I assume though the accusation will be enough to open some Title IX complaints. Unless her colleagues step up I assume she’ll be hounded out by the bureaucracy, though I hope I’m wrong.
Hooven has been all over the media, just see what she’s RTed on her Twitter account. She makes it pretty clear she’s not going to back down on the scientific questions and answers. Which is how it should be, but that sort of stance is far less common than groveling obeisance before the new red guards.
We note that our estimated TMRCA to Neanderthal within Neanderthal-introgressed segments in all non-African populations is recent, ~74 ka ago, and implies therefore that little genetic drift separates admixed humans from sequenced Neanderthals in these segments. This recent TMRCA suggests that the majority of Neanderthal ancestry in modern humans originated from Neanderthal gene flow into the ancestors of all non-Africans before populations diversified. It also suggests that at least one of the Neanderthal genomes used here is closely related to the Neanderthal(s) involved in this admixture event. The slightly elevated Neanderthal ancestry that others have described in Central and East Asian populations also appears to have originated in this first pulse, as Central and East Asian Neanderthal haplotypes are mostly shared with other, geographically distant populations. This observation favors the hypothesis that the increased Neanderthal ancestry in these populations relative to others is due to weaker selection against alleles that may be mildly deleterious (32), made possible because of smaller historical population sizes in this part of Eurasia, rather than to additional admixture events (22). Our evidence of many small-scale, population-specific admixture events, however, together with a simulation study that found a single-pulse admixture model followed by drift unable to explain the discrepancies in admixture proportions in European and Asian genomes (49), hints at a complex history of admixture throughout Eurasia not fully captured by either of these two hypotheses.
I don’t think that it’s weaker selection in East Asians. I think it’s complex demography.
I’m going to sidestep the new inference that Austronesian expansion may predate the movement out of Taiwan. I’ll revisit. Rather, let’s reflect on the Denisovans. There is strong evidence of more than one admixture from this lineage into modern humans. And, multiple papers now support a model where various Southeast Asian groups have several different pulses. Finally, the “Denisovans” have really deep divergence. Way deeper than anything in modern humans. Some of them split right after the west-east Eurasian hominin split.
All this is curious in light of small hominins in the Philippines and Flores, as well as late ‘erectus.’ I think it is likely that some of the Denisovan lineages have ‘super-archaic’ admixture, while some of the gene flow is mediated by highly admixed moderns with high Denisovan load.
The history of human inbreeding is controversial. The development of sedentary agricultural societies may have had opposite influences on inbreeding levels. On the one hand, agriculture and food surplus may have diminished inbreeding by increasing population sizes and lowering endogamy, i.e. inbreeding due to population isolation. On the other hand, increased sedentism, as well as the advent of private property may have promoted inbreeding through the emergence of consanguineous marriage customs or via ethnic and caste endogamy. The net impact is unknown, and to date, no systematic study on the temporal frequency of inbreeding in human societies has been conducted. Here we present a new approach for reliable estimation of runs of homozygosity (ROH) in genomes with ≥3x mean coverage across >1 million SNPs, and apply this to 440 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROH, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to endogamy, although singular cases of high consanguinity can also be found in the archaeogenomic record.
I think it is hard to think this is unrelated to decreased pairwise Fst between populations over the Holocene. Fst is a statistic that measures the proportion of genetic variation across two populations in relation to the total variance. In a Pleistocene world of small clans occupying a thinly populated landscape, one can envisage a scenario where gene flow is far more viscous than the more sedentary, but interconnected, world of agriculturalists.
Hunter-gatherers were probably not more xenophobic. Rather, increasing populations by an order of magnitude increases the number of potential geographically close mates a lot.
Another consequence of more gene flow and more partners is that inbreeding also declines, as people have more recent ancestors in their pedigree.
The main caveat I would put into this though is that this applies to dense Eurasian time transects. There is some reason to think that hominins on the northern Eurasian fringe were always on the knife’s edge of sustainability.
I don’t have time to blog in detail today so I’ll point you to Ann Gibbon’s story, How Neanderthals lost their Y chromosome. You can find the link to the paper in there. The big issue here is that both mtDNA and Y chromosomes were replaced due to introgression from a population closer to modern humans than the Neandersovans, though basal to any modern humans alive today. This new group may actually be basal to the “basal human” group hypothesized by some scholars (there are suggestions of its existence in autosomal admixture into Neanderthals).
