Showing posts with label Vertebrata. Show all posts
Showing posts with label Vertebrata. Show all posts

04 March 2014

Deeper Dive on the PhyloPic T-shirt

Just to review:
  •  PhyloPic is a website featuring freely-reusable silhouettes of organisms. Anybody may submit images under a Creative Commons license.
  • I am attempting to raise funds to host PhyloPic for the next two years by selling a PhyloPic T-shirt, depicting the past half-billion years of our evolutionary lineage with free silhouettes.
We've come a long way.
In this post I'll go into more detail about what, exactly, is on the shirt, starting with the final silhouette and going back in time. In each entry, the taxonomic name links to a page for the image, with artist and license information. Some terminology first: "concestor" means "most recent shared ancestor", and "stem-X" means "not X, but more closely related to X than to anything else alive".


The final silhouette is a modern human, Homo sapiens sapiens, specifically a Melanesian woman. Melanesians and other Oceanians represent one of the furthest migrations of humanity from our original geographical range.

Immediately behind her is another Homo sapiens sapiens, this one a Subsaharan African man. Subsaharan Africa is the wellspring of modern humanity. (This isn't meant to imply an ancestordescendant relationship between the two figures; they're just coexisting members of the same subspecies.)

24 February 2014

Half a Billion Years in the Making: The PhyloPic T-shirt

Yes, now you can wear PhyloPic.

The PhyloPic T-shirt
PhyloPic's silhouettes are free, but hosting the site costs money. With this shirt, I'm trying to raise enough to cover basic expenses. If 100 of you buy a shirt, you will cover PhyloPic's hosting for the next two years.

The design uses PhyloPic silhouettes to depict the evolutionary lineage of humanity, starting with the earliest bilaterian animals. All of the silhouettes are public domain, or available under a Creative Commons Attribution or Attibution-ShareAlike license (which means the design itself is under a Creative Commons Attibution-ShareAlike license). The works of ten artists are featured:

The shirt is only available through March 15. As of this morning, 25 shirts have been purchased, meaning that we are exactly one quarter of the way to the goal. So help PhyloPic out, and get a great T-shirt! Or, if you can't*, at least help spread the word.

Do you have PhyloPic's back?

* Apologies, but shipping is only available in the U.S., Canada, and Army or Fleet Post Offices. But if this campaign does well, I'll certainly look into a more global option for future shirts. (Yes, plural. Why should Homo sapiens get all the fun? PhyloPic has good coverage of many other lineages.)

16 January 2012

In Anticipation: The Evolution of the Raven, in Silhouettes

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

01 March 2010

The Great PhyloCode Land Run

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.

22 July 2009

"The Case for Human Evolution" - Illustrations

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:


Enjoy!

24 June 2009

Human-Chimpanzee Systematics

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 1758Troglodytes 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.

27 May 2009

PLoS ONE exPLoSiONE

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:
  1. Write to the editor and/or primary author and hope they have a moment to respond.
  2. Complain to whomever will listen.
  3. Write a frustrated note in the margin and move on.
  4. 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.

09 November 2007

Who Ate What Now?

Most fossils, especially the older ones, are annoyingly incomplete. They'll find a few bones, or some footprints, a smudgy outline, etc. Then there are the more-or-less complete specimens, which are rarer but still not infrequent. And finally there are real "snapshots of life" which come along once in a great while. This latest discovery, for example:


Specimens with the remains of ingested animals are sometimes found, but I've never heard of this kind of "Russian doll" fossil before. Truly remarkable.




And now that I've finished marveling at it, it's time for me to return to character and bemoan the nomenclatural inaccuracies!

First, what are the actual animals involved? It's an Acanthodes bronni, eaten by a temnospondyl, eaten by a Triodus sessili. Is the headline accurate? Let's establish a few ground rules first.

Most taxa (at least of those that have been around a while) are based on living organisms. When related fossil organisms are found, there is often some dispute as to whether to include them or not. For example, when Archaeopteryx was discovered, people couldn't decide if it was a bird or not. It had feathered wings and bird-like feet, but also had teeth and a long tail. Did it fly? Who knows.

In the past, some people have recommended letting taxa extend as far as possible, encompassing what is known as the total group. A total group includes everything sharing closer ancestry with the living members of a group than with any other living organisms. This approach can run into some serious problems, though. For example, it would make all dinosaurs birds. More generally, it lumps the earliest, barely differentiated members of a lineage in with their derived, living descendants. This encourages the use of unjustified inferences. For example, I know that all living birds have tertial feathers (long feathers along the upper arm), so, since Archaeopteryx is a bird, it should have them, too, right? WRONG. Analysis of the available fossils has yet to indicate the presence of any tertials.

