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Showing posts with label evolution. Show all posts
Showing posts with label evolution. Show all posts

01 July 2014

The Evolution of Cranial Capacity in Humans and Stem-Humans

(Hey, I'm actually writing on the blog's title subject today!)

Here's a chart I've been working on for a while:


This shows all known human and stem-human individuals, plotted according to stratigraphy and cranial capacity (endocranial volume). The fossil individuals with known cranial capacity are highlighted as white circles; other fossil individuals' probable capacity is inferred from these. The "chimpanzee range" shows the span between a normal female bonobo chimpanzee (Pan paniscus) and a normal male common chimpanzee (Pan troglodytes) (Begun & Kordos 2004); the full range for chimpanzees (Pan) is slightly larger (but not much). The "human range" shows where about 90% of living humans fall (Burenhult 1993). UPDATE: My mistake, it's the range of ~90% of living humans combined with the range of Upper Pleistocene humans (which is actually higher, on average).

Some notes:

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.)

02 January 2013

All Known Great Ape Individuals (Messinian to Present)

Happy 2013, everyone!

Recently I announced a code package I was working on, called Haeckel, for generating vector-based charts related to evolutionary biology. Here's an image I've created using it:

Known Great Ape Individuals
This chart represents all known hominid individuals (Hominidae = great apes, including humans and stem-humans) from the Messinian to the present, erring on the conservative side when the material is too poor to determine the exact number.

If you've been following this blog for a few years you may remember an earlier version of this. I've done a lot of refinement to the data since then. The earlier versions were dissatisfying to me because the horizontal axis was essentially arbitrary. For this version I used matrices from a phylogenetic analysis (Strait and Grine 2004, Table 3 and Appendix C) of craniodental characters to generate a distance matrix, and then inferred positions for other taxa based on phylogenetic proximity and containing clade. This is similar to the metric I used in this chart, except that it incorporates Appendix C, uses inference, and averages distance from humans against distance from [Bornean] orangutans. Don't be mistaken  this is still arbitrary. But it's a bit closer to something real.

Stray notes:
  • I'm pretty sure there are Pliocene stem-orangutans somewhere, right? Might have some work left to do on that data.
  • The dot with no taxon above "Australopithecus" is an indeterminate stem-human from Laetoli. It should probably go further left.
  • The Ardipithecus bubble includes the poorly-known "Australopithecus" praegens. (Although in some runs it moves outside  there's a random element to the plotting.)
  • The Holocene is barely visible up at the top. What a worthless epoch.
  • Homo floresiensis (hobbits) are far to the left of Homo sapiens because I placed them outside Clade(Homo erectus  Homo sapiens).
  • You may recall Lufengpithecus? wushanensis as "Wushan Man", as it was originally placed in Homo erectus. (Hey, it's just teeth.)
  • A couple of fossil chimpanzees, lots of fossil orangutans, but no fossil gorillas. :(
    • (Unless you count Chororapithecus, but that's pre-Messinian. Very pre-Messinian. Suspiciously pre-Messinian....)
  • Look at all that overlap between Homo, Paranthropus, and Australopithecus!
    • I have a feeling, though, that if I added another dimension, Paranthropus and Homo would jut out in opposite directions.
    • Reclassifying Australopithecus sediba as Homo sediba would also decrease the overlap. (Although its position is inferred  actually scoring it might do the same thing.)
    • It's frustrating that the type species of Australopithecus and Paranthropus are also just about the most similar species across the two genera.
  • Kenyanthropus and Praeanthropus have been provisionally sunk into Australopithecus.
  • Should we just sink Orrorin and Sahelanthropus into Ardipithecus? Why not?
  • My guess is that if I added postcranial characters, the stem-humans would all shift right (humanward). Oh, for a good matrix of postcranial characters....
Update
Oh yeah, and if you want a peek at the data, go here.

02 December 2012

Haeckel: A Code Library for Browser-Based Evolutionary Diagrams

For a while now I've been writing posts with diagrams like this one, showing the evolution of cranial capacity in mangani over the past seven million years:


How did I make them? Originally it was all ad-hoc ActionScript code, but more recently I've begun to organize the code into a library and translate it into TypeScript (which, in turn, is automatically translated into JavaScript). Although this library is still in progress, I've decided it's at a stage where I can open it to the general public.

