A Bit More Detail

io9 linked to a very interesting study of chimpanzee genetics suggesting that humans–by comparison, and notwithstanding their substantially larger numbers–are genetically much less diverse than their nearest relatives.

There are four genetically distinct chimpanzee populations, all found in two relatively small regions of Africa. And yet these populations, which are sometimes less than a mile apart, are more genetically diverse than humans that live on different continents.

Three of the common chimpanzee groups are found in very close quarters[.] While the distinct bonobo subspecies in in red on the southern side of the Congo River, the Eastern, Central, and Cameroonian subspecies form a nearly contiguous region in Central Africa, with only the Western population isolated from the others by any considerable geographic distance.

That’s why the results of a new genomic study conducted by an international team of researchers is so surprising. Based on the DNA from 54 chimps taken from across these four populations, these chimps really are genetically distinct from each other despite often being so close together. What’s more, the genetic diversity of these different chimp populations, even those who are practically right on top of each other, is significantly greater than that found in humans separated by entire continents. Oxford professor Peter Donnelly explains:

“Relatively small numbers of humans left Africa 50,000-100,000 years ago. All non-African populations descended from them, and are reasonably similar genetically. That chimpanzees from habitats in the same country, separated only by a river, are more distinct than humans from different continents is really interesting. It speaks to the great genetic similarities between human populations, and to much more stability, and less interbreeding, over hundreds of thousands of years, in the chimpanzee groups.”

The poster links to the PLoS Genetics paper “Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population”, of which a noteworthy portion is posted below.

We have applied a number of different analytical methods to an extensive set of SNP data from 54 chimpanzees. All of the methods point clearly to the existence of three distinct population groups, corresponding to three of the previously-described “subspecies” of chimpanzee P. t. verus, P. t. troglodytes, and P. t. ellioti, with the latter two groups sharing somewhat more similarity with each other than either does with P. t. verus. P. t. troglodytes and P. t. verus are two securely defined populations estimated to have diverged 0.4–0.6 million years ago. Our analyses show P. t. ellioti to be clearly distinct from P. t. troglodytes with both groups equally distinct from P. t. verus, so that whatever terminology (“population” or “subspecies”) is applied to verus and troglodytes should equally be applied to ellioti.

By way of comparison, we have shown that these three chimpanzee populations are more differentiated than even continental human populations, and also that in spite of the relatively close geographic proximity of the groups, particularly troglodytes and ellioti, the chimpanzee populations are considerably more distinct than the African populations sampled in HapMap III, suggesting rather differing demographic histories for the two sister species.

In order to compare population comparisons based on the copying model with those based on more traditional FST approaches, we also calculated pairwise FST values for each of the 100 resamples of individuals and SNPs in our analyses of the three continental population samples. The results are summarized in Table 2. We note that while the average values of pairwise FST across the 100 samples show the same pattern as copying proportions in the copying model, the sample-to-sample variation is larger. For example, the FST intervals for the central 95% of resamples for Europe-East Asia overlap those of Africa-Europe and Africa-East Asia, and for example for five of the 100 resamples the pairwise FST between Africa and Europe was actually smaller than that between Europe and East-Asia. In contrast, for the copying model analysis the 95% intervals for the proportion that Europe and East Asia copy from each other do not overlap with the 95% intervals for either copying from Africa, and the proportion that Europe copied from Africa was lower than the proportion Europe copied from East Asia in each of the 100 re-samples. This accurately reflects the fact that on average East Asia and Europe share more recent ancestry with each other than with Africa.

One weakness of our study (and some others) is that we do not have definitive information on the geographic origin of all of the chimpanzees we have studied. All our analyses point to two very distinct population groups for the chimpanzees originating from eastern Nigeria and Cameroon. In the light of other genetic evidence for distinctiveness of individuals sampled from either side of the Sanaga Riverour assignment of one of our sampled groups as troglodytes and one as ellioti seems reasonable. Whilst our data alone could not rule out two distinct populations, one or both of which extends across the Sanaga River, this seems a priori unlikely – the river provides a natural barrier between the distinct populations, whereas if both were to exist on the same side of the river there seems no reason for their reproductive isolation—and at variance to other available evidence. Notwithstanding our lack of complete geographical information on sampled chimpanzees, the clear separation between all three populations, relative to the similarities within the populations, seems hard to reconcile with the suggestion that chimpanzee genetic variation is distributed more or less continuously across the species range.

There’s a certain irony in all this: although chimpanzees currently face the threat of extinction from we their near-cousins, who are smarter or more capable generally than chimpanzees whatever their subspecies, chimpanzees don’t seem to have gone through the near-extinction events that human beings seem to have gone through at least once.

