Current Biology http://dx.doi.org/10.1016/j.cub.2016.01.028
Deep Roots for Aboriginal Australian Y Chromosomes
Anders Bergström et al.
Australia was one of the earliest regions outside Africa to be colonized by fully modern humans, with archaeological evidence for human presence by 47,000 years ago (47 kya) widely accepted [ 1, 2 ]. However, the extent of subsequent human entry before the European colonial age is less clear. The dingo reached Australia about 4 kya, indirectly implying human contact, which some have linked to changes in language and stone tool technology to suggest substantial cultural changes at the same time [ 3 ]. Genetic data of two kinds have been proposed to support gene flow from the Indian subcontinent to Australia at this time, as well: first, signs of South Asian admixture in Aboriginal Australian genomes have been reported on the basis of genome-wide SNP data [ 4 ]; and second, a Y chromosome lineage designated haplogroup C∗, present in both India and Australia, was estimated to have a most recent common ancestor around 5 kya and to have entered Australia from India [ 5 ]. Here, we sequence 13 Aboriginal Australian Y chromosomes to re-investigate their divergence times from Y chromosomes in other continents, including a comparison of Aboriginal Australian and South Asian haplogroup C chromosomes. We find divergence times dating back to ∼50 kya, thus excluding the Y chromosome as providing evidence for recent gene flow from India into Australia.
Link
February 26, 2016
February 20, 2016
Are living Africans nested within Eurasian genetic variation (?)
(Early modern human lineage detected as admixture in the Altai Neandertal, ((Asians, Europeans), Africans)),
and then there are two deeper layers of Eurasian hominins (Neandertal/Denisovans) and the "Mystery hominin" that mixed into Denisovans.
Africans are thus just a leaf of the Eurasian family tree, casting serious doubt -if this model is to be believed- to the position that H. sapiens originated in Africa and are descended from people who never left the continent. It seems much simpler to derive them from an early migration (~200kya?) from Asia which would nicely explain why the continent's first sapiens populations appear tentatively in the northeastern corner, and why they do not replace archaic hominins for most of the 200 thousand years until today. In a reversal of perspective it is not Skhul/Qafzeh that are the "migration that failed", but rather the Omo 1 outlier is.
One might argue that this is just a consequence of the fact that lots of ancient genomes have been published from Eurasia, but none from Africa. So, there are all these branches of deep archaic Eurasians simply because there are no genomes of deep archaic Africans.
But, this explanation does not really work. If Africans had any significant ancestry deeper than the split of "Early modern human lineage", then this lineage would be closer to (Asians, Europeans) than to Africans. However, Kulhwilm et al. assert that it is "equally related to present-day Africans and non-Africans". If they had any ancestry deeper than ((Denisovans, Neandertals), H. sapiens), then (Denisovans, Neandertals) would be closer to non-Africans than to Africans. Well, they are, but this is now satisfactorily explained by admixture from (Denisovans, Neandertals) into non-Africans, thanks to genomes like Ust Ishim, K14, and Oase which have big chunks of Neandertal ancestry that can't be explained any other way. No need to invoke any such lineage when a simpler well-documented alternative exists.
The presented phylogeny negates the possibility of the existence of collateral archaic African kin of the extant Africans that admixed with them, and leads to the conclusion that Africans are nested within Eurasian variation because they really are. This is, of course, incompatible with the statistically inferred archaic introgression into Africans which indeed postulates the existence of such archaic Africans and their contribution to extant ones.
I don't see any obvious flaw with Kulhwilm et al. but if its model is right, then it does lead to some rather extreme conclusions. It contradicts the evidence for archaic introgression; if Hsieh et al. is wrong (and I don't seen any evidence for that either), then Kulhwilm et al. can be saved, but only if Africans are really nested within several layers of Eurasian variation and did not admix at all with the morphologically diverse archaic Africans of the paleoanthropological record. This also doesn't seem right now that we know that sapiens-archaic admixture was a common occurrence in Eurasia. The reversal of perspective alluded to above may help here by removing the opportunity for admixture, but that too is, of course, an extraordinary claim.
In sum, I am rather convinced that the latest discoveries have muddled the origin story of our species and some major rethink is needed to evaluate the totality of the evidence.
February 19, 2016
Archaic introgression in Pygmies
We must remember that detecting archaic admixture in Africa is a statistical power game where only a particular type of such introgression can be detected:
First, it needs to be from highly diverged Palaeoafrican sources so that it will look very different from plain H. sapiens DNA. Unlike Eurasia, there's no genome of an ancient Palaeoafrican one can compare against. All inference is based on African genomes having an improbable amount of heterozygosity in parts of their genome.
