May 29, 2014

A twist in Austronesian origins

The Taiwanese origin of Austronesians is widely accepted. A new preprint confirms this theory, but adds a new twist to the story of Austronesian dispersals, as it seems that in their western expansion, Austronesians picked up some Austroasiatic ancestry. This means either that Austroasiatic speakers preceded them in islands where Austronesian languages are now spoken, or that the Austronesians picked up this kind of ancestry in the mainland before settling in the islands.

bioRxiv, doi:

Reconstructing Austronesian population history in Island Southeast Asia

Mark Lipson et al.

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the "Austronesian expansion," which began 4-5 thousand years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, focusing primarily on Island Southeast Asia, we analyze genome-wide data from 56 populations using new methods for tracing ancestral gene flow. We show that all sampled Austronesian groups harbor ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.


May 24, 2014

High genetic differentiation between populations often driven by classic selective sweeps

bioRxiv doi:

Human genomic regions with exceptionally high or low levels of population differentiation identified from 911 whole-genome sequences

Vincenza Colonna et al.

Background: Population differentiation has proved to be effective for identifying loci under geographically-localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. Results: We demonstrate that while sites of low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. Conclusions: We have identified known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.


May 22, 2014

MSMC preprint (Schiffels and Durbin)

From the paper:
In particular, the early beginning of the drop would be consistent with an initial formation of distinct populations prior to 150kya, while the late end of the decline would be consistent with a final split around 50kya. This suggests a long period of partial divergence with ongoing genetic exchange between Yoruban and Non-African ancestors that began beyond 150kya, with population structure within Africa, and lasted for over 100,000 years, with a median point around 60-80kya at which time there was still substantial genetic exchange, with half the coalescences between populations and half within (see Discussion). We also observe that the rate of genetic divergence is not uniform but can be roughly divided into two phases. First, up until about 100kya, the two populations separated more slowly, while after 100kya genetic exchange dropped faster.
If divergence between Yoruba and non-Africans began 150kya, then I wonder when divergence between Bushmen or the non-farmer ancestors of Pygmies and the Yoruba started. These dates are well within the time period when anatomical modernity was already in existence, but well before the time period when behavioral modernity first appears. This is important, as some people imagine that humans lived together for most of the time period since their first appearance ~200kya and only split recently at ~50kya, but this is obviously wrong. ~50kya seems to be the time for cessation of gene flow, with 100ky more of impeded gene flow.

As expected, the oldest split amongst out-of-Africa populations is between European and East Asian (CHB and MXL) populations, most of which occurs between 20-40kya (Figure 4b). Intriguingly there may be a small component (10% or less) of this separation extending much further back towards 100kya, not compatible with a single out-of-Africa event around 50kya.
This is the most intriguing part of this preprint as it suggests that European/East Asian genetic differentiation may not only be due to the their post-UP divergence, but also to older strands of ancestry. Such deep differentiation may be related to the ~100kya settlement of the Near East (but not East Asia) by anatomically modern humans and the recent evidence for a deep "Basal Eurasian" lineage in Europeans but not East Asians.

bioRxiv, doi:

Inferring human population size and separation history from multiple genome sequences

Stephan Schiffels, Richard Durbin

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.


May 19, 2014

The history of mtDNA haplogroup U6

BMC Evolutionary Biology 2014, 14:109 doi:10.1186/1471-2148-14-109

The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents

Bernard Secher et al.

Abstract (provisional)


Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia.


Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent.


The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.


May 16, 2014

mtDNA D1 from 12-13 thousand year old Paleoamerican

This is interesting both because it's a >12,000 year old skeleton from the bottom of the sea (!) and because it establishes that an individual with clear Paleoamerican morphology belonged to a common modern Amerindian mtDNA haplogroup. Together with the recent publication of the Anzick genome, it seems that everything points towards continuity of Native Americans since the earliest settlement, rather than a more recent arrival of the ancestors of Native Americans that replaced an earlier "Paleoamerican" gene pool.

Science 16 May 2014: Vol. 344 no. 6185 pp. 750-754 DOI: 10.1126/science.1252619

Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans

James C. Chatters

Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico’s Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.


May 15, 2014

An excess of X-chromosomal diversity in Africans

A new study provides important new data for African-Eurasian differences in the X-to-autosomal ratio of nucleotide diversity.

