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Classic 1897 painting of Diplodocus

Contemporary depiction of Diplodocus
Credit: Nobu Tamura

A few weeks ago I happened to listen to a fascinating interview on NPR with Brian Switek, the blogger behind Laelaps, and author of Written in Stone: Evolution, the Fossil Record, and Our Place in Nature. Switek was discussing his newest book, My Beloved Brontosaurus: On the Road with Old Bones, New Science, and Our Favorite Dinosaurs. To be frank I was captivated by the discussion, and immediately purchased a copy of the book. The reason is simple: despite our current divergent interests Brian Switek began at the same place I did, with dinosaurs. Though after reading My Beloved Brontosaurus I can’t assert that my dinomania matched Switek’s, it was of the same quality. The difference is that while Switek remained true to dinosaurs, my own interests wandered into other domains. Today I am focused more upon evolutionary forces operating on the scale of thousands of years within a species, rather than geological scale transmogrifications. But every now and then I wonder about dinosaurs, and whatever happened to them over the past 20 years after my “dinosaurs years” faded into the distance.

And that exactly where Switek takes me with My Beloved Brontosaurus. I read The Dinosaur Heresies in the early 1990s, but that book is now 25 years old. Yes, like everyone else I’ve seen glimmers of the controversies of the debates about dinosaur metabolism and plumage over the years, but to truly get to the guts of the matter of what people think one needs to comprehend the scientific literature, not just watch NOVA specials. And that is what Switek does, as he tours us through abstruse and esoteric journals in paleobiology to get the heart of the matter in terms of what scientists believe and know. For me the narrative was especially fascinating because I am approximately the same age as the author, and experienced many of the same cultural changes in our perceptions of dinosaurs. From lethargic large lizards to bright feathered monstrosities.

There are three primary threads in My Beloved Brontosaurus. First, a cultural history of our society’s perception of what dinosaurs looked like, how they lived, what they were in some fundamental fashion. Second, there is the cutting edge science as to what we now know of dinosaur anatomy, behavior, and systematics. Third, there is Switek’s personal biography as it relates to dinosaurs, and his reminiscences of the experience of being at various field sites.

Credit: LadyOfHats

Our perception of dinosaurs and what we know about them today in a scientific manner are obviously related. Switek’s distillation of the latest peer reviewed literature would make far less sense if we didn’t have an understanding from where we came in terms of our perceptions and preconceptions. In the late 19th and early 20th centuries dinosaurs were “terrible lizards” literally in their depction. They were green or gray sprawling reptiles, torpid and cold-blood creatures which were destined for the dust-bin of history (ergo, “he is such a dinosaur!”). Today the view is totally different. Dinosaurs are not extinct, because birds seem to be a derived lineage of theropod dinosaurs (and the extinction of the non-avian lineage is but for the grace of meteor!). It is now the majority view that many, if not most, dinosaurs were both warm blooded, and, had feathers. Not only did they have feathers, but paleontologists have been able to reconstruct the pigmentation of some dinosaurs. Would you believe they had the plumage of magpies!

If you want to know if dinosaurs were social, what they sounded like, and why they may have risen to prominence in the late Triassic, My Beloved Brontosaurus has you covered. Switek’s scope of knowledge is awesome. In Jerry Coyne’s Why Evolution is True he is referred to as a graduate student in paleontology at Rutgers. The reality is that when those words were written Switek was an undergraduate. But it’s easy to see how one could just assume he had to be a graduate student. His peregrinations across the country in search of museums and dig sites reflects a personality which one ideally would find in a graduate student, but alas far too often one does not.

One point in this book that I do want to explore is the controversy over the extinction of the dinosaurs. The public perception is that the K-T boundary exists because of a massive meteor impact. But a few years ago I saw an interview with the paleontologist Peter Ward where he denied that this was established and accepted science, which took me aback. I was interested to see that in Switek’s telling this seems a minority position, and that most scholars still accept the K-T event’s paramount importance. This is reassuring, because too often historical scientists fixate on uniformitarianism to an almost irrational extent. The wiping away of massively charismatic genera after genera all across the world over the space of a < 1 million years suggests something genuinely catastrophic. Denying the likelihood of a major exogenous shock, as opposed to a more prosaic confluence of events, bespeak a paradigmatic narrowness. If there is anything My Beloved Brontosaurus did it was to prevent me from wasting my time reading the literature in this area.

I’m hoping Switek keeps following up with these sorts of books. This is in the classic “news you can use” for nerds genre.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Dinosaurs, Evolution, Paleontology 
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Spinger et al. doi: 10.1073/pnas.0334222100

By this time I’m sure you’ve encountered articles about the reconstructed last common ancestor of all placental mammals. Greg Mayer at Why Evolution is True has an excellent review of the implications, along with a link to a moderately skeptical piece by Anne Yoder in Science. Yoder’s piece is titled Fossils vs. Clocks, while the original paper is The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals. The results clearly support the “Explosive Model” in the figure to the left for the origination of placentals. That might prompt the thought: “isn’t this what we knew all along?”