Second, it needs to have happened recently enough so that it will come in big chunks that can be distinguished from the plain H. sapiens background. Given enough time, recombination breaks down archaic segments into ever tinier bits. You can argue that an unusually long divergent haplotype with a deep TMRCA is archaic, but you can't argue that a single SNP is.
I have little doubt that most if not all of the supposedly "old divergences" between African populations are a mirage created by admixture between modern humans and archaic "Palaeoafricans" diverging and admixing at different time depths. The palaeoanthropological record is quite clear that modern humans were not the only game in town for most of the 200 thousand years since modern humans first appeared in the continent's northeastern corner.
A handful or two of archaic genomes from Eurasia needs an ever-more-complex web of admixtures to make sense of; Africa will need no less, and -if morphological variability persistence is any criterion- a lot more.
Genome Research Published in Advance February 17, 2016, doi: 10.1101/gr.196634.115
Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
PingHsun Hsieh et al.
Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.
Link
Genome Research Published in Advance February 17, 2016, doi: 10.1101/gr.192971.115
Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
PingHsun Hsieh et al.
African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.
Link
First, it needs to be from highly diverged Palaeoafrican sources so that it will look very different from plain H. sapiens DNA. Unlike Eurasia, there's no genome of an ancient Palaeoafrican one can compare against. All inference is based on African genomes having an improbable amount of heterozygosity in parts of their genome.
Second, it needs to have happened recently enough so that it will come in big chunks that can be distinguished from the plain H. sapiens background. Given enough time, recombination breaks down archaic segments into ever tinier bits. You can argue that an unusually long divergent haplotype with a deep TMRCA is archaic, but you can't argue that a single SNP is.
I have little doubt that most if not all of the supposedly "old divergences" between African populations are a mirage created by admixture between modern humans and archaic "Palaeoafricans" diverging and admixing at different time depths. The palaeoanthropological record is quite clear that modern humans were not the only game in town for most of the 200 thousand years since modern humans first appeared in the continent's northeastern corner.
A handful or two of archaic genomes from Eurasia needs an ever-more-complex web of admixtures to make sense of; Africa will need no less, and -if morphological variability persistence is any criterion- a lot more.
Genome Research Published in Advance February 17, 2016, doi: 10.1101/gr.196634.115
Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
PingHsun Hsieh et al.
Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.
Link
Genome Research Published in Advance February 17, 2016, doi: 10.1101/gr.192971.115
Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
PingHsun Hsieh et al.
African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.
Link
February 17, 2016
Ancestors of Eastern Neandertals admixed with modern humans 100 thousand years ago
If true, this is very hard to reconcile with late (60kya) out of Africa and may be a smoking gun for pre-100kya presence of anatomically modern humans in Eurasia. From the paper:
If the new discovery checks out, it will no longer be possible to assert that the deepest split in our species, H. sapiens, involves African populations. A modest interpretation of these results would assert an earlier (pre-100kya) exodus of our species from Africa, and a more bold one would seek to re-examine the geographical origin of H. sapiens itself. I don't know if anyone is working on getting DNA from the progressive Neandertals of the Near East, but they should.
Things are bound to get more interesting.
Nature (2016) doi:10.1038/nature16544
Ancient gene flow from early modern humans into Eastern Neanderthals
Martin Kuhlwilm, Ilan Gronau, Melissa J. Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernán A. Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Tomas Marques-Bonet, Aida M. Andrés, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel & Sergi Castellano
It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
Link
The inferred demographic model confirms and provides quantitative estimates of previously inferred gene flow events among modern and archaic humans2, 3 (Extended Data Fig. 1). These include Neanderthal gene flow into modern humans outside Africa (3.3–5.8%) and gene flow from an unknown archaic hominin into the ancestors of Denisovans (0.0–0.5%). Interestingly, we also detect a signal of gene flow from modern humans into the ancestors of the Altai Neanderthal (1.0–7.1%). The precise source of this gene flow is unclear, but it appears to come from a population that either split from the ancestors of all present-day Africans or from one of the early African lineages, as significant admixture rates are estimated from San as well as Yoruba individuals. This introgression thus occurred in the opposite direction from the previously reported gene flow from Neanderthals to modern humans outside AfricaAnd:
However, it is clear that the source of the gene flow is a population equally related to present-day Africans and non-Africans (Extended Data Fig. 3). We conclude that the introgressing population diverged from other modern human populations before or shortly after the split between the ancestors of San and other Africans (Fig. 3a), which occurred approximately 200,000 years ago11.The implications of this inference (if correct) for modern human origins are potentially monumental as they suggest a Eurasian modern human lineage (only detected in the Altai Neandertal) that diverges from other modern humans as early (if not earlier) than any two African ones.