In my opinion, an explanation for this phenomenon might be found in the back-migration into Africa of Eurasian males (belonging to Y-haplogroup E). If a Eurasian man has offspring with an African woman, then the autosomal diversity of his offspring will be more than his and less than hers (*). For the pairing's daughters, 1 X chromosome will be contributed by the Eurasian man and 1 from the African woman. But, for its sons, 1 X chromosome will be contributed by the African woman only. Thus, X chromosomal diversity in descendants of such a mixed population will be higher because Africans will contribute 2/3 of the X chromosomes but only 1/2 of the autosomes.

(*) It will probably not be halfway between them, because some increase in diversity will be contributed by mutations (or equivalently archaic introgressions) that occured in the Eurasian and African lineages since their separation.

AJHG doi:10.1016/j.ajhg.2014.04.011

Contrasting X-Linked and Autosomal Diversity across 14 Human Populations

Leonardo Arbiza et al.

Contrasting the genetic diversity of the human X chromosome (X) and autosomes has facilitated understanding historical differences between males and females and the influence of natural selection. Previous studies based on smaller data sets have left questions regarding how empirical patterns extend to additional populations and which forces can explain them. Here, we address these questions by analyzing the ratio of X-to-autosomal (X/A) nucleotide diversity with the complete genomes of 569 females from 14 populations. Results show that X/A diversity is similar within each continental group but notably lower in European (EUR) and East Asian (ASN) populations than in African (AFR) populations. X/A diversity increases in all populations with increasing distance from genes, highlighting the stronger impact of diversity-reducing selection on X than on the autosomes. However, relative X/A diversity (between two populations) is invariant with distance from genes, suggesting that selection does not drive the relative reduction in X/A diversity in non-Africans (0.842 ± 0.012 for EUR-to-AFR and 0.820 ± 0.032 for ASN-to-AFR comparisons). Finally, an array of models with varying population bottlenecks, expansions, and migration from the latest studies of human demographic history account for about half of the observed reduction in relative X/A diversity from the expected value of 1. They predict values between 0.91 and 0.94 for EUR-to-AFR comparisons and between 0.91 and 0.92 for ASN-to-AFR comparisons. Further reductions can be predicted by more extreme demographic events in excess of those captured by the latest studies but, in the absence of these, also by historical sex-biased demographic events or other processes.


May 14, 2014

Near Eastern roots of South Asian Neolithic

The table of dates for different sites might prove useful (pdf).

PLoS ONE 9(5): e95714. doi:10.1371/journal.pone.0095714

The Near-Eastern Roots of the Neolithic in South Asia

Kavita Gangal et al.

The Fertile Crescent in the Near East is one of the independent origins of the Neolithic, the source from which farming and pottery-making spread across Europe from 9,000 to 6,000 years ago at an average rate of about 1 km/yr. There is also strong evidence for causal connections between the Near-Eastern Neolithic and that further east, up to the Indus Valley. The Neolithic in South Asia has been far less explored than its European counterpart, especially in terms of absolute (14C) dating; hence, there were no previous attempts to assess quantitatively its spread in Asia. We combine the available 14C data with the archaeological evidence for early Neolithic sites in South Asia to analyze the spatio-temporal continuity of the Neolithic dispersal from the Near East through the Middle East and to the Indian subcontinent. We reveal an approximately linear dependence between the age and the geodesic distance from the Near East, suggesting a systematic (but not necessarily uniform) spread at an average speed of about 0.65 km/yr.


Younger Dryas/Cosmic Impact synchrony questioned

Good coverage in Nature News:
Supporters of the impact theory have put forth 29 sites, from North America to Europe and beyond, that contain a thin layer of sediments said to date to the start of the cosmic impact event. The latest study checked to see whether those sites were all really 12,800 years old.  
Only 3 of the 29 are, the researchers report today in the Proceedings of the National Academy of Sciences1. The other sites either have not been dated using the usual radiometric methods, or are much older or younger than the reported impact. “The chronology doesn’t hold up,” says team leader David Meltzer, an archaeologist at Southern Methodist University in Dallas, Texas.
Impact supporters are not about to give up. “Meltzer’s analysis of the dates is overly simplistic and clearly biased towards his conclusions,” says Richard Firestone, a nuclear chemist at Lawrence Berkeley National Laboratory in California and leader of the impact theory. Errors in radiocarbon dating mean that not all of the sites will date precisely to 12,800 years ago, Firestone argues. And much of his team's argument relies on cross-correlating various sites containing impact markers, some with good radiocarbon dates and some without.
PNAS doi: 10.1073/pnas.1401150111

Chronological evidence fails to support claim of an isochronous widespread layer of cosmic impact indicators dated to 12,800 years ago

David J. Meltzer et al.