The standard story for the last generation in the popular imagination is that a massive asteroid impact was the direct cause of the extinction of all dinosaurs (and of course a host of other groups) except the lineage which we now term birds. And yet it turns out that there is actually some debate about this, though at least in some form it seems likely that the impact is going to be important (see this Brian Switek piece for exploration of this issue, and the general opinion of the scientific literature as of now). The second aspect to focus on is timing. Contrary to the intuition of many, over the past 20 years molecular phylogenetics has inferred a very definite (on the order of tens of millions of years) pre-K-T boundary coalescence for the common ancestors of the disinct mammalian lineages. A plausible explanation for this is that these lineages diversified through allopatry, as the Mesozoic supercontinent fragmented. Morphological diversification of these mammalian lineages also may have occurred after the K-T event.

The reality is that I know little more about this domain than the “typical person off the street,” so why does this matter? It matters because the difference between model a and model b above impacts our assessment of the nature of the K-T event, and the construction of the “tree of life” in general. For example, if model a, that the diversification of placental mammals was an explosive event after the K-T boundary, with extant lineages derived from one common ancestor, is correct, was the selection of this ancestor a matter of chance, or did it have exaptations which allowed it to traverse the boundary? In contrast, if there were many different mammalian lineages which traversed the boundary than perhaps the nature of the diversification is less contingent? In regards to the K-T boundary issue, it seems on the face of it rather peculiar that anything but extreme circumstances which included the scale of an asteroid impact (perhaps with other necessary conditions). These aren’t trivial questions, and it is within this context that we need to frame our understanding of how life on earth came to be the way it came to be.

An issue which is of more direct interest to me is the long standing conflict between molecular phylogenetics and paleontology. In short, the paleontology seems to support the explosive model. This paper, using morphological traits in a phylogenetic context does just that. In contrast molecular phylogeneticists have long perceived there to be relationships on may genes which pre-date the boundary. So many in fact that it simply isn’t plausible from a genetic perspective that these groups were not reproductively isolated tens of millions of years before the K-T boundary. Yoder points out that the methods of the molecular phylogeneticists is not entirely comparable with that of this paper. And, critically, she suggests that estimation of the branch lengths in the nodes is a weak link within their argument. If you believe that paleontology speaks truly, then you believe in this paper. If you accept the robustness of molecular phylogenetic calibrations of the evolutionary rates of genetic change, than this paper’s dating of the diversification is unpersuasive.

Where do I stand? In more recent questions of human evolution (e.g., the divergence between chimps and humans) the molecular phylogeneticists won, and the bones contingent were wrong. But that is just one lineage. I have a hard time believing that the paleontologists could be wrong about such much. Obviously there’s an error in the assumptions somewhere within these scientific disciplines, but I can’t pinpoint it.

Citation: M. O’Leary et al., DOI: 10.1126/science.1229237

(Republished from Discover/GNXP by permission of author or representative)
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Update: That charlatan David Klinghoffer seems to be enjoying this. As a rule I don’t follow dishonest propagandists, but it’s interesting how appealing this sort of “two sides” story is to Creationists. End Update

Reading this article this morning, DNA and Fossils Tell Differing Tales of Human Origins, really aggravated me. I believe that it’s totally misrepresenting the tensions in the scientific process here, and misleading the public. The standard conflict/”two views” format is used, and to disastrous effect. Here are some of the sections which I found alarming:

The geneticists reached this conclusion, reported on Thursday in the journal Cell, after decoding the entire genome of three isolated hunter-gatherer peoples in Africa, hoping to cast light on the origins of modern human evolution. But the finding is regarded skeptically by some paleoanthropologists because of the absence in the fossil record of anything that would support the geneticists’ statistical calculation….

In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.

Although all known African fossils are of modern humans, a 13,000-year-old skull from the Iwo Eleru site in Nigeria has certain primitive features. “This might have indicated interbreeding with archaics,” said Chris Stringer, a paleoanthropologist at the Natural History Museum in London. “For half of Africa we really have no fossil record to speak of, so I think it’s quite likely there were surviving archaic forms living alongside modern humans.”

Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.

I could have quoted the whole piece and highlighted aspects which I think mislead in terms of public perception. There’s just so much. First, a minor factual issue: I’ve seen presentations on the East Africa Neandertal admixture, and the researchers seem to assume that that is due to “back migration” from Eurasia. In other words, the point about Neandertals being cold-adapted is irrelevant. Second, the big issue seems to be that some paleoanthropologists are unhappy. This is not a debate between all paleoanthropologists and all geneticists. In fact, some genetics are moderately skeptical of admixture because they think it might be due to population structure in the ancient African H. sapiens sapiens. Even within the article you have Chris Stringer, a paleoanthropologist, giving a straightforward reason for why there is a mild discordance here: a lacunae in the fossil coverage across much of Africa due to difficulties of preservation.

