Razib Khan One-stop-shopping for all of my content

September 30, 2018

The shadow of the Ice Age

Filed under: paleontology,Wolves — Razib Khan @ 1:55 pm

As ancient DNA becomes a more standard part of archaeological science it’s going really yield up some doozies. You’ve probably read Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, and how it’s upended old paradigms. But with the human past we probably have a better idea of the range of possibilities. When it comes to other organisms it’s going to be a weirder and wilder ride I predict.

This is why a new preliminary result does not shock me, Ancient Japanese wolf may be rare remnant of ice age wolves:

The wolf’s DNA more closely resembled that of a long-extinct wolf that lived in Siberia more than 35,000 years ago than that of living Eurasian and American wolves, Niemann reported here on Friday at the International Symposium on Biomolecular Archaeology. Most ancient wolves went extinct when the ice sheets that covered the Northern Hemisphere began to melt more than 20,000 years ago and the large mammals the wolves hunted, such as mammoth, died off. But some of their DNA lived on in the Honshū wolf, which could offer a new window on the evolution of wolves as well as dogs, says paleogeneticist Mikkel Sinding of the Greenland Institute of Natural Resources in Nuuk, who extracted the DNA.

Unfortunately the last Honshu wolves were killed more than a century ago. But for the purposes of DNA extract that’s basically yesterday.

From everything I can see the “megafauna” that inhabit the Palearctic ecozone seem to have through a lot of mass extinctions over the last 50,000 years. This extends from Neanderthals, to mammoths, to large canids and felids. Some lineages, such as that of humans and wolves, also underwent expansions from the remaining branches of the phylogenetic tree. But it’s reasonable that various relic groups of earlier diversifications might persist here and there.

April 20, 2018

Humans as the necessary but not sufficient cause of mega-faunal extinction

Filed under: paleontology — Razib Khan @ 12:57 am

The figure above is kind of hard to parse, but it’s from Body size downgrading of mammals over the late Quaternary, and it illustrates that in some periods larger animals tended to go extinct, while others there was no bias due to size (in fact, large animals tended to do quite well because of their wide ranges). I was pointed to this paper by an Ed Yong piece in The Atlantic, In a Few Centuries, Cows Could Be the Largest Land Animals Left.

One of my peeves with the overall field of natural history is that sometimes researchers just want to argue about the obvious because they can. Natural history is obviously historical, and so you can’t just run an experiment and settle things. It seems pretty clear to me looking at the pattern across the past two million years across six continents that humans are not the sufficient cause of megafaunal mass extinction but they are a necessary cause.

If it wasn’t for humans, mammoths would still be around. How do I know this? They were around for hundreds of thousands of years a minimum and made it through the Emian interglacial from 130,000 to 115,000 years ago when the world was actually warmer than it is today.

The major work of the paper above was assembling a large data set across a wide time period and geographic expanses. You can see that the emergence of Homo, and not just modern humans, is really what matters. The labels above are:  LQ, average of all late Quaternary (LP to H) extinctions; LP, late Pleistocene; EP, end Pleistocene; TP, terminal Pleistocene; H, Holocene; and F, future extinctions. The end of the Pleistocene was probably bad because the shock of the climate change probably knocked out a lot of species which were already under pressure from humans.

I’ll leave you a quote from Yong’s piece:

When hominins like Neanderthals, Denisovans, and modern humans spread through Europe and Asia, the average mass of mammals there halved. When Homo sapiens later entered Australia, the mammals there became 10 times smaller on average. And when they finally entered the Americas, with effective long-range weapons in hand, they downsized the mammals there to an even steeper degree. By around 15,000 years ago, the average mass of North America’s mammals had fallen from 216 pounds to just 17.

Addendum: The reason that Holocene extinctions have a smaller size average is that there weren’t as many big mammals to kill. We’re pretty much moving down the trophic layers now….

April 18, 2018

The braided estuary of human evolution

Filed under: Genetics,Human Evolution,paleontology,science — Razib Khan @ 2:22 pm

Metaphors matter because they evoke images, and images are often one of the best ways to understand something in a deep fashion. Consider Charles Darwin’s musing:

“It is interesting to contemplate a tangled bank…

He brought something memorable and familiar to make evocative the dynamics at play in his novel theory of evolutionary change through natural selection. The tangled bank has haunted us for over 150 years, though as a friendly apparition to be sure.

Other metaphors are less useful, and even downright destructive. The great chain of being hooks into deep human intuitions about our “special” place in nature and centrality in the universe. “Previously made in the image of our Creator” in the 19th century, science confirmed peoples’ expectations that modern humans are the pinnacle of evolution and the end of a long process of change; from the slouching ape, to the shuffling caveman, and finally, to the upright and thinking man.

The earlier view of Neanderthals was typical and illustrative of where we once were. Originally relegated to a primitive dead-end of our family tree, Neanderthals were depicted as bestial half-men at best. As late as the 2000s many researchers, such as the influential paleoanthropologist Richard Klein, doubted that humans and Neanderthals could produce offspring. There was skepticism from these quarters that Neanderthals could speak, or that they even used fire!

