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john hawks weblog

paleoanthropology, genetics and evolution

Photo Credit: Contemporary human skull compared to the Kabwe cranium. John Hawks CC-BY-NC 2.0

Looking for the vulture assist with Neolithic burials

The archaeological site of Çatalhöyük, in present-day Turkey, is one of the most significant early Neolithic villages to have been excavated. It was occupied between around 7100 and 6000 BC, and at its height was occupied by more than 3500 people. An array of human skeletal remains have been found at the site. Many of them were buried in the floors of houses in flexed pit burials.

One interesting aspect of the burials is that many were in an extremely flexed position. Legs were tucked against the chest in a tight position that seems anatomically unlikely if flesh had been on the skeletons at the time they were buried. This has given rise to the hypothesis that the bodies had been defleshed in some way before they were buried.

Marin Pilloud and coworkers in 2016 published a paper suggesting that the Çatalhöyük bodies were possibly defleshed by vultures. A brief excerpt from the conclusion gives the gist of their argument:

The burial practices at Çatalhöyük (i.e., removal of cephalic extremity, limb removal, tight flexion) as observed in the archaeological record are often consistent with some manner of flesh removal prior to interment. It seems possible based on current forensic experimental work that the people of Çatalhöyük may have employed vulture excarnation prior to interment. Based on human studies, vultures are unlikely to leave marks on the bone that would be visible 9000 years later.

It’s an interesting concept. The paper goes into some of the symbolic meanings of vultures and the possibility that bodies were exposed on the roofs of residences for vultures to approach.

Getting species diagnoses non-destructively from collagen

A neat paper by Naomi Martisius and coworkers in Scientific Reports: “Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals”.

The introduction of the paper presents the problem that the researchers set out to solve. How can we get biological identifications of modified bone fragments without drilling into them to extract protein? The answer is provided by a new method that can examine the trace amounts of collagen that adhere to plastic surfaces after they contact a bone. This includes the plastic bags that are used to store artifacts and archaeological bone samples.

ZooMS has been useful for identifying ancient animal remains when fragmentary bones present a challenge for more traditional methods. The method has been used to identify fragmented animal and human remains from Paleolithic sites, as well as cultural artifacts from various time periods, including bone tools and parchment. Such objects frequently have been significantly altered from their original form making taxonomic identifications based on morphology nearly impossible. At the same time, conventional ZooMS extraction procedures involve drilling or cutting a bone sample (less than 20 mg), thereby altering often unique and fragile artifacts (Supplementary Fig. S1). Recently, a non-destructive approach based on the triboelectric effect occurring between collagen and plastic surfaces has been developed to sample parchment for ZooMS analysis. The concept behind this approach has been applied to plastic storage bags containing bone artifacts as well, as the use of erasers carries the risk of modifying bone surfaces through abrasion. Here, we show that collagen molecules adhering to the plastic surfaces allow us to infer species selection of Middle Paleolithic lissoirs made by Neandertals, which then permits the consideration of competing hypotheses about the selection of ribs as the raw material for making lissoirs.

This is a significant advance. For those of us who grapple with decisions about destructive sampling, every non-destructive approach provides us with the potential of making better decisions. It won’t always be the right thing to use these non-destructive approaches. Some biological and anthropological questions will merit a fuller examination of larger samples. But the availability of a non-destructive method means that we can be deliberate in choosing the best method for each scientific question. We can better leverage the knowledge we gain from some samples to conserve others.

The result of the study is itself interesting. The fact that Neandertals were consistently choosing bovid ribs for these specialized tools, even though bovid remains are rare at the site, gives useful insight into the entire process behind their use of technology. They planned for later use of tools and curated material to make effective use of hides from later kills.

How mice became house mice

A new paper from Thomas Cucchi and coworkers in Scientific Reports probes the early history of the house mouse: “Tracking the Near Eastern origins and European dispersal of the western house mouse”.

A quick taxonomy of house mouse subspecies:

Although often overlooked compared with commensal rats (Rattus rattus, R. norvegicus and R. exulans), this elusive mammal has been a much more successful invasive rodent, becoming almost as ubiquitous as H. sapiens. Originating in the Indo-Pakistan subcontinent and neighbouring Afghanistan and Iran, house mice differentiated during the Pleistocene climatic oscillations into three main Mus musculus subspecies (M. m. domesticus, M. m. musculus and M. m. castaneus). All these subspecies are human commensals, facilitating their long-distance colonization and ultimately their cosmopolitan range.