A key element underpinning the controversial hypothesis of a widely destructive extraterrestrial impact at the onset of the Younger Dryas is the claim that 29 sites across four continents yield impact indicators all dated to 12,800 ± 150 years ago. This claim can be rejected: only three of those sites are dated to this window of time. At the remainder, the supposed impact markers are undated or significantly older or younger than 12,800 years ago. Either there were many more impacts than supposed, including one as recently as 5 centuries ago, or, far more likely, these are not extraterrestrial impact markers.


May 09, 2014

Ancient DNA from the Balkans (Iron Age Thrace)

A new paper in PLoS Genetics presents new data from two Iron Age Thracian individuals and puts the Sardinian-ness of Oetzi in new context. The authors write:
The results of the analyses including additional ancient genomes provide mounting evidence that the Iceman's genetic affinity with Sardinians reflects an ancestry component that was widespread in Europe during the Neolithic. Despite their different geographic origins, both the Swedish farmer gok4 and the Thracian P192-1 closely resemble the Iceman in their relationship with Sardinians, making it unlikely that all three individuals were recent migrants from Sardinia. Furthermore, P192-1 is an Iron Age individual from well after the arrival of the first farmers in Southeastern Europe (more than 2,000 years after the Iceman and gok4), perhaps indicating genetic continuity with the early farmers in this region. The only non-HG individual not following this pattern is K8 from Bulgaria. Interestingly, this individual was excavated from an aristocratic inhumation burial containing rich grave goods, indicating a high social standing, as opposed to the other individual, who was found in a pit [15]. However, the DNA damage pattern of this individual does not appear to be typical of ancient samples (Table S4 in [15]), indicating a potentially higher level of modern DNA contamination. On the other hand, the Swedish and the Iberian hunter-gatherers show congruent patterns of relatedness to the modern populations of Northern Europe, which is consistent with the previous results using those samples.
Also of interest, given previous suggestions that the Iceman had more Neandertal ancestry than modern Europeans:
However, all D-tests involving another non-African population do not significantly deviate from zero, suggesting that the Iceman genome contains levels of archaic ancestry that are comparable to that of other non-African populations.
A model of European history is seen on the left. Some details are probably incorrect (e.g., Sardinian Neolithic probably followed the Cardial/Mediterranean route rather the one shown in C). There are no good ancient DNA from Cardial Neolithic farmers, so the fact that Sardinians are similar to the Iron Age Bulgarian, the Stuttgart LBK German, and the Swedish TRB farmers may mean that the Mediterranean/Cardial farmers were related to the ones that went into Europe following the inland route from the Balkans.

In any case, the fact that there are now data from Bulgaria is great, because it means that southern Europe is not hopeless for ancient DNA preservation and hopefully more is on its way.

UPDATE: Did anyone see a link to the new data? It appears that there are only ~1,000 SNPs in common with the HGDP. [A link to the data will become available at the Bustamante lab website]

PLoS Genet 10(5): e1004353. doi:10.1371/journal.pgen.1004353

Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

Martin Sikora et al.

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.


May 08, 2014

Psychological differences in China predicted by rice/wheat agriculture

Science 9 May 2014: Vol. 344 no. 6184 pp. 603-608
DOI: 10.1126/science.1246850

Large-Scale Psychological Differences Within China Explained by Rice Versus Wheat Agriculture

T. Talhelm et al.

Cross-cultural psychologists have mostly contrasted East Asia with the West. However, this study shows that there are major psychological differences within China. We propose that a history of farming rice makes cultures more interdependent, whereas farming wheat makes cultures more independent, and these agricultural legacies continue to affect people in the modern world. We tested 1162 Han Chinese participants in six sites and found that rice-growing southern China is more interdependent and holistic-thinking than the wheat-growing north. To control for confounds like climate, we tested people from neighboring counties along the rice-wheat border and found differences that were just as large. We also find that modernization and pathogen prevalence theories do not fit the data.


May 05, 2014

SPAMIX for spatial localization of admixed individuals

A new preprint on the bioRxiv suggests that it is possible to geographically localize the location of a person's four grandparents. This is often a problem for persons of mixed ancestry who often tend to plot in PCAs in some average location between their ancestors (so someone who is Swedish+Italian+Spanish+Russian might end up somewhere in central Europe even though none of his ancestors are central European).