With the confirmation through myriad genetic analyses published from 2010 onward that in fact humans outside of Africa carry 1–2% Neanderthal ancestry, a transformation occurred in our perceptions of our cousins…or rather, our ancestors.

Clearly our understanding of human evolution is conditioned by our cultural preconceptions, our biases. Evolutionary biologists have long warned of the tendency to see in the “tree of life” directionality or purpose, but in the public’s mind the purpose of the universe is manifested in our own lineage. All of the pitfalls that we’ve attempted to avoid when considering evolutionary biology became stark and endemic in the study of humanity.

Unfortunately, paleoanthropology often fed into this narrative because of the paucity of remains.There was very little data, and an empire of theory and supposition cropped up in its place. The prominence of superstar researchers and their associated singular remains, Raymond Dart and the Taung child, Richard Leakey and the Turkana boy, and Donald Johansen and Lucy, highlighted the almost artisanal quality of the field.

As a result of only a few individuals being able to analyze the material evidence for the evolution of our own species, we eventually assembled a relatively neat ascending tree, with a few stray side branches. Like modernist architecture, paleoanthropology constructed a spare and elegant scaffold within which to understand the emergence of what we call humanity. Our story was simple, singular, and implicitly progressive. All paths led to us.

But just as genetics has changed our understanding of the origins of our species, so paleoanthropology itself is undergoing a revolution of sorts because of the veritable flood of data. Remains.

At the end of 2013 I happened to have been present when Lee Berger, a South African paleoanthropologist, presented work that reported on a deep cave where copious remains of a new hominin, Homo naledi, were being assembled and analyzed. Whereas previous researchers often focused on fragments, or the skeleton of a single individual, Berger explain that many remains were to be found in the cave system. This was going to be statistically-sound science, because he had much more than one sample.

To assemble the team that was small and nimble enough to venture into the cave, he reached out to paleoanthropology researchers via social media. And once the data came in, he published it quickly, at the same time releasing the information to other researchers.

The implications for paleoanthropology as it was practiced were revolutionary in and of themselves, but the results were also ground-breaking. H. naledi stood at five feet or shorter. Their cranial capacities were 30% those of modern humans. Meanwhile, their skeletal features were an assemblage of characteristics which seemed both very modern or very ancient. A simple role in a simple story did not present itself.

H. naledi reconstruction

This hominin confounded expectations. If the sample was singular, no doubt there would be skeptics. But Berger had the numbers, so that could not be denied. When the dates came back there was also another shocker: H. naledi flourished a bit over ~200,000 years ago. The reality though is that species invariably are found after and before the datings of particular remains. H. naledi almost certainly occupied the same landscape as early modern humans, who were developing within Africa 200-300 thousand years ago.

Meanwhile, far to east, on the island of Flores, were the Hobbits — H. floresiensis, a diminutive hominin that flourished until modern humans arrived in the region more than 50,000 years ago.

H. floresiensis

The reason that naledi and the Hobbits are important is that they shatter our image of an ascending chain of evolution progressing from lower to higher. The reality that modern human have genes from ancient Eurasian hominins, such as Denisovans and Neanderthals, also refute a simple model whereby humans were born, they came, and they conquered. Humans were both the conquered and conqueror.

Hundreds of thousands of years ago our lineage was highly speciose, with many diverse branches. Modern genetic technology implies that human lineages branch and come back together again and again, like an eternal cycle. The proliferation of ancient remains that are startling in their novelty and shocking in their recency also suggests that the shift in human evolution from slouching, small-brained apes to tall, large-brained apes was not the only way to be human. After all, the largest-brained hominins of all were Neanderthals, who eventually merged back into the much more massive stream of African humans who are our primary forebears.

Maybe you have some Neanderthal or Denisovan in your DNA. Discover your story today with Neanderthal by Insitome.

The braided estuary of human evolution was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

March 21, 2018

The Others were people too

Filed under: Genetics,Human Evolution,paleontology,science — Razib Khan @ 12:25 pm
Neanderthals, cousins we knew.

In 2010, our understanding of Neanderthals, our human cousins, changed forever. Before this year, there was a live debate about whether they were human at all, whether they had fully elaborated language, or even culture.

When A Draft Sequence of the Neanderthal Genome was published in Science, we found out that all humans outside of Africa, and some within Africa, had some ancestors who were Neanderthal. In the wake of this finding, a renaissance of Neanderthal humanization occurred. Previously, Neanderthals were just a ‘dead-end’ in our ancestral lineage.

Denisova Cave

In December of the same year, Nature published Genetic history of an archaic hominin group from Denisova Cave in Siberia. While Neanderthals had been part of our cultural landscape for over 150 years, these hominins discovered in Denisova cave were a shot out of the dark. Debates about Neanderthals’ humanity raged for years, and this discovery certainly promoted more.

Called Denisovans, after the Siberian cave they were discovered in, what we know about these mysterious people comes from only a few bones and teeth.