Human language may well have originated in the African continent with the human species. One recent study even claimed that it was possible to determine the part of Africa where language evolved. A recent (summarized) study in Science suggests that this recent study made overblown claims.

In the beginning was the word – yes, but where exactly? Last year, Quentin Atkinson, a cultural anthropologist at Auckland University in New Zealand, proposed that the cradle of language could be localized in the southwest of Africa. The report, which appeared in Science, one of the world’s leading scholarly journals, was seized upon by the media and caused something of a sensation. Now however, linguist Michael Cysouw from Ludwig-Maximilians-Universitaet (LMU) in Munich has published a commentary in Science which argues that this neat “Out-of-Africa” hypothesis for the origin of language is not adequately supported by the data presented. The search for the site of origin of language remains very much alive.

Atkinson based his claim on a comparative analysis of the numbers of phonemes found in about 500 present-day languages. Phonemes are the most basic sound units – consonants, vowels and tones – that form the basis of semantic differentiation in all languages. The number of phonemes used in natural languages varies widely. Atkinson, who is a biologist and psychologist by training, found that the highest levels of phoneme diversity occurred in languages spoken in southwestern Africa. Furthermore, according to his statistical analysis, the size of the phoneme inventory in a language tends to decrease with distance from this hotspot. To interpret this finding Atkinson invoked a parallel from population genetics. Biologists have observed an analogous effect, insofar as human genetic diversity is found to decrease with distance from Africa, where our species originated. This is attributed to the so-called founder effect. As people migrated from the continent and small groups continued to disperse, each inevitably came to represent an ever-shrinking fraction of the total genetic diversity present in the African population as a whole.

So does such a founder effect play a similarly significant effect in the dispersal and differentiation of languages? Michael Cysouw regards Atkinson’s finding as “artefactual”. Cysouw, whose work is funded by one of the prestigious Starting Grants awarded by the European Research Council (ERC), heads a research group that studies quantitative comparative linguistics in LMU’s Faculty of Languages and Literatures. He says he has no objection in principle to the use of methods borrowed from other disciplines to tackle questions in linguistics, but that problems arise from their inappropriate application. For example, he finds that if Atkinson’s method is employed to examine other aspects of language, such as the construction of subordinate clauses or the use of the passive mood, the results “do not point in the same direction”.

Indeed, in their article in Science, Cysouw and his coauthors Steven Moran (LMU) and Dan Dediu of the Max Planck Institute for Psycholinguistics in Nijmegen show that, depending on the features considered, Atkinson’s method places the site of origin of language in eastern Africa or the Caucasus or somewhere else entirely. As Cysouw points out, linguists have long sought to throw light on the origin of language by analyzing patterns of language distribution. The problem is that such relationships can be reliably traced only as far back as about 10,000 years before the present.

It’s notoriously difficult to come up with hard data on languages in deep historical time, with the various efforts to construct ur-languages predating the earliest recorded languages (i.e. Sumerian, Akkadian, Chinese) or plausible reconstructions (i.e. Indo-European) tending to be mutually contradictory. The data is too sparse and the time too deep, at least for the methods we’ve developed so far.

All that said, I wonder if the different results reported in the summary of Cysouw’s paper–language originated in southwest Africa as defined by this trait, in east Africa according to that, in the Caucasus as shown by a third–might actually constitute a point against the monogenesis of language, against the idea that language evolved in a single region or even a single community before being picked up by the remainder of the human species. If different widely separated populations developed language independently and then came into contact with each other, the resulting contact languages might retain each source language’s distinctive traits. (Might. I speculate at the limit of my knowledge.)

Thoughts?

The headline of Traci Watson’s National Geographic News article sensationalizes the news a bit–it would have been a one-time migration to Iceland, on medieval Europe’s extreme western periphery, and the effects are limited to Iceland–but it’s still fascinating to think that there might have been pre-Columbian migration between the two hemispheres of the world with lasting effects.

Five hundred years before Columbus sailed the ocean blue, a Native American woman may have voyaged to Europe with Vikings, according to a provocative new DNA study.

Analyzing a type of DNA passed only from mother to child, scientists found more than 80 living Icelanders with a genetic variation similar to one found mostly in Native Americans.

This signature probably entered Icelandic bloodlines around A.D. 1000, when the first Viking-American Indian child was born, the study authors theorize.

Historical accounts and archaeological evidence show that Icelandic Vikings reached Greenland just before 1000 and quickly pushed on to what is now Canada. Icelanders even established a village in Newfoundland, though it lasted only a decade or so.