The major dynamic to me seems to be that Richard Klein, admittedly a very prominent paleonanthropologist, is also very ticked off. He has some reason to be. Much of the framework within which he has worked is now being shifted (see The Dawn of Human Culture). Klein’s model is that modern humans emerged as a singular speciation event within Africa, and rapidly expanded and replaced other human lineages in totality due to their peculiar genetic innovations (e.g., language). This is hard to align with the current genomic data. But Klein’s views are not the only ones within paleoanthropology. People like John Hawks, Milford Wolpoff, and Erik Trinkaus are no doubt excited by the new statistical inference techniques because they supports their own models, more or less.

What are you seeing here is a battle within paleoanthropology. It is probably correct that statistical geneticists should take more care to integrate fossils into their interpretative frameworks, but there are still plenty of fossil people who feel vindicated by the new genomic findings even granting this objection. Additionally, even those who don’t necessarily taking heart from these findings, such as Chris Stringer, are revising their own viewpoints. You can see the “other perspective” (i.e., not Klein’s) in this paper in Journal of Human Evolution: Did a discrete event 200,000–100,000 years ago produce modern humans?.

I do want to be clear here that I think Richard Klein and his camp are free to feel aggrieved. Science is about dispute and disagreement in many ways. But I think The New York Times does a disservice by confusing what is really a within field controversy into one between two scientific teams.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, Paleontology 
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There’s a new paper out, Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. The primary results are above. Basically, using 13 mtDNA samples the authors conclude that it looks as if there was a founder effect for Neanderthals in Western Europe ~50 K years ago, generating a very homogenized genetic background for this particular population before the arrival of modern humans. Perhaps it’s just me, but press releases with headlines such as “European Neanderthals Were On the Verge of Extinction Even Before the Arrival of Modern Humans” strike me as hyperbolic. I’m also confused by quotes like the one below:

“The fact that Neanderthals in Europe were nearly extinct, but then recovered, and that all this took place long before they came into contact with modern humans came as a complete surprise to us. This indicates that the Neanderthals may have been more sensitive to the dramatic climate changes that took place in the last Ice Age than was previously thought”, says Love Dalén, associate professor at the Swedish Museum of Natural History in Stockholm.

There are several points that come to mind, from the specific to the general. First, from what I gather Neandertals were actually less expansive in pushing the northern limits of the hominin range than the modern humans who succeeded them. From this many suppose that despite the biological cold-adapted nature of the Neandertal physique they lacked the cultural plasticity to push the range envelope (e.g., modern humans pushed into Siberia, allowing them to traverse Beringia). One might infer from this that Neandertals were more, not less, sensitive to climate changes than later human populations. Second, there is the fact that as the northern hominin lineage one would expect that Neandertals would be subject to more population size variations than their cousins to the south during the Pleistocene due to cyclical climate change. This is not just an issue just for Neandertals, but for slow breeding or moving organisms generally. The modern human bottleneck is in some ways more surprising, because modern humans derive from a warmer climate. Finally, there is the “big picture” issue that though we throw these northern adapted hominins into the pot as “Neandertals,” one shouldn’t be surprised if they exhibit structure and variation. Non-African humans have diversified over less than 100,000 years, at a minimum the lineages which we label Neandertals were resident from Western Europe to Central Asia for ~200,000 years. Wouldn’t one expect a lot of natural history over this time?

Presumably the authors focused on mtDNA because this is copious relative to autosomal DNA, making ancient DNA extraction easier. I’m a bit curious how it aligns with the inference from the Denisovan paper that Vindija and Mezmaiskaya Neandertals both went through a population bottleneck using autosomal markers. The dates from the paper’s supplements are not clear to me, though it seems possible that they may have sampled individuals where the Vindija population may have been post-resettlement. At some point presumably we may be able to get a better sense of the source population of the Neandertal admixture into our own genomes if the genomic history of this population is well characterized.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Human Evolution, Neanderthals, Paleontology 
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I missed this piece in Edge from Chris Stringer in November, Rethinking “Out of Africa”. He sums up his current thinking at the end:

We’ve got the lineage of the hobbit, ‘Homo floresiensis’ (in quotation marks because its human status in not yet clear), perhaps diverging more than two million years ago, evolving in isolation in southeast Asia, and apparently going extinct about 17,000 years ago.

We’ve got Homo erectus, most likely originating in Africa, giving rise to lineages which continue in the Far East in China and Java, but which eventually go extinct. In Europe, it perhaps gave rise to the species Homo antecessor, “Pioneer Man,” known from the site of Atapuerca in Spain. Again, going extinct.