This has appeared shortly after the GPS method of Elhaik et al. (2014) which presents evidence of being more accurate than SPA, so it will be interesting to see a comparison between SPAMIX and GPS. My experience in the Dodecad Project suggests that this is a useful feature (the Dodecad Oracle could sometimes be used for this purpose and e.g., could infer that a person that had one Ashkenazi Jewish grandparent and 3 English ones was a ~3/4 British+~1/4 Jewish mix, but it is limited to mixtures of two populations, so it could not cope with the case of 3-4 grandparents with different origins). There is an under-appreciated pool of adoptees who would love a tool like that, and there are also obvious forensic implications if something like this really works.

bioRxiv doi: 10.1101/004713

Spatial localization of recent ancestors for admixed individuals

Wen-Yun Yang et al.

Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over non-model-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum. We devise efficient algorithms based on hidden Markov models to localize on a map the recent ancestors (e.g. grandparents) of admixed individuals, joint with assigning ancestry at each locus in the genome. We validate our methods using empirical data from individuals with mixed European ancestry from the POPRES study and show that our approach is able to localize their recent ancestors within an average of 470Km of the reported locations of their grandparents. Furthermore, simulations from real POPRES genotype data show that our method attains high accuracy in localizing recent ancestors of admixed individuals in Europe (an average of 550Km from their true location for localization of 2 ancestries in Europe, 4 generations ago). We explore the limits of ancestry localization under our approach and find that performance decreases as the number of distinct ancestries and generations since admixture increases. Finally, we build a map of expected localization accuracy across admixed individuals according to the location of origin within Europe of their ancestors.


May 04, 2014

Genealogical vs. Evolutionary Y-STR mutation rate

Long-time readers will remember my Y-STR series which was inspired by my desire to figure out why some papers used the directly observed mutation rate for Y-STRs while others used a 3-times slower "evolutionary" one. My conclusion was that the evolutionary rate was misapplied because its theoretical justification hinged on an assumption of constant population size that was wrong for modern humans and even modest amounts of growth led to a mutation rate that was closer to the genealogical one.

My enthusiasm for Y-STR based dating waned in 2011 when Busby et al. (2011) published a study which showed the effect of microsatellite choice on TMRCA estimates due to the fact that Y-STRs don't follow the the unconstrained strict symmetrical stepwise model (i.e., increase by +/- 1 steps per mutational event with equal probability). This meant that various published age estimates depended on the cocktail of slow/fast Y-STRs used as well as the age of the target node in the phylogeny (because deviations from linearity were more egregious for older nodes). Additionally, at that time it was clear that whole Y chromosome sequencing was around the corner and so the issue would soon be resolved by a new technology.

A new preprint presents an interesting coda to this long-standing controversy and basically agrees that the genealogical rate is better than the evolutionary one in the sense that it produces age estimates that are closer to those from resequencing. The evolutionary rate is good only for the very deep split in the tree which is not surprising since this is the domain where deviations from linearity plague the genealogical rate so a slower rate will do better.

One comment to the authors is that the generation length of 25 years is not applicable to modern humans, but rather a male generation length of 31-32 years has been estimated across different cultures. The authors estimate the "super-Eurasian" CT clade at 56.26kya (using sequence data) which would correspond to ~71 thousand years if we apply a 31.5/25 multiplier. This would bring it closer to the age estimate for Eurasian M+N mtDNA which has been estimated without an assumption of generation length using ancient DNA. (There is of course no a priori reason that the two should match, but the dates seem to match with the drying up of the Sahara-Arabia zone c. 70kya. As I've argued before, the population contraction that must have accompanied such a traumatic event would be a good opportunity for drift to shed genetic lineages and leave the CT/M+N pair as the inheritors of Eurasia).

bioRxiv doi: 10.1101/004705

Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates

Chuan-Chao Wang, Li Hui

We have compared the Y chromosomal lineage dating between sequence data and commonly used Y-SNP plus Y-STR data. The coalescent times estimated using evolutionary Y-STR mutation rates correspond best with sequence-based dating when the lineages include the most ancient haplogroup A individuals. However, the times using slow mutated STR markers with genealogical rates fit well with sequence-based estimates in main lineages, such as haplogroup CT, DE, K, NO, IJ, P, E, C, I, J, N, O, and R. In addition, genealogical rates lead to more plausible time estimates for Neolithic coalescent sublineages compared with sequence-based dating.