The authors frame their work as ultimately an inquiry into the domestication and spread of cats:

The earliest and most striking evidence of cat domestication comes from 9,500 cal BP in Pre-Pottery Neolithic (PPN) Cyprus. Its introduction onto the island is thought to be tied to the control of the proliferation of the house mouse populations, present on the island since the Early PPNB26. The appearance of the domestic cat in western European archaeological contexts during the Iron Age, around 3,000 years ago, is synchronous with the strong evidence for the house mouse biological invasion of western Europe. This co-dispersal of cats and house mice has also been mentioned in literary sources, describing the deliberate transport of domestic cats on ships to control rodent pests, inducing its worldwide distribution. This co-phylogeography supports the premise that understanding the house mouse’s origin and dispersal can lead to insights pertaining to the origin of domestic cats and their subsequent dispersal.

Honestly I think that the process by which species become commensal with people is even more interesting than domestication. Humans exert intentional control over domestication. Commensal animals adapt to human-created environments largely on their own with little or no intentional human selection. Many would argue that cats are commensal rather than domesticated, and that may well have been true for much of the early history of domestic cats. Global house mouse (Mus musculus) populations exist in human-created habitats and are specialists within them.

The paper is mostly a straightforward review of first appearance dates and range expansion of the house mouse across the Levant and southeastern Europe. It’s not a full history. The authors have done work to understand which mice were inhabiting pre-agricultural sedentary populations of the Levant, followed by the spread of those mice into the eastern Mediterranean more broadly.

Most interesting, the mice adapted to human settlements before people started keeping granaries:

The earliest commensal populations of M. m. domesticus found in Natufian sedentary settlements (14,500 cal BP) confirm that the impact of sedentism on ecosystems and the ecology of organisms (i.e. reduction of predation and competition pressures, climatic buffer etc) was the catalyst for the commensal relationship between mice and humans rather than the emergence of agriculture systems with large-scale grain storage, which emerged two millennia later. Nevertheless, M. m. domesticus was identified only in the largest, long-term Natufian settlements such as ‘Ain Mallaha in the Southern Levant and Mureybet in the Northern Levant between 14,500 and 12,000 BP. In smaller and shorter term Natufian sites in the Southern Levant, only the native mouse Mus macedonicus was identified. This pattern suggests that dense human occupation in large open air settlements was the prerequisite for M. m. domesticus to eventually outcompete other potential anthropophilous rodent like M. macedonicus from the Natufian ecological niche.

That suggests that the protection that human settlements provided from other nonhuman predators may have been more important than human-accumulated food resources that mattered to mice. Sure, there was plenty of trash to eat around human settlements even without large-scale grain storage. But a reduction in predation from raptors and small carnivores created a very attractive environment for a small rodent.

Goat immunity modified by introgression during and after domestication

Goat domestication may provide another example in which introgression brought new genetic variations conferring advantages for immunity into a population. A new paper in Science Advances by Zhuqing Zheng and collaborators looks at modern domesticated goats and wild relatives from several species, and also a handful of ancient goat genomes: “The origin of domestication genes in goats”.

Here’s the abstract:

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene, which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7200 and 8100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanisms of animal domestication.

The abstract understates the evidence for introgression on genes related to immunity. The mucin gene mentioned in the abstract stands out because the current frequency of the introgressed allele is near fixation, indicating strong selection since its introduction into domesticated goats. But many other genes influencing immunity have also come into domesticated goats by introgression.

A passage later in the paper presents some of the complexity that Zheng and coworkers found:

D statistics reveal that all four ibex-like species have significant signals of allele sharing with ancient and modern goats, indicative of admixture (Fig. 2C and table S8). We then examined this genome-wide pattern of admixture between ibex-like species and domestic goats using D statistics and identity by state in 20-kb sliding windows. We further verified candidate introgressed regions using Sprime and maximum likelihood (ML) phylogenetic trees. Using a conservative criterion (namely, only keeping putative introgressed haplotypes with a frequency higher than 0.1 in goats), we identified 112 genomic segments overlapping with 81 protein-coding genes with signatures of introgression from ibex-like species (Fig. 2D, fig. S16, and data file S1). A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for these genes shows that the most significantly enriched category is amoebiasis (hypergeometric test, adjusted P < 5.28 × 10−3: table S10), which is related to parasite invasion and immunosuppression, including four genes (SERPINB3, SERPINB4, CD1B, and COL4A4). Three additional genes (BPI, MAN2A1, and CD2AP) are also involved in immune function (19–21). In these segments, we observed a pronounced signature of putatively introgressed alleles from the West Caucasian tur (fig. S17), consistent with this species showing the greatest genome-wide allele sharing with domestic goats (Fig. 2C).