In the western part of the Old World, we get the development of a new species, Homo heidelbergensis, present in Europe, Asia and Africa. We knew heidelbergensis had gone two ways, to modern humans and the Neanderthals. But we now know because of the Denisovans that actually heidelbergensis went three ways—in fact the Denisovans seem to represent an off-shoot of the Neanderthal lineage.

North of the Mediterranean, heidelbergensis gave rise to the Neanderthals, over in the Far East, it gave rise to the Denisovans. In Africa heidelbergensis evolved into modern humans, who eventually spread from Africa about 60,000 years ago, but as I mentioned, there’s evidence that heidelbergensis populations carried on in Africa for a period of time. But we now know that the Neanderthals and the Denisovans did not go genetically extinct. They went physically extinct, but their genes were input into modern humans, perhaps in western Asia in the case of the Neanderthals. And then a smaller group of modern humans picked up DNA from the Denisovans in south east Asia.

We end up with quite a complex story, with even some of this ancient DNA coming back into modern humans within Africa. So our evolutionary story is mostly, but not absolutely, a Recent African Origin.

Now, I know that Milford Wolpoff has still not totally buried the hatchet with Stringer, but their views are actually converging a great deal. What does that tell us? Well, paleoanthropology most definitely is a science, reality and results are dictating to the intellectual antagonists.

(Via Ruchira Paul)

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Human Evolution, Paleontology 
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Paintings at Lascaux, Prof saxx

Behavioral modernity:

Behavioral modernity is a term used in anthropology, archeology and sociology to refer to a set of traits that distinguish present day humans and their recent ancestors from both living primates and other extinct hominid lineages. It is the point at which Homo sapiens began to demonstrate a reliance on symbolic thought and to express cultural creativity. These developments are often thought to be associated with the origin of language.

First, I’d like to put into the record that I suspect that Neanderthals had language as we’d understand it. I suspect within the next few decades genomics may clarify the issue, because people with congenital linguistic defects will probably be sequenced to the point where we’ll get a sense of all the many regions of the genome necessary for language competency. We can then crosscheck that against the Neanderthal genome. So let’s take that off the table, even if it’s under dispute.

The term “behavioral modernity” is important because “anatomically modern humans” predate them by tens of thousands of years in Africa. Over 2 million years there had been a gradual increase in cranial capacity in the hominin lineage up until a leveling off ~100,000 years or so before the present. It is stated by many that in fact that the maximal cranial capacity of any hominin lineage was attained by the Neanderthals.

In the post below I suggest that perhaps the transition to modern humans as we understand them had less to do with a switch in “human universals” than a more complex change on the margins of a few individuals here and there. Greg Cochran has wondered if the majority of humans today would actually be termed “behaviorally modern” by an objective third-party observer. To bring the point home: consider how many humans can actually describe in any detail how an automobile works, as opposed to using an automobile? Cultural production as we know it today is almost magical in the way complex systems arise out of the coordinated activities of many people who have no idea as to the nature of the whole. This mysterious productive endeavor seems likely to distinguish behaviorally modern humans from their predecessors. But I suspect that this required far less change on a per person basis than we might think. The average modern human understands the inner working of a computer as well as a H. erectus.

(Republished from Discover/GNXP by permission of author or representative)
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Image credit:ICHTO

Recently something popped up into my Google news feed in regards to “Neanderthal-human mating.” If you are a regular reader you know that I’m wild for this particular combination of the “wild thing.” But a quick perusal of the press release told me that this was a paper I had already reviewed when it was published online in January. I even used the results in the paper to confirm Neanderthal admixture in my own family (we’ve all been genotyped). One of my siblings is in fact a hemizygote for the Neanderthal alleles on the locus in question! I guess it shows the power of press releases upon the media. I would offer up the explanation that this just shows that the more respectable press doesn’t want to touch papers which aren’t in print, but that’s not a good explanation when they are willing to hype up stuff which is presented at conferences at even an earlier stage.

A second aspect I noted is that except for Ron Bailey at Reason all the articles which use a color headshot use a brunette reconstruction, like the one here which is from the Smithsonian. But the most recent research (dating to 2007) seems to suggest that the Neanderthals may have been highly depigmented. This shouldn’t be too surprising when one considers that they were resident in northern climes for hundreds of thousands of years.

But there are some new tidbits, from researchers in the field of study:

“There is little doubt that this haplotype is present because of mating with our ancestors and Neanderthals,” said Nick Patterson of the Broad Institute of MIT and Harvard University. Patterson did not participate in the latest research. He added, “This is a very nice result, and further analysis may help determine more details.”