The probability of fixation of a newly introduced allele is the frequency of that allele, so how is it that these paleo-modern variants swept into Neanderthals? Perhaps on one locus, but two? One solution offered is naturals selection. This seems plausible, but the possibility of natural selection on Y and mtDNA lineages has always been a “wild card” that would make us rethink a lot of our phylogeography in general.
Finally, though it looks like the vast majority of modern ancestry outside of Africa is derived from a relatively recent (60,000 years ago) rapid expansion, it is clear that the picture at any given time is more complex than the signal we see today. It seems more and more likely that there was more a continuum between the African and Neandersovan lineages, and I strongly suspect that some of the paleo-modern lineages will at some point be detected in some modern groups once we have ancient DNA (the closer genetic distance and low fraction makes it hard for these segments to be identified in extant modern lineages using standard inference).
One of the oldest group of loci investigated for variation in humans are the ABO antigen markers. There are several reasons for this. First, you can assay them with pre-DNA methods. Second, they vary a lot. Third, they’re very important for things like blood donation.
The fact that they vary a lot means that researchers in the early 20th century used these markers to try and figure out population history. This was not workable for two reasons. First, looking at a locus here and there is not really informative. Y and mtDNA have special characteristics, but even these markers are really informative in a broader context. Second, the ABO locus is subject to natural selection. More precisely, it looks like a lot of immunological markers the ABO locus is subject to balancing selection which keeps it quite diverse.
What does this mean? Basically, variation at any locus is going to turnover. All the polymorphism will “coalesce” back to a common ancestor. The date of coalescence is going to be conditional on parameters such as genetic drift, and selection. Strong sweeps mean all the variance is removed and the coalescence is shallow. Similarly, bottlenecks mean short lifetimes for lineages, since drift cranks away variation. Balancing selection results in the opposite effect. At immunological loci the coalescence is often deeper than the time between the separation of species. The reason is that frequency-dependent selection prevents rare alleles from going extinct (the fitness goes up the rarer the allele).
Variation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. As one of the first genetic markers, variation at the ABO gene has been studied for over 60 years, and yet there are some aspects of its evolution that remain mysterious. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We analyze coding variation at the ABO locus from next-generation sequences in ~2,500 individuals from 28 populations, including three Neanderthal and one Denisovan individuals. We use the modern human haplotypes to impute ABO genotypes for the four archaic human genomes. We found that the Siberian Neanderthals, Altai and Chagyrskaya, are both homozygous for a derived Neanderthal variant of the O allele, while the European Neanderthal, Vindija, is a heterozygote for two derived Neanderthal variants, an O variant different from Altai and Chagyrskaya, and a rare cis-AB variant. The Denisovan individual is homozygous for an ancestral variant of the O allele, similar to variants found widely in modern humans. Perhaps more surprisingly, the derived O allele variant found in the Altai Neanderthal can be found at low frequencies in modern European and Southeast Asian individuals, and the derived O allele variant found in the Vindija Neanderthal is also found at very low frequency in East Asian individuals. Our genetic distance analyses suggests both alleles were introgressed through Neanderthal-human gene flow. In summary, our study identifies the genetic variation of the ABO gene in archaic humans, we find that ABO allele diversity in Neanderthals was likely high, and that some of these alleles still survive in modern humans due to inbreeding with Neanderthals.
The results are in alignment with theoretical expectations (which were probabilistic though). Alleles from these Eurasian hominins are probably beneficial in some way. Admixture with diverged lineages is a way to “rescue” diversity that may have been lost. The interesting point in the discussion though is that the Neanderthal population that the rare alleles were obtained had more variation than the small samples of European and Altai Neanderthals that we have now. This is not surprising, as it was probably a Near Eastern extension of European Neanderthals, and may even had have a larger long-term effective population than the groups further north.
The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic super-archaic species, Homo luzonensis and H. floresiensis, were present around the time anatomically modern humans (AMH) arrived in the region >50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA, a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.