This library includes functionality for:

  • Modeling scientific concepts such as taxa, phylogeny, character states, stratigraphy, and geography.
  • Processing scientific data (notably calculating morphological distance and inferring unknown character states).
  • Rendering data into charts as Scalable Vector Graphics, using RaphaëlJS.
For a while I struggled with what to call this library. It's neither purely about science nor purely about graphics. Finally I got my inspiration from RaphaëlJS, a graphics library named after a great artist. I named my library after a man who was both a great artist and a great biologist:

21 August 2012

Closest to Humans: The Skull & Tooth Version

Previously I posted a diagram showing how different various primates are from humans, based on soft tissue characters.  Here is a similar diagram, but using the craniodental characters from Strait & Grine's (2004) matrix. Unlike the soft-tissue diagram, this includes fossil taxa.



This black lines indicate the probable distance, as inferred from the phylogeny. The gradients show the actual range of uncertainty. (They'd also show polymorphism, but this matrix has none.) Ordering is according to probable distance—using the mean of the range of uncertainty yields slightly different results.

As in the soft-tissue diagram, chimpanzees are closer to humans than any other living primates are. But, oddly, gibbons and colobus monkeys are closer to humans than gorillas and orangutans! My guess is that this is because gorillas and orangutans are more derived from the ancestral catarrhine state than gibbons or colobus monkeys. (This probably also explains why the Paranthropus species, a.k.a. "robust australopithecines", are further than chimpanzees, although it is strange that the earliest one, P. aethiopicus, is furthest.)

To the right of chimpanzees is a very unsurprising pattern: "gracile australopithecines", then basal Homo species, then the large-brained Homo ergaster, and finally the huge-brained Homo sapiens.

You can also see how well-known the fossil crania are, ranging from the very well-known Australopithecus africanus to the crushed skull of Kenyanthropus platyops. Note that Ardipithecus ramidus is much better known now than when this study was done.

Again a disclaimer: this is not an objective measure of morphological similarity (there is no such thing), and it is definitely not a phylogenetic analysis (even if the data is taken from one).



References



  • Strait & Grine (2004). Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa. Journal of Human Evolution 47:399–452. doi:10.1016/j.jhevol.2004.08.008

17 August 2012

Refinement: Primate Anatomical Similarity

Earlier, I posted a chart showing how similar humans are to other primates (and other euarchontoglires),  as measured from Diogo & Wood's (2011) soft-tissue character matrix. A problem with the earlier version was that it doesn't reflect uncertainty in that matrix. (It also wouldn't show polymorphisms, although that matrix doesn't have any, anyway.) I've created a new version that shows the maximum and minimum possible distance, given the uncertainties in the matrix.




08 August 2012

How similar are we, anatomically, to other primates?

There is no objective way to measure anatomical similarity, but you can get a sense by converting character matrices into distance matrices. I've done this for the matrix used by Diogo & Wood (2011), which looked at soft tissue anatomy. Here is a bar chart showing how similar each taxon is to humans:


Dangit, 2011, not 2010. I'll fix it later.
Click for full size.
As you can see, the distances for great apes are well-marked and exactly what you'd expect based on phylogeny, but past that it gets a bit fuzzy. Moving outward from the great apes we get to Old World monkeys, then gibbons (from phylogeny you'd expect gibbons first, but the difference is so minor I'm sure it's meaningless), then a mixture of non-catarrhine primates, and finally non-primates.

This figure was generated using a JavaScript library I'm developing. I'll say more later, but rest assured it will be free and open source.

Expect to see some more stuff like this on A Three-Pound Monkey Brain soon.

References


  • Diogo & Wood (2011). Soft-tissue anatomy of the primates: phylogenetic analyses based on the muscles of the head, neck, pectoral region and upper limb, with notes on the evolution of these muscles. J. Anat. 219:273359. doi:10.1111/j.1469-7580.2011.01403.x

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

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.)




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.



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:

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.

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!

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!

23 December 2010

What is a human?

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 (ArdipithecusOrrorinSahelanthropus). 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, ArchaeopteryxIchthyornis
  • 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 46% 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 complexthe 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 itour 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 23:449480. [PDF]
  • Green & al. (2010). A draft sequence of the Neandertal genome. Science 328:710722. 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 491503 iEarly Modern Humans at the Moravian Gate. Springer Vienna.  doi:10.1007/978-3-211-49294-9_17

04 January 2010

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

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 200th 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)

CollectionUppsala domkyrka, Uppsala, Sweden (Sverige), Europe
NameCarl Linnaeus
Other NamesCarolus Linnaeus (Latin)
Carl von Linné (after ennoblement)
Carolus von Linné (Latin, after ennoblement)
L. (standard abbreviation in botanical literature)
Remainsinterred corpse
Geographyborn in Älmhult, Småland, Sweden (Sverige), Europe
died in Uppsala, Sweden (Sverige), Europe
Chronologyborn 1707 CE May 23
died 1778 CE January 10
Sexmale
Age71 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, 4th 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 (2nd 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.

20 November 2009

More Human Evolution Diagrams

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.
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