David Reich, a Harvard Medical School geneticist, added, “Dr. Labuda and his colleagues were the first to identify a genetic variation in non-Africans that was likely to have come from an archaic population. This was done entirely without the Neanderthal genome sequence, but in light of the Neanderthal sequence, it is now clear that they were absolutely right!”

The modern human/Neanderthal combo likely benefitted our species, enabling it to survive in harsh, cold regions that Neanderthals previously had adapted to.

“Variability is very important for long-term survival of a species,” Labuda concluded. “Every addition to the genome can be enriching.”

Since Nick comments here on occasion I probably should have asked him what he thought of these results back in January, but it goes to show that I’m not thinking like a journalist. Yet.

(Republished from Discover/GNXP by permission of author or representative)
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Yesterday Dienekes had a post up, Homo erectus soloensis fades into the past…. In it he states:

Every year or so there seems to be a redating of a key fossil in human evolution. It’s nice to see scientific self-correction in action, and soon after Neandertals got a little older, casting doubt on their supposedly long co-existence with modern humans, we now have a redating of Homo erectus soloensis from Java to about 150-550 thousand years ago, but certainly long before there were any anatomically modern humans in the area.

I think Dienekes is jumping the gun a bit in terms of the solidity of any given finding in knocking down prior consensus. That being said, the very young ages for Southeast Asian H. erectus, on the order of ~30-50,000 years B.P., always seemed strange to me. The paper Dienekes is referring to, The Age of the 20 Meter Solo River Terrace, Java, Indonesia and the Survival of Homo erectus in Asia, is rather technical in the earth science, as it involves dating and interpreting confounds in the stratigraphy. But this section of the discussion gets to the gist of the matter if you can’t follow the details of fossil dating:

If the middle Pleistocene40Ar/39Ar ages better reflect the age of the Solo River 20 meter terrace deposits and hominins, the site of Ngandong remains a relatively late source of H. erectus; however, these H. erectus would not be the contemporaries of Neandertals and modern humans, and their chronology would widen the gap between the last surviving H. erectus and the population from Flores – whose source population has been argued to be Indonesian H. erectus…although this point is contested…Instead, the Ngandong hominins would be contemporaries of the H. heidelbergensis from Atapuerca, Spain and elsewhere in Europe, and, possibly the archaic H. sapiensspecimen from Bodo (Ethiopia), which might favor arguments that they are more closely affiliated with these taxa and differ from H. erectus…S uch ages for Ngandong would suggest that a series of geographically relatively isolated lineages of hominins lived during the middle Pleistocene.

About three years ago I went to a talk given by Tim White, famed paleoanthropologist who was the maestro behind Ardi. He began by observing that fossils are real, concrete, and they matter. My own suspicion that is that White was taking a mild swipe at the prestige accorded to genetic inference in reconstructing the human past. In some ways White’s assertion would seem to be be validated. Svante Pääbo subsequently gave a talk at the conference where he very confidently ruled out Neandertal admixture into the modern human lineage. Pääbo famously did an about face on this issue later, because new data compelled him to do so. But, observe that the inferences generated are sensitive to the inputs you have available at any given moment.

Fossils are concrete and can be absorbed in a Gestalt fashion. You can visually see how much more robust earlier hominin lineages were when you look at their skulls! But the reality is that this sort of innate understanding of the general nature of a fossil has its limitations. Recall the conflicts of interpretation between paleoanthropologists which raged across the decades. Part of the issue is the matter of sample size. So much hinges on just a few specimens. And very few people alive have a command of the details of all these specimens to make an intuitive assessment of the issues at hand.

And just because the fossil is concrete, it doesn’t mean that all the contextual issues around the fossil are so cut and dried. Just like geneticists make inferences of facts unseen from patterns of variation they do see, so paleontologists need to make inferences as to the geology of a locale to accurately assess dates and fossil succession. Because of modern radiometric dating the errors are far less than they were in the past, but when you’re talking human evolutionary history the margin is far less than in other situations. A few tens of thousands of years here, and a few tens of thousands of years there, and pretty soon you’re talking a very long span indeed.

With the confused state of the understanding of modern human origins today fossils are even more important in pegging some of the parameters to fixed values in our models. Consider the possibility of admixture across human lineages. Genetics can tell us that two different lineages which were isolated from each other eventually co-mingled at some point in the future, but it’s a much sketchier thing to pinpoint where that event occurred. To do so is a matter of elimination of the possibilities. If the fossils tell us that other hominin lineages were thick on the ground in eastern Eurasia then the possibilities for admixture naturally present themselves. On the other hand, if it seems that hominins were very rare or extinct before modern humans, then they do not.

There are two extreme scenarios for the exotic ancestral elements in modern humans, the ~2.5% Neandertal in all humans outside of Africa, as well as the ~5% Denisovan in Melanesian populations. In one model the admixture event occurred outside of Africa, after modern humans left that continent. The distinctiveness between the two genetic lineages is a simple matter of geographic distance. Another model, which I believe Dienekes’ favors, is that the admixture is simply a reflection of the structure within the continent at the time of the “Out of Africa” event. In other words, ancient Africans were themselves compounds of different hominin lineages.