May 03, 2014

Did Men cause the demise of the Hobbits?

An interesting tidbit from an interview with Chris Stringer:
There was also a population of a very small human-like species on the island of Flores in Indonesia—often called "hobbits." It had been thought they were around until about 17,000 years ago, but unpublished evidence suggests they could have disappeared earlier, in which case the spread of modern humans might correlate with their demise.
My model is that modern humans came out of Africa 60,000 years ago and moved very quickly into the territory of the Neanderthals, later into the territory of the Denisovans, and soon after that into the territory of the "hobbits." Within 20,000 years, as far as we can tell, those other populations have gone, all of them. 

May 02, 2014

Human STR variation (Willems et al. 2014)

bioRxiv doi: 10.1101/004671

The Landscape of Human STR Variation

Thomas F. Willems et al.

Short Tandem Repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across over 1,000 individuals in phase 1 of the 1000 Genomes Project. This process nearly saturated common STR variations. After employing a series of quality controls, we utilize this call set to analyze determinants of STR variation, assess the human reference genome?s representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations. The resource is publicly available at both in raw format and via a graphical interface. 


May 01, 2014

Archaic admixture in Eurasians with hominins that diverged 0.9 and 3.5 million years ago?

One of the interesting stories of the Neandertal Genome Project is how earlier evidence of archaic introgression into Eurasians was later confirmed when the Neandertal genome was published. It is always trickier to make a case for archaic introgression in the absence of an actual archaic genome, so I expect this paper to be subjected to a high level of scrutiny. In any case, I'm glad that it's on the arXiv so that the scrutiny process can begin by anyone who cares about the subject.

arXiv:1404.7766 [q-bio.PE]

Genome-wide Scan of Archaic Hominin Introgressions in Eurasians Reveals Complex Admixture History

Ya Hu, Yi Wang, Qiliang Ding, Yungang He, Minxian Wang, Jiucun Wang, Shuhua Xu, Li Jin

Introgressions from Neanderthals and Denisovans were detected in modern humans. Introgressions from other archaic hominins were also implicated, however, identification of which poses a great technical challenge. Here, we introduced an approach in identifying introgressions from all possible archaic hominins in Eurasian genomes, without referring to archaic hominin sequences. We focused on mutations emerged in archaic hominins after their divergence from modern humans (denoted as archaic-specific mutations), and identified introgressive segments which showed significant enrichment of archaic-specific mutations over the rest of the genome. Furthermore, boundaries of introgressions were identified using a dynamic programming approach to partition whole genome into segments which contained different levels of archaic-specific mutations. We found that detected introgressions shared more archaic-specific mutations with Altai Neanderthal than they shared with Denisovan, and 60.3% of archaic hominin introgressions were from Neanderthals. Furthermore, we detected more introgressions from two unknown archaic hominins whom diverged with modern humans approximately 859 and 3,464 thousand years ago. The latter unknown archaic hominin contributed to the genomes of the common ancestors of modern humans and Neanderthals. In total, archaic hominin introgressions comprised 2.4% of Eurasian genomes. Above results suggested a complex admixture history among hominins. The proposed approach could also facilitate admixture research across species.


Doggerland inhabitants destroyed by tsunami (?)

I hope someone is studying ancient DNA from these two Mesolithic ladies from Brittany. The caption reads:
These two young Mesolithic women from Teviec, Brittany, were brutally murdered. As sea levels rose there may have been increased competition for resources
Prehistoric North Sea 'Atlantis' hit by 5m tsunami
The wave was generated by a catastrophic subsea landslide off the coast of Norway.
Analysis suggests the tsunami over-ran Doggerland, a low-lying landmass that has since vanished beneath the waves. 
"It was abandoned by Mesolithic tribes about 8,200 years ago, which is when the Storegga slide happened," said Dr Jon Hill from Imperial College London. 

The wave could have wiped out the last people to occupy this island. 
The research has been submitted to the journal Ocean Modelling and is being presented at the European Geosciences Union General Assembly in Vienna this week.
Dr Hill and his Imperial-based colleagues Gareth Collins, Alexandros Avdis, Stephan Kramer and Matthew Piggott used computer simulations to explore the likely effects of the Norwegian landslide. 
He told BBC News: "We were the first ever group to model the Storegga tsunami with Doggerland in place. Previous studies have used the modern bathymetry (ocean depth)."
As such, the study gives the most detailed insight yet into the likely impacts of the huge landslip and its associated tsunami wave on this lost landmass.

