19 December 2011

Season's Greetings

Season's Greetings 2011

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.

16 November 2011

What Is and Is Not a Stem Group

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 (sadlyit'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!

04 November 2011

Lucy Gwyn Havens

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!

11 October 2011

Human Clades: A Look at a Complex Phylogeny

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 examplewhile 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.)


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.

15 September 2011

Soft Tissue Characters Supporting the Great Ape Clades

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 200:349. 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:

31 August 2011

Characters that Support the Great Ape Clades

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:

30 August 2011

Guest Post: Similarities Between Macaque and Human Brains

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 Monkeys
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
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.

27 May 2011


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.

08 March 2011

To Flash or not to Flash

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.

05 March 2011

PhyloPic Week 2: Lineages, Browsing, and API

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:
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.


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!

28 February 2011

The First Week of PhyloPic

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:

Evolution of the Human

(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!

21 February 2011

Introducing PhyloPic: An Open Database of Reusable Silhouettes

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...

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

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

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.)

04 January 2011

Hybridizing Stem-Humans: Or, Is Everyone Right?

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 Homocould 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.


  • 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 328:710722. 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