Obviously the nature of the fossil record matters a lot in weighing the probability of the disparate scenarios. Right now much of the world is a large blank spot. West and Central Africa, large swaths of East Asia after the earliest erectus finds, for example. So it is critical that the fossils that we do have are well dated. And because of the paucity of the fossil record much can ride on a solid date for a few specimens here and there. As a civilian it can get very frustrating, because it’s not really possible to adduce which side hast he right of a matter if there’s a conflict. But often that’s just how science is.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Human Evolution, Paleontology 
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Kennewick Man produced a cottage industry of journalism ~10 years ago, thanks to the political controversy around the science. Today the stakes are different. Consider this from John Hawks, “Agriculture, population expansion and mtDNA variation”:

I am less sanguine about their results for Europe. They show a gradual period of growth associated in time with the Younger Dryas (around 12,000 years ago), which could make sense in the archaeology. But I am not convinced that the “European” haplogroups here are really European to that time depth. We know that the Neolithic and post-Neolithic saw some large-scale shifts in the frequencies of mtDNA haplogroups in Central and Western Europe. Some Upper Paleolithic Europeans probably contributed mtDNA to this later population, but I have no confidence that the proportion was great enough to accurately infer the demography of that pre-Neolithic population. (This is also a problem with the current paper in Current Anthropology by Peter Rowley-Conwy. I’ll discuss this sometime soon.)

The next frontier in reconstructing the population history of Europe will be ancient DNA. A good sample of Neolithic and pre-Neolithic whole mtDNA genomes would settle this question and allow inferences about the kind of demographic recovery Europe underwent after the Last Glacial Maximum….

An open letter to Science highlights the same issue with Native Americans, Unexamined Bodies of Evidence:

In his News & Analysis story “Do island sites suggest a coastal route to the Americas?”…M. Balter discusses the implications of evidence that more than 10,000 years ago, people used marine resources and specialized technology on California’s Channel Islands. He mentions that some archaeologists, citing Spanish ethnohistorical observations, argue against interpreting the evidence as support for a coastal route from Alaska, suggesting instead that mainlanders used the islands seasonally. Later in the story, Daniel Sandweiss notes the need for DNA studies and states, “we need to find where the bodies are.”

Two such bodies, a rare double burial, were recovered during archaeological excavations at the University of California, San Diego, chancellor’s residence in 1976….

Unfortunately, the University of California administration has failed to honor research requests for the study of these unique skeletons. Instead, the University of California favors the ideology…of a local American Indian group over the legitimacy of science. In contrast, the 2004 Kennewick case verdict stated that there was insufficient evidence to establish that the skeleton was Native American or related to any living American Indian group (6). The potential loss of the La Jolla skeletons would have a profoundly negative impact on our knowledge of the peopling of the Americas and the antiquity of coastal adaptations

There are few points here. First, I’m a little confused as to why the letter was sent to Science. This is preaching to the choir. Perhaps for mobilization? You can find an ungrated screenshot here. But sending this letter to a more widely readable (to the public) journal might have been best. You need to get the masses on your side by raising broader consciousness. Despite all the talk of “hegemonic” science, I’m not sure I’d bet on the paleoanthropologists in a battle between them and Native American tribes purely on the plain of politics.

Speaking of politics, I think the scientists themselves have an ideological ax to grind: that of objective truth. I happen to share this value, this ideology. And I think broadly this value is shared by the broader public, with qualifications (alas). Science does not always hit upon objective truth, but when it comes to reality it’s the best bet we have. In a very concrete manner “folk positivism” is the ascendant ideology of our day. We shouldn’t pussyfoot around this point, if we push the issue on the normative grounds of truth, we’ll win. They have their ideology. We have ours. The truth will win out.

Third, John Hawks touches upon a major broader possibility when it comes to the migration of peoples: that the past was characterized by more population genetic turnover than we had previously thought. The mythologies of many peoples, such as the ancient Athenians, assert a rooted indigenous origin, which just isn’t true upon further reflection. So the claims of a local resident native population upon the bones of “ancestors” is a highly time sensitive assertion. 50 years makes sense. 5,000 years is open to contention.

Rex Dalton has more in Wired. The science is actually more interesting than the politics, in terms of what the skeletons might tell us. But it might never happen because of politics.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, Paleontology 
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There was a reference to complex pre-Cambrian life in a book I’m reading, Kraken, and it made me double-check Wikipedia’s Cambrian explosion entry. Lacking total clarity, I decided to read a new paper which was published in Nature, Earth’s earliest non-marine eukaryotes. The Cambrian explosion is pegged to ~500 million years ago, but these data indicate a freshwater ecosystem which predates ~1 billion years before the present. Also, there was weird stuff in the discussion which startled me:

…Early eukaryotes were clearly capable of diversifying within non-marine habitats, not just in marine settings as has been generally assumed. This idea directly supports phylogenomic studies which find that the cyanobacteria evolved first in freshwater habitats and later migrated into marine settings….

