonnodes.org. No, it's not Names on Nodes itself, unfortunately. The project is taking a huge amount of time. But I thought I'd post something, so here's a little Flex application I made (using the new Flash Builder 4 Beta!) using a smidgen of the technology behind Names on Nodes.

Have you ever been discussing phylogeny online and wished there was an easy way to make a readable cladogram? (95% of readers leave.) Those of you who are left, check this out: Text Tree Maker. Just type in a Newick tree string, and voilá! Okay, so typing in a Newick tree string is not that easy in the first place, but it is easier.

Well, I'll be using it, anyway. Check this one out!


Ardipithecus
|--ALA-VP 2/10
`--+--ARA-VP 6/1
   |--KNM-T1 13150
   `--Praeanthropus
      |--KNM-KP 29281
      `--+--AL 288-1
         |--KNM-WT 40000
         |--KT 12/H1
         |--LH 4
         `--+--BOU-VP 12/130
            |--Australopithecus
            |  |--Taung 1
            |  |--Australopithecus (Paranthropus)
            |  |  |--SK 6
            |  |  `--TM1517
            |  `--Australopithecus (Zinjanthropus)
            |     |--KNM-WT 17000
            |     |--OH 5
            |     `--Omo 18
            `--Homo
               |--KNM-ER 1470
               |--KNM-ER 1813
               |--OH 7
               |--OH 9
               `--Homo (Homo)
                  |--D 2600
                  |--KNM-ER 992
                  |--LB 1
                  `--+--Ceprano 1
                     |--Trinil 2
                     `--Homo (sapiens)
                        |--ATD 6-5
                        `--+--Mauer 1
                           `--+--Neandertal 1
                              `--+--Florisbad 1
                                 |--Kabwe 1
                                 `--Uppsala domkyrka: Carolus Linnaeus

NOTE: Right-click on the application and select "View Source" if you want to see some of the code behind it.

Human-Chimpanzee Systematics

2009-06-24T00:52:00.000-07:00

I've been working on a couple of projects to do with stem-humans. Naturally, these efforts necessitate creating a working phylogeny. I thought I'd post what I more or less have so far. I haven't done any rigorous work here; I'm just trying to piece things together from various publications.

This is a phylogeny of all known species within Clade(Homo sapiens Linnaeus 1758 ← Troglodytes gorilla Savage vide Savage & Wyman 1847), including some unnamed, fragmentary species that can only be differentiated from other species by location and/or time. (Note: Sahelanthropus tchadensis Brunet & al. 2002 is excluded because it doesn't seem to be clear that it does fall within this clade.) I've included links for all citations with permanent identifiers, when available, or popups with fuller information, when not. The phylogeny is interspersed with a rank-based taxonomy. (Unfortunately, there are no published phylogeny-based names to apply here.) Outlined circles indicate that the species may be ancestral to what are shown as sister groups. Species names are listed with their original prenomina (genera), regardless of current placement. I've added a note when the listed species is the type of its prenominal genus or another genus.

- ?Orrorin tugenensis Senut & al. 2001 [typus]
- ≅ Tribus Hominini Gray 1825
  - Ardipithecus kadabba Haile-Selassie 2001
  - ≅ Genus Pan Oken 1816
    - Pan sp. innom. McBrearty & Jablonski 2005
    - Pan paniscus Schwarz 1929
    - Simia troglodytes Blumenbach 1776 [typus Pan]
  - ≅ Subtribus Hominina Gray 1825
    - Australopithecus ramidus White & al. 1994 [typus Ardipithecus]
    - - Australopithecus anamensis Leakey & al. 1995 (?= praegens)
      - Homo praegens Ferguson 1989
      - Australopithecus afarensis Johanson & al. 1978 [typus Praeanthropus]
        Australopithecus bahrelghazali Brunet & al. 1995 (?= afarensis)
        Australopithecus garhi Asfaw & al. 1999
        Kenyanthropus platyops Leakey & al. 2001 [typus] (?= afarensis)
        ≅ Genus Australopithecus Dart 1925
        Australopithecus aethiopicus Olson 1985
        Australopithecus africanus Dart 1925 [typus]
        Zinjanthropus boisei Leakey 1959 [typus]
        Australopithecus robustus Broom 1938 [typus Paranthropus]
        ≅ Genus Homo Linnaeus 1758
        Homo sp. innom. Kimbel & al. 1996
        Homo habilis Leakey & al. 1965
        Homo rudolfensis Alexeev 1986
        ≅ Subgenus Homo (Homo) Linnaeus 1758
        Anthropopithecus erectus Dubois 1892 [typus]
        Homo ergaster Groves & Mazák 1975
        ?Homo floresiensis Brown & al. 2004
        Homo georgicus Vekua & al. 2002
        ≅ Superspecies Homo (sapiens) Linnaeus 1758
        Homo antecessor Bermúdez de Castro & al. 1997
        Homo cepranensis Mallegni & al. 2003 (?= antecessor)
        Homo heidelbergensis Schoetensack 1908
        Homo neanderthalensis King 1864
        Homo rhodesiensis Woodward 1921 (?= heidelbergensis)
        Homo sapiens Linnaeus 1758 [typus]

One Name, One Taxon

2009-05-29T17:00:00.000-07:00

One of the primary goals of a nomenclatural code should be to make sure that names refer to one taxon and one taxon only. This principle is mentioned in the ICZN's preamble (emphasis added):

The objects of the Code are to promote stability and universality in the scientific names of animals and to ensure that the name of each taxon is unique and distinct. All its provisions and recommendations are subservient to those ends and none restricts the freedom of taxonomic thought or actions.