If the new discovery checks out, it will no longer be possible to assert that the deepest split in our species, H. sapiens, involves African populations. A modest interpretation of these results would assert an earlier (pre-100kya) exodus of our species from Africa, and a more bold one would seek to re-examine the geographical origin of H. sapiens itself. I don't know if anyone is working on getting DNA from the progressive Neandertals of the Near East, but they should.
Things are bound to get more interesting.
Nature (2016) doi:10.1038/nature16544
Ancient gene flow from early modern humans into Eastern Neanderthals
Martin Kuhlwilm, Ilan Gronau, Melissa J. Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernán A. Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Tomas Marques-Bonet, Aida M. Andrés, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel & Sergi Castellano
It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
Link
February 12, 2016
Phenotypic effects of Neandertal admixture
Now that we know that Neandertal-introgressed DNA had (deleterious) functional consequences for modern humans, I think we also need a study on "useful stuff" conferred by Neandertal admixture. So far, the Neandertal genome has been used (mostly) as our closest relative, in order to identify novel gene variants shared by all modern humans but absent in Neandertals: the goal is to find things that "made us special". Pickings of this search have been slim.
Doubtlessly, as we begin to better understand the genetics underlying positive human traits, some of these will end up having come from archaic humans. Neandertal admixture was a huge injection of "new stuff" into the Eurasian modern human gene pool, and there is every reason to think that even if the "bad stuff" outweighed the "good", there was still plenty of room for functionally beneficial variants to be acquired from them.
Science 12 Feb 2016:
Vol. 351, Issue 6274, pp. 737-741
The phenotypic legacy of admixture between modern humans and Neandertals
Corinne N. Simonti et al.
Many modern human genomes retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence of this admixture on human traits is largely unknown. We analyzed the contribution of common Neandertal variants to over 1000 electronic health record (EHR)–derived phenotypes in ~28,000 adults of European ancestry. We discovered and replicated associations of Neandertal alleles with neurological, psychiatric, immunological, and dermatological phenotypes. Neandertal alleles together explained a significant fraction of the variation in risk for depression and skin lesions resulting from sun exposure (actinic keratosis), and individual Neandertal alleles were significantly associated with specific human phenotypes, including hypercoagulation and tobacco use. Our results establish that archaic admixture influences disease risk in modern humans, provide hypotheses about the effects of hundreds of Neandertal haplotypes, and demonstrate the utility of EHR data in evolutionary analyses.
Link
Doubtlessly, as we begin to better understand the genetics underlying positive human traits, some of these will end up having come from archaic humans. Neandertal admixture was a huge injection of "new stuff" into the Eurasian modern human gene pool, and there is every reason to think that even if the "bad stuff" outweighed the "good", there was still plenty of room for functionally beneficial variants to be acquired from them.
Science 12 Feb 2016:
Vol. 351, Issue 6274, pp. 737-741
The phenotypic legacy of admixture between modern humans and Neandertals
Corinne N. Simonti et al.
Many modern human genomes retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence of this admixture on human traits is largely unknown. We analyzed the contribution of common Neandertal variants to over 1000 electronic health record (EHR)–derived phenotypes in ~28,000 adults of European ancestry. We discovered and replicated associations of Neandertal alleles with neurological, psychiatric, immunological, and dermatological phenotypes. Neandertal alleles together explained a significant fraction of the variation in risk for depression and skin lesions resulting from sun exposure (actinic keratosis), and individual Neandertal alleles were significantly associated with specific human phenotypes, including hypercoagulation and tobacco use. Our results establish that archaic admixture influences disease risk in modern humans, provide hypotheses about the effects of hundreds of Neandertal haplotypes, and demonstrate the utility of EHR data in evolutionary analyses.
Link
February 08, 2016
mtDNA from 55 hunter-gatherers across 35,000 years in Europe
Another justification for the "Asia-first" model was the presence of Y-haplogroup C in Australians and Asians. But, that too was found in UP Europeans (K14).
So, I think things are looking good for my theory that Eurasians came out of Arabia northwards, interbred with Neandertals, headed both west and east, populating both Europe and Asia. The inferred date for both M and N (55kya) is on the cusp of the 50kya technological transition.
The authors also propose a major turnover in Europe at 14.5kya that replaced (not necessarily completely) the previous occupants. The authors write:
In European hunter-gatherers, our model best explains this period of upheaval as a replacement of the post-LGM maternal population by one from another source. Although the exact origin for this later population is unknown, the inferred demographic history (Figure 3 and 2b in Figure S2) suggests that it descended from another, separate LGM refugium.Where was this LGM refugium?