Cyanobacteria are the ubiquitous blue-green algae which were’t familiar with. New Scientist has some quotes from paleontologists who seem to think that this paper is credible. There’s a good and a bad to this. The good, I’ll have to read up on this area which I’m so fuzzy about in terms of details. The bad is that it slices my finite time pie even more.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Natural History, Paleontology 
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I was thinking a bit about H. floresiensis today. Probably my thoughts were triggered by John Hawks’ post on the propensity for paleontologists to be “splitters,” naming new finds as species when they’re not. The issue with H. floresiensis is a little more cut & dried: if they weren’t a separate species they were obviously pathological. The original paper on the Flores hobbits came out in 2004. Is it too much to ask for a little clarity here six years on? Carl Zimmer has covered this story in depth before, so perhaps he’ll have some insights or inside sources who can shed some light at some point in the near future. John Hawks was sure that the specimens were pathological in the early days, but he hasn’t said much for a bit now. And from what I hear there are new controversies about “Ardi”. I was at a talk years ago where Tim White played up the importance of fossils as the final word, as opposed to the more indirect inferential methods of statistical genetics, but this is getting ridiculous. After the Neandertal admixture paper and the Denisova hominin, genomic inferences are looking pretty good. I assume there’s more coming in the near future (though Svante Pääbo may have kidnapped family members of people working in his lab to gain leverage, so word probably won’t start leaking until a few weeks before the paper breaks). Ötzi the Iceman is going to have his genome published next year.

With all that as preamble, here’s a new paper, Post-Cranial Skeletons of Hypothyroid Cretins Show a Similar Anatomical Mosaic as Homo floresiensis. It’s in PLoS ONE, so read it yourself. Does anyone care? I don’t know enough about about anatomy and osteology to make well-informed judgments about these sorts of things, so to the experts I absolutely defer. But frankly some of the experts strike me jokers. Here’s the problem: I don’t know who the jokers are!

I just went back and reread some of the press when the hobbit finds were revealed. New member of the human family tree! Evolution rewritten! And so forth. If H. floresiensis turns out to be pathological, I don’t know what to think about paleontology. More honestly, I might start slotting the discipline in with social psychology or macroeconomic modeling.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, Hobbits, Human Evolution, Paleontology 
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551px-Monito_del_Monte_ps6Though I don’t blog about the topic with the breadth and depth of individuals such as Brian Switek or Darren Naish I do take some interest in natural history. This is the domain which was my original focus as a child when it came to science, and I continue to observe it from afar with great fondness. General questions, such as the role of contingency and necessity in the arc of evolution, are obviously the sort of issue which natural history can be brought to bear upon. But I also have a fascination with specific, often anomalous details. For example, the Monito del Monte of Chile is generally held to be more closely related to the marsupials of Australia than those of the New World. It is the only extant member of the order Microbiotheria, and its connection to Australian marsupials is one of those surprises which go to show you why science is done in the field, and not just theorized from your a priori beliefs. It’s why you play the game, and don’t simply allow the handicapping professionals to decide wins and losses.

A new paper in PLoS Biology explores the phylogenetic relationship of Australian and New World marsupials through a more robust genomically focused technique. Though the method has a “in silico” spin, the basics seem to be grounded in cladistics. Look for derived characters which can indicate monophyly. Monophyly simply means that all of a set of organisms descend from one common ancestor. So, famously, the class of reptiles is not monophyletic. Some of the descendants of the common ancestors of all reptiles are not included within the class, birds. Earlier generations of taxonomists tended to classify organisms based on their characters, and the set of characters which they chose for reptiles included groups, such as crocodiles and tortoises, which were genetically very distant (when compared to crocodiles and birds). Though anatomically informative, these sorts of taxonomic classifications misled one as to evolutionary history. Not a minor matter. Ergo, the rise of cladistic techniques which replaced intuition with a more formal hypothetico-deductive framework. Because of its generality as a method naturally you can substitute genetic loci for morphological character traits, and so you get papers such as the one below.