In defense of Neandertals

Here is an article that could very well be included in John Hawks' impressive collection of Neandertal anti-defamation files.

I am personally rather disinclined to accept the theory of Neandertal inferiority (or its correlate, that modern humans must have had some genetic adaptation that made them superior and facilitated their success). The main reason for leaning in this direction is that history abounds in examples of vanquished and marginalized peoples and it's hard to argue that this was due to any superiority of the people that replaced them. In ancient times all it took was a bad commander in war or getting a vital piece of military tech too late and a whole nation might be destroyed. Or, more simply one might find themselves on the wrong side of the numbers game and big groups of people tend to replace smaller ones even if individual members of big and small groups are not particulary different in any measurable way.

PLoS ONE 9(4): e96424. doi:10.1371/journal.pone.0096424

Neandertal Demise: An Archaeological Analysis of the Modern Human Superiority Complex

Paola Villa, Wil Roebroeks

Neandertals are the best-studied of all extinct hominins, with a rich fossil record sampling hundreds of individuals, roughly dating from between 350,000 and 40,000 years ago. Their distinct fossil remains have been retrieved from Portugal in the west to the Altai area in central Asia in the east and from below the waters of the North Sea in the north to a series of caves in Israel in the south. Having thrived in Eurasia for more than 300,000 years, Neandertals vanished from the record around 40,000 years ago, when modern humans entered Europe. Modern humans are usually seen as superior in a wide range of domains, including weaponry and subsistence strategies, which would have led to the demise of Neandertals. This systematic review of the archaeological records of Neandertals and their modern human contemporaries finds no support for such interpretations, as the Neandertal archaeological record is not different enough to explain the demise in terms of inferiority in archaeologically visible domains. Instead, current genetic data suggest that complex processes of interbreeding and assimilation may have been responsible for the disappearance of the specific Neandertal morphology from the fossil record.


The Mystery of Language evolution (Hauser et al. 2014)

Many big names grace this paper which appears to pretty much say that know close to nothing about how language has evolved. The authors don't seem to buy into the theory that the hyoid bone of the Kebara Neandertal proves that H. neanderthalensis had language (which would probably push the origin of language to a time much earlier than the invention of recognizably modern human culture).

In a sense we have no data because our evidence for language is from recent millennia of our own species and older hominins did not exhibit behaviors that would unambiguously require language. So, the origin of language may remain obscure unless some breakthrough identifies the genetic substrate of language whose existence in different ancient hominins can then be ascertained.

Front. Psychol. | doi: 10.3389/fpsyg.2014.00401

The mystery of language evolution

Marc D. Hauser1*, Charles Yang2, Robert C. Berwick3, Ian Tattersall4, Michael Ryan5, Jeffrey Watumull6, Noam Chomsky3 and Richard Lewontin7

Understanding the evolution of language requires evidence regarding origins and processes that led to change. In the last 40 years, there has been an explosion of research on this problem as well as a sense that considerable progress has been made. We argue instead that the richness of ideas is accompanied by a poverty of evidence, with essentially no explanation of how and why our linguistic computations and representations evolved. We show that, to date, 1) studies of nonhuman animals provide virtually no relevant parallels to human linguistic communication, and none to the underlying biological capacity; 2) the fossil and archaeological evidence does not inform our understanding of the computations and representations of our earliest ancestors, leaving details of origins and selective pressure unresolved; 3) our understanding of the genetics of language is so impoverished that there is little hope of connecting genes to linguistic processes any time soon; 4) all modeling attempts have made unfounded assumptions, and have provided no empirical tests, thus leaving any insights into language’s origins unverifiable. Based on the current state of evidence, we submit that the most fundamental questions about the origins and evolution of our linguistic capacity remain as mysterious as ever, with considerable uncertainty about the discovery of either relevant or conclusive evidence that can adjudicate among the many open hypotheses. We conclude by presenting some suggestions about possible paths forward.


Chris Stringer on Recent Out-of-Africa

An interesting new opinion piece by Chris Stringer in which he affirms the recent Out-of-Africa theory. Some predictions of the multiregionalists were certainly wrong (e.g., they did not predict that East Asians would have any Neandertal ancestry, let alone more than Europeans; and the ancestry of mankind may be even more jumbled than they'd imagined as e.g., it is not Siberians that have regional continuity with Denisovans but rather the faraway Papuans and Australians). On the other hand, the evidence does seem to point for a mostly African origin of Homo sapiens with important details of when and how that remain to be filled.