Most paleonathropologists seem convinced now that Flores and the island of Luzon in the Phillipines were host to deeply diverged lineages of humans. By “deeply diverged” we’re talking well over one million years. Homo itself is only two million years ago. If they are deeply diverged there are ways to probe the genome for outlier segments of DNA which seem to have “come in” from outside lineages in relation to the main branch of ancestry. The more deeply diverged the ancestry, the easier it is to pick up the signal with even small amounts of admixture.
The authors could not find such ancestry in the various population across Southeast Asia and Australia, at least not to a greater extent than elsewhere. This implies that if luzonensis and floresiensis are deeply diverged they did not mix with anatomically modern humans. Or, the other option is that luzonensis and floresiensis are themselves Denisovans! In other words, luzonensis and floresiensis underwent strong adaptation to local conditions and changed so much that a standard morphological comparison will yield greater phylogenetic distance than what the whole genome might indicate. As we do not have ancient DNA from luzonensis and floresiensis this hypothesis cannot be tested.
But the model which the preprint seems to favor is that there are regions of island Southeast Asia with rich megafaunal survival, Sulawesi and Mindoro (an island off the coast of Luzon), that are also likely candidates for Denisovan remains. I would like the biogeographic element of the preprint fleshed out more before publication, though perhaps my relative confusion here is due to the fact that the evolutionary genomics is quite familiar to me.
I will note that the authors cite super-archaic admixture into the Andamanese, but from what I can tell most researchers in the area are skeptical of that particular paper. Basically, it looks like direct super-archaic admixture is unlikely. That being said, there are more complex models of indirect admixture through Neanderthals and Denisovans, and “first wave” modern humans, which I find possible.
Nature recently came out with two blockbuster papers establishing a better chronology on the settlement of the New World by humans. More precisely, the papers seem to push the likely date back by over 15,000 years. The figure above is from one of the papers. It shows human-derived artifacts from sites that date to 25,000 years BP and even 32,000 years BP.
I have recorded a podcast with the first author of one of the papers (she is second on the other). The podcast should post later today. Nevertheless, talking to the author I am more than 50% convinced that humans were present in the New World 32,000 years ago, and 90% convinced they were here 25,000 years ago. This is well before what is needed and expected from the standard “Beringian standstill” model.
The Beringian standstill alludes to the fact that the proto-Amerindians, a mix of Paleo-Siberian (ANE) and diverged East Asian, may have occupied Beringia for thousands of years before finally pushing southward ~15,000 years ago. The sites in the database of these papers show that a huge explosion of human occupation characterized North America during this period. But these were not the first humans.
I believe these new results likely open the possibility for a resolution of the mystery of why some groups in the Amazon seem to have “Australasian” genetic affinities. The result is robust. But it was hard to resolve with the Beringian standstill. The new chronology offers up an opportunity. Clearly the earlier populations before 20,000 years ago may have been the ancestors of the “Australasians” that are still hinted at in the Amazonians. I believe that these early people were members of what I have termed Clade-2 East Eurasians. This clade was dominant in South, Southeast Asia, Tibet, and present in coastal East Asia (Japan), during the Pleistocene. It has closer affinities to Oceanians than East Asians to the north.
If the first humans in the New World arrived as coastal fringe dwellers, it is clearly plausible that populations from Japan and points south could simply have done a circum-Pacific arc. We’ve seen lots of mass replacements in the ancient DNA, and the WST-Clovis groups seem to have been very numerous. Weak to no genetic signature of Clade-2 New World peoples is not surprising. There is no evidence of Oase Aurignacians in modern Europeans.
Charles Darwin famously posited the origin of species through adaptation driven by natural selection. The theory of evolution as we understand it. But another of Darwin’s major ideas was that sexual selection was very important in driving diversity within species. More specifically Darwin thought that female choosiness was critical and explained why in species such as birds the males were so much more “showy.”
Sexual selection is a huge field of study, and it’s hard to deny that it is a real thing. But, there has long been an argument about the efficacy of sexual selection within humans. Depending on how you define it, it does not seem that humans are particularly sexually dimorphic compared to common chimpanzees and gorillas, for example. This goes back to whether we are polygynous or monogamous. Because of high reproductive variation for males in polygyny sexual selection can drive changes really fast (e.g., one super-fit male can produce huge numbers of offspring). The situation in monogamy is more difficult since there is less reproductive variance.