The idea that a Native American woman sailed from North America to Iceland during that period of settlement and exploration provides the best explanation for the Icelanders’ variant, the research team says.

“We know that Vikings sailed to the Americas,” said Agnar Helgason of deCODE Genetics and the University of Iceland, who co-wrote the study with his student Sigrídur Ebenesersdóttir and colleagues. “So all you have to do is assume … that they met some people and ended up taking at least one female back with them.

[. . .]

Through genealogical research, the study team concluded that the Icelanders who carry the Native American variation are all from four specific lineages, descended from four women born in the early 1700s.

Those four lineages, in turn, likely descended from a single woman with Native American DNA who must have been born no later than 1700, according to study co-author Ebenesersdóttir.

The genealogical records for the four lineages are incomplete before about 1700, but history and genetics suggest the Native American DNA arrived on the European island centuries before then, study co-author Helgason said.

The DNA in question doesn’t have precise parallels with any existing First Nations population, although many similar mutations do exist.

The whole story is remarkable inasmuch as the historical consensus is that relations between the Vikings and the First Nations of the Arctic and Newfoundland, the so-called Skræling, were profoundly hostile.

Complicating matters, the historical record contains no evidence that Icelandic Vikings might have taken a Native American woman back home to their European island, scholars say.

“It makes no sense to me,” said archaeologist and historian Hans Gulløv of the Greenland Research Centre in Copenhagen.

For one thing, experts say, nothing in excavations or the Icelandic sagas—thought to be rooted in fact but not entirely reliable—suggests a personal alliance of the kind reported in the new study, published online November 10 in the American Journal of Physical Anthropology.

The Saga of Erik the Red does tell of four Skraeling boys—the Norse term for the American Indians—who were captured by an Icelandic expedition and taken back to Greenland, said Birgitta Wallace, an emeritus archaeologist for Parks Canada who has written extensively about the Norse.

But Icelanders spent little time in North America, and their relations with the people they found living there seem to have been mostly hostile, she said. The stories “talk in not very flattering terms about [Native Americans'] looks,” Wallace said.

One saga, she added, tells of explorers “who found some sleeping natives—and they just killed them.”

“What we have is a big mystery,” study co-author Helgason admitted.

But still, the DNA evidence suggests that all it took was a single woman’s child. Spike on Facebook, who linked to the article, theorized that the woman likely belonged to either to the Dorset in the Arctic or the Beothuk culture in Newfoundland, both areas contacted by the Vikings in the medieval period. I’d be inclined to bet on the woman coming from the Dorset culture, since the Viking pattern of occasional trade with the inhabitants of the Arctic would support migration better than the violently failed settlement in Newfoundland.

I’d meant to comment on this very interesting story on basic differences in behaviour between humans and the chimpanzees that arguably constitute the most closely related primate species, provided by Wired Science’s Danielle Venton. Finding the real differences between human intelligence and non-human intelligences, not making broad sweeping judgements, is always necessary.

Might altruism be more distinctly human that we’d previously conceived?

Primate researchers, working with semi-free ranging chimpanzees at a sanctuary in Uganda, found chimpanzees recruit a helping partner only if it gets them more food than they’d get alone. The study, described in Animal Behavior, Sept. 7, is part of a current trend in primatology to unpick how motivation and mental state affects an animal’s interactions.

“It looks like motivation plays a very important role in how we behave,” said Anke Bullinger, primary author. “And it gives a hint that even though species might be cognitively capable of doing certain things, they might not show the behavior, because they just don’t want to.”

The extent of human cooperation is unique, but not cooperation itself. Chimpanzees, bonobos, elephants, and many birds work together for joint rewards.

“The interesting thing is that there isn’t much research on the motivational aspects of this,” Bullinger said. “I suspect that motivation plays a role in many aspects of cognition, not just in cooperative behavior, but also in social learning, in communication.”

For the study, Bullinger and her colleagues set food boards out of the chimpanzee’s direct reach. To bring the banana-bearing platforms close, the chimps pulled on a rope resting on the ground. Chimpanzees had two options. One board they could pull close solo. On another board, loose rope threaded between loops. To get these boards, both ends had to be pulled, so the chimpanzee had to go get their partner, waiting in an adjoining room.

When Bullinger placed two banana pieces on the single board, and four pieces on the partner board, amounting to the same payoff for each chimpanzee, the animals chose to work alone the vast majority of the time. If another banana piece for each was added to the partner board, the chimpanzees overwhelmingly choose to collaborate.

“We were a bit surprised that just one more piece made such a difference,” Bullinger said.

The study implies that chimpanzees view others as social tools, as a means of maximizing their own rewards.