It’s not obvious to me how the authors ruled out the hypothesis of reverse introgression from domesticated goats into some of the wild relatives as a cause for some similarities that they found. Certainly domesticated goats have been more numerous in recent times than the wild species. The authors did show some evidence for introgression among the wild species prior to domestication. I suspect there is more of a story to be found there.

The evidence from ancient genomes here is very slight. It did, however, show the presence of the introgressed alleles in the domesticated goat material from before 7000 years ago. The complexity of the domestication process seems to have been quite impressive in this case, drawing in adaptive variation from multiple species of wild caprids.

When I wrote about introgression in my 2006 paper, I spent a lot of time investigating the phenomenon in cattle, including the four wild species of cattle and the progressive spread of zebu genes into taurine cattle that followed domestication. I knew very little about goats. Goats seem like an even more complicated scenario in some ways.

Twins from an adaptive point of view

The biological anthropologist Rebecca Sear looks at the evolution of human twinning in a post for This View of Life: “Solving the Evolutionary Puzzle of Twinning”.

She reviews the results of a recent paper modeling the fitness costs and benefits of multiple ovulation in a cycle, or polyovulation.

Twinning is a relatively rare event, varying from around 0.6 to 4% of all births, and this new paper suggests that its rarity is because it is an ‘accident’ arising from a strategy of polyovulation to counteract very high rates of foetal loss. Many questions still remain about this phenomenon: such as why foetal loss is so high, and why twinning rates vary around the world – because of differences in the likelihood of foetal loss, perhaps? But regardless of the explanation for the existence of twins, mythology, literature and the human experience is much richer because of this fascinating phenomenon."

Humans have a very high late of early pregnancy loss, which is itself an evolutionary problem. The idea of a bet-hedging strategy revolving around polyovulation is one possible explanation.

But there are a couple of things that this explanation is less good for. I’m less convinced than the authors of the study about bet-hedging for older mothers. The fact that twinning increases with maternal age seems more consistent with a progressive decline in the strength of selection against it, rather than an adaptation for twinning for older mothers.

More critically in my view is the fact that monozygotic twinning in humans is approximately the same frequency as dizygotic twinning in many populations, even though they originate from very different mechanisms. Polyovulation should have no effect on the rate of monozygotic twins, so why should they be around the same frequency?

Knowing more precise numbers about the rate of these in different populations and the genetic correlates of them will be helpful.

Link: Online learning metaconversation

I’ve been thinking a lot over the last few weeks about how to help students transition more effectively to online learning. Obviously this is a topic on the minds of many teachers and professors this year.

I was pointed to a post where Martin Weller reacts to some conversations he’s seeing in his Ed Techie blog: “It’s forever 1999 for online learning critics”.

Online and distance learning does generally require more self-motivation from the learner, away from the physical cues that prompt learning. It also requires more organization of their time and study environment and so retention may always be an issue compared to f2f. But it also offers opportunities for other forms of teaching. The least interesting thing you can do is replicate the not very effective model of the lecture. We had these discussions back in 1999, and people explored problem based learning, constructivism, collaborative learning, and then later connectivism and flipped learning. I’m not proposing any one of these approaches as a magic bullet, and some students will like them and others hate them. But different approaches are achievable and have been realised for a long time. Just because you’ve been dumped off your lectern and feel aggrieved, is no need for another ‘online learning sucks’ hot take.

I appreciated the (short) comments section on the post, where a commenter made the point that most students have spent more than a dozen years in classrooms learning how to learn. Obviously a shift to online interactions will seem difficult because it is easy to forget how much time students have spent learning to learn in classroom settings.