Genome-wide sequencing of human populations has revealed substantial variation among genes in the intensity of purifying selection acting on damaging genetic variants. While genes under the strongest selective constraint are highly enriched for Mendelian disorders, most of these genes are not associated with disease and therefore the nature of the selection acting on them is not known. Here we show that genetic variants that damage these genes reduce reproductive success substantially in males but much less so in females. We present evidence that this reduction is mediated by cognitive and behavioural traits, which renders male carriers of such variants less likely to find mating partners. Our findings represent strong genetic evidence that Darwin’s theory of sexual selection is shaping the gene pool of contemporary human populations. Furthermore, our results suggest that sexual selection can account for about a quarter of all purifying selection acting on human genes.
The figure to the right gets at the major finding. More mutations mean a far more rapid drop in fitness for males than females. Why? The major reason seems to be that males can’t find a partner. If they can find a partner, the effect is much weaker. Basically, this is detecting an increase in childlessness.
A plausible explanation is that it impacts fertility, but the above indicates that that is not the case. And, the deleterious mutations aren’t enriched in the testes, nor does pruning out loci with known reproductive effects remove the impact. The authors also looked at intelligence. Those with mutations were not as intelligent, but that can’t explain most of the effect (and obviously it didn’t have much of an impact on women). The same with known conditions such as schizophrenia. Rather, what’s going on is that people are picking up on overall “genetic quality.”
There are major limitations of course. This is in British people. And, the samples from the Biobank tend to be somewhat healthier than average. There is a lot more work to be done with a lot more samples. But this is an awesome result in that it synthesizes the power and methods of modern genomics with a classical evolutionary hypothesis about the shape of human variation.
The main question I have regarding sexual selection then is what will the results in other societies be? As per Joe Henrich’s recent book, The WEIRDEST People in the World, the British have been in enforced monogamy for 1,000 years. Purifying selection could be much stronger in some non-WEIRD societies (and in inbred Arab cultures cousin-marriage would also ‘expose’ recessive alleles faster). That might mean there aren’t as many deleterious alleles. Or, it could be the effect is much stronger in those who have no children (males).
This is just the beginning. Perhaps it’s time to reread Geoffrey Miller’s The Mating Mind?
Archaeologists contend that it was our aptitude for symbolic, technological, and social behaviors that was central to Homo sapiens rapidly expanding across the majority of Earth’s continents during the Late Pleistocene. This expansion included movement into extreme environments and appears to have resulted in the displacement of numerous archaic human populations across the Old World. Tropical rainforests are thought to have been particularly challenging and, until recently, impenetrable by early H. sapiens. Here, we describe evidence for bow-and-arrow hunting toolkits alongside a complex symbolic repertoire from 48,000 years before present at the Sri Lankan site of Fa-Hien Lena—the earliest bow-and-arrow technology outside of Africa. As one of the oldest H. sapiens rainforest sites outside of Africa, this exceptional assemblage provides the first detailed insights into how our species met the extreme adaptive challenges that were encountered in Asia during global expansion.
The most interesting aspect of this is that it is pretty close (a few thousand years earlier) to the date for the arrival of modern humans in Europe. The admixture with Neanderthals seems to be about 10,000 years earlier than this date, while that with Denisovans around this date. Something happened around 50,000 years ago, as a group of modern humans in and around the Near East seem to have radiated rapidly all across Eurasia, and later Oceania.
I assume that modern(ish) humans were present in Southeast Asia, but most of the ancestry dates to this period and pulse. A decade ago I might posit some incredible biological change, but cultural innovations in the Holocene triggered massive demographic shifts. There’s no reason the same couldn’t apply to the Pleistocene.
Carole Hooven has a new book, T: The Story of Testosterone, the Hormone that Dominates and Divides Us. I’ll be honest and admit I was only vaguely aware of the book until yesterday when a social media controversy erupted over her “transphobic comments” on Fox & Friends. You can watch the clip yourself, and see that she’s not transphobic at all.