“It seems they care about what they want,” said David Watts, a primate researcher and Yale anthropologist, not involved in the study. “They don’t get a partner involved because they enjoy that, or because they care about what their partner wants. While, in human cases, we are often motivated to get someone else involved, just for the sake of having them involved.”

If this represents a fundamental difference between humans and other animals, it could help explain why humans evolved to be better problem solvers, and use a wider range of habitats.

“If you have a species that is psychologically predisposed to work with others, and get them involved, that opens up possibilities,” Watts said. “There is a wider range of goals they can accomplish, the population can do much better ecologically and evolutionarily.”

Razib Khan’s post at Discover‘s GNXP taking a look at the origins of Homo sapiens. This is a surprisingly complicated question, especially now that it’s well-known Homo sapiens sapiens includes representatives from at least two highly distinctive hominid populations, the Neandertals and the recently-found Denisova.

One of the terms in paleoanthropology which can confuse is that of archaic Homo sapiens (AHS). This is in contrast to anatomically modern humans (AMH). A simple Out of Africa “recent-origin-with-replacement” model allowed to sidestep the semantic imprecision in tossing disparate populations into a generic category such as AHS (similarly, the term “animal” as opposed to “human” has some colloquial utility, but it’s not scientifically useful). But the possibility of admixture from archaic lineages in modern human populations forces us to grapple with the dichotomy between AHS and AMH, as modern humans may be a compound of these two categories (not to mention the idea of behaviorally modern humans, who are a subset of AMH).

I assume that fleshing out the details of a new paradigm which is both precise and accurate will be a project for the coming years. But before we move on we need to fix more sturdily our understanding of the genealogical relationships of contemporary human populations. Over the past few years there have been major strides in this domain, confirming the broad outline of a dominant African heritage for modern humans. Geneticists have moved from classical markers to SNP data, focusing on hundreds of thousands of genetic variants. But now they’re shifting to whole genome sequences, which with errors excepted encapsulate the totality of the lowest order aspect of human genetic variation.

Razib takes a look at the paper. The conclusion? The hunter-gathering San of southern Africa are the most distinctive populations because of their very early separation from the other human populations of the world, even other Africans.

Notably, our point estimate of ~130 kya suggests that the San divergence occurred ~2.5 times as long ago as the African-Eurasian divergence, that major human population groups diverged at least ~80,000 years before the out-of-Africa migration and that the San divergence is more than one-third as ancient as the human-Neanderthal divergence…Still, human effective population sizes are sufficiently large that these divergence times are small relative to the time required for lineages to find common ancestors in ancestral populations. Indeed, of the mutations differentiating a San individual from a Eurasian individual, only about 25% are expected to have arisen since the San divergence. Thus, the ancient divergence of the San population does not alter the essential fact that far more human variation occurs within population groups than between them.

Razib continues, noting that the San/non-San and Neanderthal/AMH divergence is a matter of degree, not type.

There’s now a fair amount of data and results which indicate a deep divergence between the traditionally hunter-gatherer populations of Sub-Saharan Africa and the farmers and agro-pastoralists of the continent. If these results are correct (and they seem to be in line with the earlier genomic analysis of the Bantu and Khoisan from South Africa) then we have here a rather straightforward refutation of the very simple Out of Africa model, where one East African group replaces everyone else. The Bushmen seem to be of another lineage. Secondly, these results suggest that we should be cautious about inferring a qualitative difference between Neandertals and AMH, where the former is bracketed as “archaic”. The difference between Bushmen and non-Bushmen is far less than between Neandertal and AMH, but it is by a factor of multiples, not order of magnitude.

Fascinating. What will come next out of the labs of the geneticists and the sites of the physical anthropologists and who knows what else?

Science blogger Razib Khan at his Discover-based blog GNXP makes an argument similar to the one I made in my post this afternoon, suggesting that culture more about the replacement of the Neanderthals and other hominins than biology does. This, Razib concludes, makes the population changes of distant prehistory much more comprehensible via analogies with our documented history.

[W]e have many cases of more recent replacements and assimilations on the scale of that of the Neandertals. In the New World Europeans and Africans have replaced and assimilated the indigenous population in many regions which were ecologically suitable. In places like the Dominican Republic indigenous ancestry does persist at low levels, especially in the mtDNA, but it is not longer salient or culturally relevant in a concrete (as opposed to symbolic) sense. There were major biological differences between these Old World populations and the indigenous ones, mostly having to do with susceptibility to disease. Still, we can not separate biological advantages of the new populations from their cultural context. Malaria resistance amongst Africans became prevalent only with the rise of agriculture, as broad swaths of wilderness were cleared and transformed into farmland which was a superior environment for the mosquitoes which transmitted the pathogen. Similarly, the various infectious agents to which Europeans were inured spread via long distance contacts, which could exhibit a scale in Eurasia unmatched in the New World thanks to the emergence of a genuine ecumene.