I find when we teach laboratory sections that many students have a difficult time adjusting to this form of learning. Many are more comfortable sitting back and listening to a teaching assistant, and are hesitant to step forward and explore materials with their hands.

Online learning does sometimes put students into a more comfortable place for exploration. They do not have to explore while other students are watching them. Some of the social fear of making a mistake is taken away. But the obvious problem for a biological anthropology course is that the physical materials are really important for learning. We have to think about the ways that students can learn to do science that do not depend so strongly on handling bones, casts, and other objects first-hand.

Replicability and archiving of geological samples

In Nature this week, Noah Planavsky and coworkers, including the present director of the National Museum of Natural History, Kirk Johnson, have an opinion piece calling for mandatory archiving of geological samples that underlie published research: “Store and share ancient rocks”.

This call is analogous to the work maintaining sequence databases in genetics, or curation of paleontological samples. Planavsky and his coauthors convey the need for seriousness concerning reliability and replicability of biochemical and other examinations of rock and mineral samples.

Attempts over the past decade to answer questions using better tools and larger databases have only amplified disputes. To make matters worse, too often, rock samples are not archived or shared. It is common for samples to be held by researchers in private collections instead of in accessible, curated institutional archives or museums. That’s a problem, because different geoscience teams cannot check each other’s work to test whether published results are robust and can be replicated.

We are fast entering a world where it may be more costly in time and effort to carry out field collection of samples for replication. That means that field studies need to make more effort to record all the context necessary for interpreting the samples they collect. Many scientists have relied upon their own memory, their descriptive ability, and GPS coordinates to document samples. The field should prioritize more precise and replicable methods for collecting context with samples.

Funding agencies should require that researchers’ grant proposals include sample archival procedures and that budgets include curation fees. Critics might argue that archiving will decrease the money available for other scientific endeavours. In our view, a sample stewardship plan should be viewed as equivalent to budget-line items for data archiving, publishing fees or institutional overhead costs that support other essential components of the research workflow.

Over the past decade, funding for biological collections has declined. That has hit many museums and curating institutions hard. The role of institutions who curate and preserve samples is more and more important. We are going to rely on skilled people who know collections, and who can work with outside experts to do apply new methods to these samples. For the future of research, we need to be building these capacities now.

Tending museums through the crisis

Atlas Obscura has an article by Jessica Leigh Hester looking at how curators and staff are tending museum collections and infrastructure while hallways are empty: “The Strange, Smelly Chores That Keep Natural History Museums Running”.

The tapir bones rest in a solution of diluted ammonium hydroxide, which pulls out marrow and fat and arrests bacterial growth. They are not far from the remains of okapi and goats that are wrapped in tarps, as well as squirrels, bats, and rodents that sit in containers on shelves. In this case, a little bit of the malodorous, milky-white fluid from the tapir’s bin had trickled out and pooled on the floor. Ferguson cleaned it up and went on his way. It wasn’t a crisis, but it was a good reminder: Museums are dynamic environments, and staff members are always doing their damnedest to fend off entropy.

If you wonder about how dermestid beetle colonies are maintained, or the effects of clothing moths on mounted crustaceans, this article is for you. Entropy is a good word for the problems that are constantly sapping away collections of biological specimens.

When will we have concerts again?

Foo Fighters frontman Dave Grohl has an essay in The Atlantic reflecting on our need for live music: “The Day the Live Concert Returns”.

In today’s world of fear and unease and social distancing, it's hard to imagine sharing experiences like these ever again. I don’t know when it will be safe to return to singing arm in arm at the top of our lungs, hearts racing, bodies moving, souls bursting with life. But I do know that we will do it again, because we have to. It’s not a choice. We’re human. We need moments that reassure us that we are not alone. That we are understood. That we are imperfect. And, most important, that we need each other. I have shared my music, my words, my life with the people who come to our shows. And they have shared their voices with me. Without that audience—that screaming, sweating audience—my songs would only be sound. But together, we are instruments in a sonic cathedral, one that we build together night after night. And one that we will surely build again.

Hunting the ghost dogs with camera traps

Cara Giaimo in the New York Times covers a recent research paper that combines camera trap evidence from across a large swath of the western Amazon to examine an elusive canine: “The Ghost Dogs of the Amazon Get a Bit Less Mysterious”.