The Denisovans were a total surprise scientifically. The result was not answering any questions because there was no foreknowledge of them. It turned out that about 5 percent of the ancestry of people in places like Papua New Guinea came down from the Denisovans!

Later work, which looked far more closely at mainland populations, showed that there were traces of Denisovan ancestry across the whole of South, Southeast, and East Asia — as well as into the New World. All these populations presumably descend from an African migration which swept east until it reached the Pacific, and then north and south. While Papuans had about 5 percent Denisovan ancestry, these groups had less: 0.1% to 0.5%.

Oddly, the only evidence we have for the Denisovans is in Siberia, but the greatest proportion of their ancestry is found beyond Wallace’s Line, in Oceania. It is very likely then that the Denisovan sequence from Siberia is from a particular population, and this species ranged far and wide across eastern Eurasia — just as Neanderthals did to the west.

A new paper in Cell, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture, adds a further twist by reporting that there were two interbreeding events with Denisovans. One group of Denisovans contributed to Papuans, Southeast Asians, South Asians, and some of the ancestry of East Asians. It turn out, however, that another group contributed ancestry only to East Asians — up to half the Denisovan ancestry is in Han Chinese.

The way the authors did this is by first compiling a list of sequences, which likely came from Denisovans or Neanderthals. They did this by looking for regions which were anomalously different from modern Africans, who have no Denisovan or Neanderthal ancestry. Once they had this list, they compared them to the genomes of the Neanderthals and Denisovans.

Not surprisingly, Europeans had matches with Neanderthals only. Papuans had more matches with Denisovans than Neanderthals. South, Southeast, and East Asian populations had many more matches with Neanderthals, but a small number with Denisovans.

So far so good.

But the authors noticed that some of the populations had Densiovan matches to the Siberian sequence that were much better than those in other populations. In South and Southeast Asia, and Oceania, there were no high quality matches with the Denisovans. In the Han Chinese, about half the matches were much better with the Siberian Denisovan genome — while half the matches were similar to the ones found in other populations.

This could mean that in Northeast Asian populations, two groups of Denisovans contributed their ancestry, while in southern Asia and Oceania only one did.

These results show us that the human past was complicated even if the early genetic results painted a simple picture. Modern humans in eastern Asia interacted with Denisovans twice. We know from a genome in Europe that there were several admixture events with Neanderthals, but it seems only one persists down to the present — as the first Europeans with additional admixture left no descendants. Perhaps the same is true in Asia, maybe there were more than two admixtures with Denisovans.

The pattern of where Denisovan admixture is found is intriguing. It is found in highest frequency among Han Chinese and somewhat lower in Japanese and the Dai people of South China. It is entirely absent in the Vietnamese. Combined with the fact that Tibetans obtained a high altitude adaptation from Denisovans, this is circumstantial evidence that the admixture occurred in the interior of Eurasia.

Denisovans are a major twist in the understanding of our species, but their widespread distribution, and multiple interactions with modern humans, points to intriguing possibilities. Perhaps the Denisovans persisted down to relatively recent times, and interacted a fair amount with modern humans? We know they interacted enough to mix with us twice. Denisovans complexify our understanding of the past, but they may simplify and illuminate myth!

Maybe you have some Neanderthal or Denisovan in your DNA. Discover your story today with Neanderthal by Insitome.

The Others were people too was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

July 26, 2012

The New York Times is ginning up fake controversy

Filed under: Anthroplogy,paleontology,Richard Klein — Razib Khan @ 9:46 am

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 ...

February 26, 2012

Neandertal population structure

Filed under: Human Evolution,Neanderthals,paleontology — Razib Khan @ 6:04 pm

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.

January 7, 2012

Science evolves

Filed under: Human Evolution,paleontology — Razib Khan @ 10:55 am

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 thatheidelbergensis 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)

November 6, 2011

Are most people “behaviorally modern”?

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.

July 18, 2011

Neanderthal-human mating, months later….

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 ...

June 29, 2011

Why hominin fossils matter

Filed under: Homo erectus,Human Evolution,paleontology — Razib Khan @ 11:57 pm

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 ...

May 24, 2011

Is the University of California putting politics before science?

Filed under: Anthroplogy,paleontology — Razib Khan @ 11:54 pm

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 ...

April 27, 2011

1 billion year old freshwater life

Filed under: Cambrian explosion,Natural History,paleontology — Razib Khan @ 11:10 am

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.

February 3, 2011

Dragon Bone Hill: An Ice-Age Saga of Homo erectus

Link to review: Dragon’s Battles

Dragon Bone Hill: An Ice-Age Saga of Homo erectus

Link to review: Dragon’s Battles

September 28, 2010

The hobbits were cretins. Perhaps. Or perhaps not

Filed under: Anthroplogy,H. floresiensis,Hobbits,Human Evolution,paleontology — Razib Khan @ 12:53 am

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.

August 4, 2010

Monophyletic Australian Marsupials

Filed under: Evolution,Marsupial evolution,paleontology — Razib Khan @ 2:52 am

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

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