The Columbian Exchange looms large in part because it is well documented and concerns Europeans, but genetic, linguistic, and archaeological data from Southeast Asia strongly implies that the ancient hunter-gatherers of both the mainland and the maritime zones have been assimilated by successive waves of agriculturalists issuing from the margins of southern China. There is also now evidence of massive population shifts in Europe and India due to the spread of agriculturalists. If an alien archaeologist examined the data I do think they might posit that were a biological speciation events which might explain this, as new traits arose which allowed the farming population to expand and replace the hunter-gatherers. Some of this is actually straightforwardly plausible. Consider the spread of lactase persistence or the ability of farming populations to digest amylose.

[. . .]

If there was a great leap forward to behavioral modernity ~40,000 years ago, then I think one should logically assert that there was another “great leap forward” ~10,000 years ago in the Middle East with the first farmers. There was also another “great leap forward” ~5,000 years ago ago with the invention of writing. There was another “great leap forward” ~300 years ago in Western Europea with the crystallization of a genuine scientific community.

I’m not actually suggesting that what happened 10,000 years ago was a speciation event. What I’m suggesting is that the near past may be more similar to the distant past than we imagine. This makes the near past more exotic, and the distant past less exotic.

Until quite recently, the general consensus was that the sustained interest in the Neanderthals, a kindred subspecies at the very least, were inherently inferior to homo sapiens sapiens–technologically, biologically–and that their destruction come the end of the Ice Age was inevitable and so thorough that not a trace of the Neanderthal genome was left. Remarkable advantages in the sequencing of ancient DNA have revealed that Neanderthals (and other hominin species) did interbreed with non-African homo sapiens sapiens, leaving an actually existing genetic legacy, and suggest that Neanderthals were intellectually comparable to homo sapiens sapiens. Why the disappearance of a discrete Neanderthal population? Wired Science writer Kate Shaw’s article “Sheer Numbers Gave Early Humans Edge Over Neanderthals” presents new evidence that the Neanderthals were simply wildly outnumbered.

Two archaeologists from Cambridge University analyzed data from the Aquitaine region of southern France, which has Europe’s highest density of sites from this era, and one of the most complete archeological records. They used data from three time periods that encompassed the transition between Neanderthals and modern humans: the Mouterian and Chatelperronian eras, during which Neanderthals lived, and the Aurignacian period, which was dominated by modern humans. By examining differences between land use during these time periods, the researchers hoped to determine whether population dynamics played a role in the transition between these two hominins.

Because of the difficulties in estimating long-ago populations, the researchers used a few different proxies for population sizes and densities. They analyzed the number of occupied sites in each era, the size of these sites, and the accumulation rates of stone tools and animal food remains. Through these proxies, the researchers could get good estimates of population dynamics during the transition from Neanderthals to modern humans in Aquitaine.

[. . .] Since these archaeological proxies was developed independently, the estimations can be looked at cumulatively to get a better idea of the different population sizes. When evaluated as a whole, these estimations show that the population size and densities of modern humans may have been more than 9 times those of the Neanderthals around the time of the population’s transition. It’s very likely that a numerical advantage that large played a significant role in modern humans’ dominance over their earlier counterparts.

All this has interesting implications. Looking at this, I’m reminded of the way that some homo sapiens sapiens hunter-gatherer cultures in historical time ended up giving way to agricultural civilizations. Certain hunter-gatherer populations, particularly those in pre-modern Japan and the North American Pacific Northwest before white settlement in the mid-19th century, were so well adapted to a bountiful environment that they had large enough surpluses to support materially and organizationally quite complex cultures. It was only at a late date, as agriculture-using civilizations finally these former frontiers with their superior technologies and numbers, that they succumbed, eventually becoming overwhelmed and assimilated as with the Ainoid Emishi of northeastern Japan, leaving only a relatively few traces far outnumbered by the impact of implanted agricultural civilization.

Other hominin species have left legacies in the human gene pool, as noted, but these legacies are fairly rare, on the level of low single digit percentages. One traditional model would have it that this low percentage reflects sustained inter-population conflicts that allowed only a select minority of Neanderthal survivors to reproduce. If Neanderthals were so substantially outnumbered by homo sapiens sapiens, however, this relatively low percentage might reflect a much more thorough assimilation of more of the Neanderthal population than traditionally believed.