Daniel Rocha, a graduate student at the University of California, Davis, and the study’s lead author, became interested in the short-eared dog in 2015, when he began working in the southern part of the Amazon. He and his colleagues set up camera traps to study the local mammal community. As they looked through the footage, “these dogs would appear,” he said. With pricked ears and furrowed brows, they almost look surprised to be caught on camera.
It surprised him, too. Even locals who spend a lot of time in the Amazon don’t often see short-eared dogs, which were assumed to be quite rare. They also evade career researchers focused on this region: Mr. Rocha, who spent years leading this study, said, “I’ve never seen the dog in the jungle, ever.”

The article briefly describes the broad collaboration that is making it possible to collect data on this species and study its distribution.

How much of the Neandertal genome came from contemporaries in Africa?

Back in June of last year, Melissa Hubisz, Amy Williams, and Adam Siepel coworkers put out a preprint with a new method for looking at introgression using the ancestral recombination graph: “Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph”.

The paper has not yet appeared in a journal, but at the time I noted one interesting conclusion:

Applying this method to modern and archaic hominins, we confirm that a significant proportion of the Neanderthal genome consists of regions introgressed from ancient humans. While we identified 3% of the Neanderthal genome as introgressed, a rough extrapolation based on our estimated rates of true and false positives suggests that the true amount is around 6%. Thus, the Neanderthal genome was likely more influenced by introgression from ancient humans, than non-African human genomes are by Neanderthal introgression. Our follow-up analysis suggests that the Hum→Nea gene flow occurred between 200-300kya. This time estimate is largely based on the frequency of introgressed elements among the two diploid Neanderthal genomes, and thus will be sensitive to the accuracy of the demographic model we used for simulation, as well as other factors such as mutation rate and generation time.

With the first sequencing of the first Neandertal genome, and for several years afterward, many geneticists promoted a scenario in which gene flow between Neandertals and modern humans had been a one-way arrangement. The idea was that moderns got some DNA from Neandertals, but the Neandertals never got any from modern humans. This conclusion was based on some data, but it was premature. The early methods applied to the Vindija low-coverage genomes could not detect “modern” genetic input into the Neanderthal population unless that modern input came from the ancestors of some modern populations and not others. The data did rule out that the Vindija Neandertals had genetic input from the immediate ancestors of living Europeans. But the analyses could not test for older introgression from African-derived populations not closely related to one living population or another.

In the last year or two, a number of analyses have started to identify introgression of particular segments of the genome. Geneticists have also added larger samples of DNA from today’s African populations. African peoples are still badly underrepresented in genetic datasets, and the recent additions are a drop in the bucket of what is needed. But it’s impressive how a better representation of African variation and better methods have started to illuminate deeper phases of population mixture in human evolution.

One of those is the deep introgression into Neandertals from their African contemporaries. The African origin of Neandertal mitochondrial DNA, revealed a few years ago, was the first major element of our emerging understanding. Mitochondrial DNA was not alone. Neandertals were repeatedly connected to African populations in the time after 350,000 years ago. They derive a substantial fraction of their genetic variation from such contacts with African populations.

The paper from Lu Chen and coworkers earlier this year provided strong evidence of the importance of gene flow from Africans into Neandertals in the period after 150,000 years ago (“Neandertal ancestors of African populations”). This new paper from Hubisz and coworkers is pointing to gene flow in an earlier period of time, more similar to that time when the Neandertal mtDNA introgressed.

The genetic ancestry of modern lions

Marc de Manuel and coworkers have a new paper in PNAS that presents some new findings about lion population history from whole-genome sequencing. The paper has the title, “The evolutionary history of extinct and living lions”.

This is a paper on a fascinating biological topic where the title promises a bit more than it delivers. Their sample includes six modern lions from Africa and India, 12 lions from historical populations that are now extinct in Africa and West Asia, and 2 cave lions, one from Siberia and one from Yukon. A truly “evolutionary history of extinct and living lions” would include a larger sample of living lion diversity and at a minimum European cave lions and American lions (Panthera atrox).

Lions have a great fossil record that this paper mostly neglects. I’m more and more dismayed by the intellectual divisions between paleontologists and geneticists on the evolution of familiar mammal groups. In this case, with a title that calls up the “evolutionary history” of lions, it would be nice to have fossils as more a part of the story.