The fundamental question for me is the balance of divergence and synthesis in human history. Certainly, the fact that Denisova cave and thereabouts in Siberia had at least four divergent human lineages in the last 100-40 thousand years (unknown archaic Eurasians, Denisovans, Neandertals, and finally modern humans) makes modern Eurasians look like twins by comparison. In more recent times, Europeans of a few thousand years ago living in Sweden were more divergent from each other than any two European populations living today. And, while many models would have modern humans and Neandertals splitting from each other and going their separate ways until very recent times, this is hard to reconcile with the fact that apparently Neandertals and Africans became more similar over time during the period where they were supposedly diverging from each other. Was the situation in Africa any different? Morphology does not suggest homogeneity for that continent either.

Certainly, both replacement and gene flow have played a role in human history. The "English" and "Spanish" packages were assembled in Europe by gene flows from hunter-gatherers, farmers, and more recently Anglo-Saxons, Celts, Vikings, Goths, Romans, and Celtiberians (to name a few), but was then exported from Europe. Human history probably abounds in examples of populations that emerge out of a multiregional matrix (even if that matrix does not encompass the entire globe) and then explode in population numbers due to a lucky break or some behavioral or technological advantage.

Trends in Ecology & Evolution Volume 29, Issue 5, p248–251, May 2014

Why we are not all multiregionalists now

Chris Stringer


•DNA data show that archaic introgression into modern human genomes occurred.
•Such introgression is claimed to support the multiregional model for modern human origins.
•This introgression is also claimed to support the lumping of distinct human species into Homo sapiens.
•Comparing models and data still validates a recent African origin model for modern humans and the use of a restricted diagnosis for H. sapiens.

Recent revelations that human genomes contain DNA introgressed through interbreeding with archaic populations outside of Africa have led to reassessments of models for the origins of our species. The fact that small portions of the DNA of recent Homo sapiens derive from ancient populations in more than one region of the world makes our origins ‘multiregional’, but does that mean that the multiregional model of modern human origins has been proved correct? The extent of archaic assimilation in living humans remains modest, and fossil evidence outside of Africa shows little sign of the long-term morphological continuity through to recent humans expected from the multiregional model. Thus, rather than multiregionalism, a recent African origin (RAO) model for modern humans is still supported by the data.


The Geographic Position Structure (GPS) algorithm of Elhaik et al. (2014) is basically wrong

In the previous post I showed that the new paper by Elhaik et al. presents as its own (without citation) two of my ideas that were published on the web ~2 years before the paper was submitted.

I also took some time to evaluate the new aspect of their "geographical positioning system" (GPS) which is an algorithm to determine the geographic position of samples given their genetic distances to a group of reference populations. This is described under the heading "Calculating the biogeographical origin of a test sample" of their paper and I include a screenshot of it on the left to help you follow along.

From Equation (2) it is easy to see that the predicted position of the test sample is shifted away from the position of the best matching reference population (Positionbest) and towards the other reference populations (Position(m)) with the contribution of each reference population being weighted by wm which is the ratio of the distance of the closest population to the distance of the m-th reference population.

A little basic geometry (right) informs us that points on the circle have a constant ratio of distances (d2/d1) to points B and A.

That is, BC/CA = BD/DA = BP/PA

In terms of the Elhaik et al. (2014) algorithm this constant ratio is wm, so if A and B are two reference populations, and the test sample is e.g., either C or D, then the same constant weight applies (and this is true for all points on the circle).

In practical terms, the algorithm of Elhaik et al. (2014) will predict the same geographical locations for all points on the circle. This will be perfectly accurate for C and biased for every other point on the circle (with D being the absolute worst).

It is actually easy to test whether the test population is like C or like D; in the case of C it is CA+CB=AB. This is a simple test of collinearity that exploits the fact that not only the distance of the test population to reference ones, but also the distance of the two reference populations from each other. And, indeed, it's easy to see that for a test population P we can estimate genetic distances AP, PB, and AB and these uniquely define the circle on which the point must lie. Do this for all pairs of reference populations, find the distribution of the intersections of these circles, find a peak of this distribution (if such exists) et voila you have a sound mechanism for localizing individuals based on genetic distances. I expect to see something like this in Nature Communications circa 2016.