This point is reiterated in Article 52:

52.1. Statement of the Principle of Homonymy. When two or more taxa are distinguished from each other they must not be denoted by the same name.

Yet there are numerous cases in zoological nomenclature where this rule is flagrantly ignored. A few:

"Echinoidea" is the name of a superfamily containing Echinus (a sea urchin genus), but also the name of a class containing that superfamily.
"Ophiuroidea" is the name of a superfamily containing Ophiura (a brittle star genus), but also the name of a class containing that superfamily.
"Chelonia" is a genus of turtle, but also used as the name of the order containing all turtles.
"Pterodactyloidea" is the name of taxon given various ranks (usually suborder) including most short-tailed pterosaurs, but also the name of a superfamily within that taxon.

This is getting to be an actual problem for me, because parts of Names on Nodes rely on the principle that a name only has one meaning under a given authority. When I create a database entry for urn:isbn:0853010064::Pterodactyloidea, is it for a suborder or a superfamily? ICZN rules actually dictate that the superfamily has precedence, since Family Pterodactylidae Meyer 1830 has precedence over Suborder Pterodactyloidea Plieninger 1901. (The ICZN considers the naming of any taxon whose rank is in the family group as implicitly naming taxa for all ranks of the family group; thus, naming Family Pterodactylidae implicitly names Superfamily Pterodactyloidea, Subfamily Pterodactylinae, Tribe Pterodactylini, and Subtribe Pterodactylina.) People who use "Pterodactyloidea" for a suborder, beware! You are violating the rules of the ICZN! (WhooOOOOoo!!)

The situation with "Echinoidea" is even worse. As near as I can tell, Family Echinidae was named by Gray in 1825 (thus implicitly naming Superfamily Echinoidea), but Class Echinoidea was already named by Leske in 1778. And the ICZN mandates that the superfamily including Echinus must be named "Echinoidea" if the family is named "Echinidae". I'm not sure how this is supposed to play out ... does Echinus simply not get a name for its superfamily? Those poor wee urchins....

(And people wonder why I support an alternative nomenclatural code without mandated suffixes for ranks!)

In the case of Chelonia, people are generally using another name ("Testudines") for the order nowadays, but in other cases I've got a real problem, especially if I hope to automatically pull a lot of this data from other databases.

PLoS ONE exPLoSiONE

2009-05-27T16:50:00.000-07:00

Others have said it before me, but I think PLoS ONE and online journals like it represent the future of scientific publishing. Quick turnaround, open access, unlimited space (not just for text, but also images, data files, etc.)—I just don't see how the older forms of journal can possibly persist for long.

Perhaps the most useful feature, though, is sadly underutilized. Imagine this—you're reading a paper and you come across an error, or a questionable inference, or an unclear point. With printed journals, you have the following options:

Write to the editor and/or primary author and hope they have a moment to respond.
Complain to whomever will listen.
Write a frustrated note in the margin and move on.
Fume silently.

But with PLoS ONE, you can accomplish #1–3 all at once. (And #4, if you want.) Simply log in, highlight the text you want to comment on (or click on "Leave a general comment"), and you can leave a publicly-visible note that anyone, authors and editors included, can respond to.

People have been slow to take advantage of this wonderful system, but it's starting to take off, I think. As many are aware, there's been a big media hubbub about a new fossil primate (Darwinius masillae) that may or may not be a stem-haplorhine (i.e., part of the group that gave rise to tarsiers and monkeys, including apes, including humans). I've seen a lot of discussion of it in various venues, and some of that is finally starting to spill over into the paper's comments section. (You may note a couple of comments left by myself.)

One notable outcome of the discussion on Darwinius is the rectification of an incompatibility between PLoS ONE's publication methods and the current requirements of the ICZN. This meant that the new scientific names published in the journal (e.g., "Darwinius", "Darwinius masillae") were nomenclaturally unavailable. Happily, this was quickly resolved, and the remedy was also carried out for the names introduced in some earlier papers.

Other discussions, on such topics as the scoring of characters as "Derived" or "Primitive", are still ongoing.

PLoS ONE also allows readers to rate the articles and leave reviews. (As of this writing, there is one review by Andy Farke, and I think he makes some excellent points.)

Science open to everyone! Go ahead—get involved.

'Nother Toolshop Animatic: The Head Map

2009-05-05T15:25:00.000-07:00

I created a sort of "mashup" of the previous two and added a temporary music track. (The ultimate version will have something different.) Click on the thumbnail (might take a moment to load):

Still clunky, but I'm just fleshing out the ideas at this point. Enjoy!

March of Man: The Toolshop

2009-05-04T10:33:00.000-07:00

My somewhat ambitious web app, March of Man, has not been proving too successful. The idea behind the project is to illustrate human and chimpanzee evolution using hundreds of figures. The web app includes tools for submitting images and generating collages. But there are only a couple dozen images right now. At this rate, the project will be completed by the time I am an old man. Time for a new approach!

I'm going to leave the site up as is, but I am also going to be working on a CG animation. I've made a new area of the website called "The Toolshop" where I'll be posting progress. Here are the first two mockups, using vector animation (click on the image to see the animation):

Human/chimpanzee evolution depicted as streams of bubbling heads.

The ranges of various taxa over time.

Enjoy!