The lion story is fascinating right now precisely because what is emerging from the genetics does not seem to line up with long-standing ideas based on the fossil record. De Manuel and colleagues show that today’s African and Asian lions are markedly limited in their diversity. All living lions appear to stem from a Late Pleistocene common ancestry:

The deepest divergence within modern lions was between the northern and southern lineages (Fig. 1B), which shared an ancestor ca. 70,000 y ago (52,000 to 98,000 y ago; SI Appendix, Table S3 and Fig. S9). This date is consistent with previous estimates based on mtDNA sequence variation (5, 14), although slightly younger than prior estimates based on autosomal markers (9). Interestingly, through a PSMC analysis of the individuals from the northern and southern groups, we inferred a sudden decline in Ne in the northern genetic lineage at roughly the same time as the split between the 2 groups (ca. 70,000 y ago, Fig. 3A). This severe population bottleneck in the northern genetic lineage suggests that regions north of the Sahara were populated by only a few migrants from the southern lineage at some point in the Late Pleistocene (1, 9, 14).

That means that most fossil lions are likely outside the bounds of modern lion diversity. Lions have existed for a long time in Asia, Europe, and North and South America. Cave lions go back to 750,000 years or more in Europe. Not only these but fossil African lions also lie outside of the envelope of today’s African and Asian lions. That’s saying something. Lions have been a hugely successful evolutionary lineage, and they appear to have a population history that is much more constrained than that of modern humans.

It is notable in this study that lion populations that were considered as phenotypically divergent, such as the Cape lions and Berber lions, show no matching genetic differentiation. They are all part of the same Late Pleistocene diversification.

De Manuel and coworkers estimate that the cave lions diverged from modern lions around 500,000 years ago. Their data do not show any evidence of gene flow into cave lions from modern lions after their divergence. This is a bit of an idiosyncracy in comparison to the broader picture of cat phylogeny, which has extensive ancient hybridization among lineages. My impression is that the big story here, that today’s African and Asian lions all derive mostly from Late Pleistocene population diversification, means that gene flow that might once have happened between Asian (or American) lions and these cave lions from Siberia and Yukon is not going to register in today’s data. European lions might be more interesting, but the very recent common ancestry of today’s lion populations predicts that any gene flow between their stem population and cave lions is not going to show up on D-statistic type tests.

A half million years of genetic diversification for cave lions and modern lions is not enough to account for the fossil record of cave lions. Some cave lions have been around since the Early Pleistocene. I would guess that there were multiple dispersals of lions that may have been accompanied by introgression.

Many of the authors of this new paper were also authors of a paper describing the mitochondrial genome of the same Yukon cave lion specimen back in 2016. That paper was “Mitogenomics of the Extinct Cave Lion, Panthera spelaea (Goldfuss, 1810), Resolve its Position within the Panthera Cats” by Barnett and coworkers. In that paper, they provided a divergence date for cave lions and modern lions at 1.89 million years ago. Now, the comparisons of the nuclear genome suggest a much more recent date.

At this point in history, we all know that initial mtDNA comparisons between species may look quite different from later, more complete comparisons using the nuclear genome. Sometimes the divergence of mtDNA appears disproportionately great, Denisovans being an obvious example. This case with the cave lion is a big difference, and it reminds me of the differences we saw early on between chimpanzee mtDNA divergence and the first nuclear genome comparisons.

The difference matters to interpreting the cave lion fossil record, which extends much older than a half million years. De Manuel and coworkers do examine the discrepancy between mtDNA and nuclear comparisons to some degree. They mention in their supplement that previous attempts to date the divergence of cave lions and modern lions used the first appearance date of cave lions in Europe as a calibration point, while this study does not. The use of a fossil calibration assumes that the earliest fossil cave lions are genetic ancestors of later cave lions. That may be a bad assumption. The hominin record is now full of examples where the later inhabitants of a region come from later migrations with little input from earlier populations in the same region. If lions did they same, they would be a parallel to the population history of hominins.

On the whole,though, I’d like to see a fuller consideration of these different sets of data. The present sample of lion genome diversity is not yet enough to evaluate whether today’s lions may retain small contributions from divergent populations that may once have existed. I’m interested in whether the modern lions have to some extent absorbed ancient lion populations across Africa and possibly Asia, in the way that modern humans have absorbed many archaic hominin populations.