This is why many others encourage the use of crown groups for common taxonomic names. A crown group is the final common ancestor of certain living organisms, and all descendants of that ancestor. Using a crown group definition for Aves, for example, would limit it to the clade of modern birds, thereby excluding Archaeopteryx. This practice has the effect of discouraging unjustified inferences.

One other term to note here is stem group. This is simply a total group minus its included crown group. For example, a stem-avian is anything sharing closer ancestry with birds than with other living organisms (e.g., crocodylians), but outside the crown group Aves. Archaeopteryx and all the classic dinosaurs are stem-avians, as are (probably) pterosaurs.

Archosauria
|-Pan-Crocodylia (including Crocodylia)
`-Pan-Aves
|-Pterosauria *
`-+-Marasuchus *
`-+-Silesaurus *
`-Dinosauria *
|-Ornithischia *
`-+-Herrerasauridae *
`-+-Sauropodomorpha *
`-+-Eoraptor *
`-+-Coelophysoidea *
`-+-Dilophosauridae *
`-+-Ceratosauria *
`-Tetanurae

Tetanurae
|-Spinosauroidea *
`-+-Carnosauria *
`-+-Compsognathidae *
|-Tyrannosauroidea *
`-+-Ornithomimosauria *
`-+-Oviraptoriformes *
`-+-Deinonychosauria *
`-+-Archaeopterygidae *
`-+-Confuciusornithidae *
`-+-Enantiornithes *
`-+-Hesperornithes *
`-+-Ichthyornithes *
`-Aves

* extinct stem-avian taxon

Cladograms (somewhat abridged) showing the avian stem group.


Is Acanthodes a fish? Well, yes, they got that right. "Fish" is a really, really broad category, tantamount to "any craniate that isn't a tetrapod" (more or less). Specifically it is an acanthodian, which makes it a stem-osteichthyan (Osteichthyes being the crown group that includes bony vertebrates, e.g., ray-finned fishes, lungfishes, coelacanths, and tetrapods).

Are temnospondyls amphibians? O.K., this is harder. Traditionally, Amphibia was used as a "wastebasket taxon" for any tetrapod that was not an amniote. More recently, it has been limited to one of two groups: the total group including frogs, salamanders, and caecilians; or the crown group including frogs, salamanders, and caecilians. There is actually quite a bit of debate on this matter and I don't expect it to be resolved any time soon. According to the crown group usage, temnospondyls are definitely not amphibians. But according to the total group usage, they might be. (But they might also be stem-tetrapods or stem-amniotes.)

Is Triodus a shark? "Shark" is a really abused term in paleontology. (In fact, acanthodians are sometimes called "spiny sharks" even though they're not even chondrichthyans.) Among modern animals, the term is generally limited to Selachii, the flatter members of which are called skates or rays. Triodus is a stem-selachian, closer to sharks, rays, and skates than to ratfishes (Holocephali). So is it a shark? If we want to limit unjustified inferences, then we should say no.

Gnathostomata (jawed vertebrates)
|--Chondrichthyes (cartilaginous fishes)
| |--Holocephali (ratfishes)
| `--+--Triodus *
| `--Selachii (sharks, rays, skates)
`--+--Acanthodes *
`--Osteichthyes (bony vertebrates)
|--Actinopterygii (ray-finned fishes)
`--Sarcopterygii (flesh-finned vertebrates)
|--Dipnoi (lungfishes)
|--Latimeria (Recent coelacanths)
`--Apo-Tetrapoda (limbed vertebrates)
|?-Temnospondyli *
`--Tetrapoda
|--+?-Temnospondyli *
| `--Amniota
`--Amphibia sensu lato
|?-Temnospondyli *
`--Amphibia sensu stricto

* extinct

Cladogram of the taxa in question, with related extant taxa.


Okay, smarty, how would YOU dumb this down? Argh, that's pretty hard. Personally I think the lay public might be ready for the term "stem-", but I seem to have a bad habit of overestimating the lay public. Anyway, the best I can come up with is "Stem-Shark Ate Limbed Creature Ate Fish." Doesn't roll off the tongue, you say? Well, I guess this is why I'm not a journalist....



(References to be added later, if I have time.)