ResearchBlogging.orgTracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions:

Ever since the first Europeans reached the Australian shores and were fascinated by the curious marsupials they found, the evolutionary relationships between the living Australian and South American marsupial orders have been intensively investigated. However, neither the morphological nor the more recent molecular methods produced an evolutionary consensus. Most problematic of the seven marsupial groups is the South American species Dromiciops gliroides, the only survivor of the order Microbiotheria. Several studies suggest that Dromiciops, although living in South America, is more closely related to Australian than to South American marsupials. This relationship would have required a complex migration scenario whereby several groups of ancestral South American marsupials migrated across Antarctica to Australia. We screened the genomes of the South American opossum and the Australian tammar wallaby for retroposons, unambiguous phylogenetic markers that occupy more than half of the marsupial genome. From analyses of nearly 217,000 retroposon-containing loci, we identified 53 retroposons that resolve most branches of the marsupial evolutionary tree. Dromiciops is clearly only distantly related to Australian marsupials, supporting a single Gondwanan migration of marsupials from South America to Australia. The new phylogeny offers a novel perspective in understanding the morphological and molecular transitions between the South American and Australian marsupials.

Retroposons are genetic elements which insert randomly throughout the genome, and rarely in the same location in across lineages. This avoids “false positives” where you observe genetic features across taxa which you incorrectly infer to indicate a phylogenetic relationship. The pattern of variation of randomly distributed distinctive retroposons can theoretically be used to map the sequence of relatedness of the same genes (orthologous) across species. Retroposon insertions copious within the marsupial genome, so naturally they’re a good candidate for markers which might exhibit the distinctiveness necessary to explore deep time evolutionary relationships. Additionally retroposons can nest within each other, within newer insertion events overlain over older ones, so that they create a sort of genetic palimpsest. These researchers filtered the loci harboring retroposons down to 53 which were particularly informative for relationships across the marsupial species for which they had genomic data, two species per order excluding orders without more than one species. The two species within each order were selected from lineages which were presumed to exhibit the deepest evolutionary split within the clade.

Granted, it isn’t as if taxonomists haven’t been interested in the relationships of marsupial mammals. As noted in the paper the nature of the phylogenetic tree frames plausible hypotheses which explain the current biogeographic pattern we see. Where there are two sets of marsupial mammals separated by the Pacific, but where the spatial pattern does not perfectly correspondent to the phylogenetic relationship. Here is a figure from a 2004 paper:


Australian and South American marsupials are color coded. As you can see, Dromiciops, Monito del Monte, is nested within the monophyletic clade which includes all the Australian mammals. But, the aforementioned paper was based on mitochondrial DNA. The DNA passed along the maternal lineage, easy to extract and amplify, as well as analyze (because of the lack of recombination). But for the purposes of exposing such deep time relationships mtDNA may not be optimal, and should not be the last word.

Much of the “guts” of the paper was obviously computational, and wasn’t explored in detail within the text. So let’s jump to the outcome, the new branch of the tree of life for marsupials:


Ah, now you see that Australian marsupials are a monophyletic clade! The Monito del Monte is no longer nested within their own lineage, but is now an outgroup. It would be peculiar if it was not the closest of the outgroups, so its positioning is reasonable in terms of what we’d expect. From the discussion:

Given the limitations just mentioned, the retroposon marker system identified a clear separation between the South American and Australasian marsupials. Thus, the current findings support a simple paleobiogeographic hypothesis, indicating only a single effective migration from South America to Australia, which is remarkable given that South America, Antarctica, and Australia were connected in the South Gondwanan continent for a considerable time.

The search for diagnostic South American or Australidelphian marsupial morphological characters has been so far confounded by the lack of a resolved marsupial phylogeny…The newly established marsupial tree can now be applied not only to morphological and paleontological studies but also to clearly distinguish genomic changes.

Life is not always parsimonious, but when more powerful techniques which can resolve issues to a greater degree of precision produce more parsimony, then the world is as it should be in science. The main curiosity I have is to wonder if the outcome isn’t a little too convenient for the generation of more elegant paleontological models. I’m not casting doubt on the integrity of the researchers, but with methods which require such heavy cognitive lifting, and operationally are a touch opaque because of the technical component, one would be assuaged by replication. I believe we will be in the future. If we have $1,000 genomes for human beings in a few years, NSF grants for taxonomists who lean on genomics may go a lot further in 2020.

Image Credit: José Luis Bartheld from Valdivia, Chile

Citation: Nilsson MA, Churakov G, Sommer M, Tran NV, Zemann A, Brosius J, & Schmitz J (2010). Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS biology, 8 (7) PMID: 20668664

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Evolution, Paleontology 
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That’s what Kambiz Kamrani is saying. Significance:

Owen Lovejoy is one of the authors of the paper, and he says that the fossil changes the notion that humans and chimps, our closest genetic cousins, both trace their lineage to a creature that was more like today’s chimp and we’ll have to be rewriting our text books soon. This is big folks. What this means is that our common ancestor was a bipedal forest forager and that chimps were an evolutionary offshoot.

Update: John Hawks & Carl Zimmer.

Update II: Science‘s Ardipithecus page is up. You can get the papers free with registration.

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• Category: Science • Tags: Paleontology 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"