Link: Bioarchaeology and the resilience of past societies

Gwen Robbins Schug has a piece in Anthropology News looking at the lack of any simplistic relationship between climate change, crisis, and cultural change in the past: “The Long View of Climate Change and Human Health”.

The subhead summarizes the theme of the essay pretty well:

The deterministic view that climate change invariably causes migration, competition, violence, and collapse is overly simplistic. Bioarchaeology shows us that human responses are far more complex and diverse.

I like the way that the essay closes, reflecting upon the failure of the big history view of the fate of societies. Instead, it’s a “little history” that we should be thinking about – the way that individuals matter, and the way that chance turns of events at the microscale make a difference.

These tiny decisions may appear mere turbulence to the historical picture. Yet if we take the long view seriously, every society is on the edge of survivability in geological time. At the threshold of the lifting edge, turbulence matters.

Broadly speaking, bioarchaeology demonstrates that there are no grand narratives in human history. Small-scale societies are often resilient in the face of environmental change; mobility, flexibility, and adaptive diversity are a largely successful strategy for avoiding negative consequences (see for example, Berger and Wang 2017; Temple and Stojanowski 2019). Complex societies, in contrast, are often much more rigid and they are built on social inequality. When these large-scale societies overshoot—undergo rapid population growth and practice unsustainable agricultural overproduction in the context of rapid climate and environmental changes—those who are resilient and who survive the short-term crisis may experience other forms of suffering (see for example, Robbins Schug, Parnell, and Harrod 2019; Tung et al. 2016).

People survive and sometimes thrive in the face of huge challenges. Other times, people fail despite their best efforts. Failure may result from a cultural system that sets people up for failure. But often it’s bad luck.

Neandertal ancestors of African populations

Earlier this year, Lu Chen and coworkers from Joshua Akey’s research group published an assessment of the amount of Neandertal ancestry in the genomes of present-day African people: “Identifying and Interpreting Apparent Neandertal Ancestry in African Individuals”.

In the wake of the initial Neandertal genome sequencing in 2010, journalists and many scientists spread the misconception that African people have no Neandertal genetic ancestry. That was wrong at the time and many people pointed out how wrong it was.

The research itself, from Svante Pääbo’s team, did not propagate this misconception. All of the authors were pretty consistent in noting that their tests could only measure the difference between sub-Saharan and other populations in Neandertal ancestry, and could not rule out Neandertal contributions to sub-Saharan African peoples.

Still, in the first year or two of genome-powered scientific conversation about Neandertal introgression, other scientists focused upon an alternative explanation: incomplete lineage sorting from a structured African population. As this idea was debated, again and again geneticists defended the introgression hypothesis by arguing that introgressed DNA was not found in Africa. As this genuine debate about incomplete lineage sorting was reported by journalists, they also reinforced the misconception that Neandertal introgression only exists in peoples outside Africa.

Through this period, I was one of the people working to debunk the myth that African populations have no Neandertal ancestry. A look at my 2010 post, “NEANDERTALS LIVE!”, shows me giving the correct answer for this question, “Do living Africans have Neandertal ancestry, too?”

The fact that living Africans are less genetically similar to the Neandertals is extremely important evidence of the Neandertals’ genetic contribution to populations outside Africa. But it doesn’t bear on how much back-migration into Africa may have happened.
We know that the answer is nonzero, because Africa has received immigrants from other parts of the world during historic times. The same genetic patterns that reflect population contacts up and down the East African coast, and across the Sahara into West Africa, show the possible conduits for the flow of Neandertal-derived genes into African populations.

I had actually grappled with this problem in my earlier paper (with Greg Cochran) in 2006, looking at what we should expect Neandertal introgression to look like: “Dynamics of Adaptive Introgression from Archaic to Modern Humans” (PDF). A number of scientists over the years suggested that any gene flow from Neandertals should be absent from Africans. That simply wasn’t true, and we pointed out why introgressed genes from Neandertals or other archaic humans might be found broadly across Africa.

Research over the last ten years has looked into the amount of Eurasian gene flow into Africa over the last 30,000 years, adding a good bit to our understanding of human population structure. That Eurasian gene flow was part of the big story of 2017, as early Holocene ancient DNA data from South Africa reinforced the finding that today’s southern African peoples have a good fraction of ancestry from Eurasian sources over the last 5000 years.

Now Chen and coworkers have given us a new set of estimates for how much Neandertal ancestry occurs in African populations. Their results are sketched out in the following figure:

Figure showing the total length of Neandertal-derived DNA segments in varied populations, from Chen et al. 2020
Figure 2a from Chen et al. 2020. This shows "violin plots" depicting the amount of Neandertal sequence identified in various populations per individual. East Asian (EAS), South Asian (SAS), European (EUR) and Native American (AMR) groups average between 50 and 60 megabases per individual, which is just under 2 percent. African populations have between 15 and 20 megabases.

These comparisons are limited to 1000 Genomes Project samples, and those are mostly in the northern parts of sub-Saharan Africa, from Gambia, Sierra Leone, Nigeria, and Kenya. Chen and colleagues identify between 15 and 20 megabases of Neandertal DNA per genome in these samples. That’s around a third the amount that the authors find in Eurasian and Native American population samples.

Europeans and Asians have around 2% Neandertal ancestry, and sub-Saharan Africans have around 0.6%.

The Neandertal DNA in African populations comes from two sources. Most of it comes from so-called “back-migration” of Eurasian modern humans into Africa. That gene flow can mostly be traced to the last 50,000 years. It’s not yet clear how much that gene flow into Africa may have accelerated over time. The population growth of the Holocene, with cattle pastoralism spreading southward across Africa, has helped fuel the spread of Eurasian genes in historic times. Yet a green Sahara during later parts of the Pleistocene also enabled contacts and dispersals that became more difficult in the recent, more arid North African landscape.

The other source of Neanderthal DNA in Africa is a kind of incomplete lineage sorting. This ILS, however, marks Neanderthal-African shared haplotypes that are absent in the rest of the world. Chen and coworkers look at the mutational differences among these and find that they have a peculiar age distribution. They do not date to the founding of the Neanderthal lineage more than 600,000 years ago. Instead, they are haplotypes that were transferred from African populations into Neanderthals by gene flow prior to 100,000 years ago.

Our own data are most consistent with models of human-to-Neanderthal gene flow between 100 and 150 ka, as IBDmix does not detect any signal in simulations with earlier gene flow. However, our results do not preclude earlier instances of gene flow, only that IBDmix is not powered to detect them. Thus, it is tempting to speculate that perhaps there were multiple waves of pre-OOA dispersals and admixture between modern humans and Neanderthals, although additional data are needed to make more definitive inferences.

Multiple waves of gene flow from Africa into Neandertals seem likely, and are corroborated by fossil discoveries like those from Misliya and Apidima.

This paper has many additional interesting things to say about Neandertal introgression. The one that I want to mark before ending is that Chen and colleagues look back at the “extra” amount of Neandertal similarity in Asian genomes compared to European genomes. This “extra Neandertal” has been estimated as much as 20% in previous work, but that assumed that Africans had no Neandertal ancestry. The Neandertal ancestry that does occur in Africa today comes in large part from gene flow out of western Eurasia, which means it is shared more with Europeans, Arabs, and other western Eurasian people than with East Asian populations. Looking at this effect, Chen and coworkers estimate that East Asian populations still have a bit more Neandertal than western Eurasian people, but only about half the previous bonus, around 8%.

It’s a cool paper that answers a number of worthwhile questions. It will be great to see larger samples applied to this and other similar problems. As I reflected in the Iceland Denisovan genetics post, we will learn much more when large samples can better characterize the haplotypes that have come from Neandertals and other populations.

I suspect when we have equivalently large samples in Africa, it will reveal a small amount of direct Neandertal introgression during the period of modern human emergence.

Quote: Robert Broom has no apologies

Robert Broom, in the first paragraph of his paper, “Further Evidence on the Structure of the South African Pleistocene Anthropoids”, says it better than I could.

NO apology need be given for publishing to the world at the earliest possible moment all new evidence that is discovered which seems to throw additional light on the structure of the apes that apparently are related to the ancestors of man. Every month reveals some new facts of importance, and it seems to me better that these should be announced at once, than that they should be held back for perhaps years in the hope of publishing a detailed account.

Next time you hear someone say that “real paleontologists take time to do quality science”, you can pull this one out of your pocket.