Exactly where this new population came from is still unclear, but it seems likely that they came from warmer areas further south. “The main hypothesis would be glacial refugia in south-eastern Europe,” says Johannes Krause at the Max Planck Institute for the Science of Human History in Jena, Germany, who led the analysis.
Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2016.01.037
Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe
Cosimo Posth et al.
How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [ 1, 2 ]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [ 3–5 ]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [ 6–9 ]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [ 3–5, 8, 9 ]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.
Link
February 02, 2016
Admixture within and into Africa
bioRxiv, http://dx.doi.org/10.1101/038406
Admixture into and within sub-Saharan Africa
George Busby, Gavin Band, Quang Si Le, Muminatou Jallow, Edith Bougama, Valentina Mangano, Lucas Amenga-Etego, Anthony Emil, Tobias Apinjoh, Carolyne Ndila, Alphaxard Manjurano, Vysaul Nyirongo, Ogobara Doumbo, Kirk Rockett, Domnic Kwiatkowski, Chris Spencer, The Malaria Genomic Epidemiology Network
Understanding patterns of genetic diversity is a crucial component of medical research in Africa. Here we use haplotype-based population genetics inference to describe gene-flow and admixture in a collection of 48 African groups with a focus on the major populations of the sub-Sahara. Our analysis presents a framework for interpreting haplotype diversity within and between population groups and provides a demographic foundation for genetic epidemiology in Africa. We show that coastal African populations have experienced an influx of Eurasian haplotypes as a series of admixture events over the last 7,000 years, and that Niger-Congo speaking groups from East and Southern Africa share ancestry with Central West Africans as a result of recent population expansions associated with the adoption of new agricultural technologies. We demonstrate that most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of large-scale population movements over the last 4,000 years. Our in-depth analysis of admixture provides an insight into haplotype sharing across different geographic groups and the recent movement of alleles into new climatic and pathogenic environments, both of which will aid the interpretation of genetic studies of disease in sub-Saharan Africa.
Link
Admixture into and within sub-Saharan Africa
George Busby, Gavin Band, Quang Si Le, Muminatou Jallow, Edith Bougama, Valentina Mangano, Lucas Amenga-Etego, Anthony Emil, Tobias Apinjoh, Carolyne Ndila, Alphaxard Manjurano, Vysaul Nyirongo, Ogobara Doumbo, Kirk Rockett, Domnic Kwiatkowski, Chris Spencer, The Malaria Genomic Epidemiology Network
Understanding patterns of genetic diversity is a crucial component of medical research in Africa. Here we use haplotype-based population genetics inference to describe gene-flow and admixture in a collection of 48 African groups with a focus on the major populations of the sub-Sahara. Our analysis presents a framework for interpreting haplotype diversity within and between population groups and provides a demographic foundation for genetic epidemiology in Africa. We show that coastal African populations have experienced an influx of Eurasian haplotypes as a series of admixture events over the last 7,000 years, and that Niger-Congo speaking groups from East and Southern Africa share ancestry with Central West Africans as a result of recent population expansions associated with the adoption of new agricultural technologies. We demonstrate that most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of large-scale population movements over the last 4,000 years. Our in-depth analysis of admixture provides an insight into haplotype sharing across different geographic groups and the recent movement of alleles into new climatic and pathogenic environments, both of which will aid the interpretation of genetic studies of disease in sub-Saharan Africa.
Link
January 26, 2016
History of extant populations of India
The differentiation of the four main components seems clear enough on the figure (left). The big question is how and in what order the different components got into India. I would wager that ASI was first and I modify my New Year's wish to ask for some ancient DNA from India too.
An interesting bit from the paper:
...that the practice of endogamy was established almost simultaneously, possibly by decree of the rulers, in upper-caste populations of all geographical regions, about 70 generations before present, probably during the reign (319–550 CE) of the ardent Hindu Gupta rulersHow plausible is that to anyone familiar with Indian history?
PNAS doi: 10.1073/pnas.1513197113
Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure
Analabha Basu, Neeta Sarkar-Roya, and Partha P. Majumder
India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform.
Link
January 16, 2016
Humans in the central Siberian Arctic ~45,000 years ago
The lack of such northerly sites prior to 45,000 years ago makes it quite likely that this mammoth kill was made by modern humans (it would be quite a coincidence if it was made by Neandertals at the same time as the expansionary Homo sapiens make their appearance all over the rest of Eurasia). If this is right, it's quite remarkable that by the mid to late 40,000s, modern humans were at ease from the equator to the arctic and from Europe to the remotest parts of Asia.
Science 15 Jan 2016:
Vol. 351, Issue 6270, pp. 260-263
Early human presence in the Arctic: Evidence from 45,000-year-old mammoth remains
Vladimir V. Pitulko, Alexei N. Tikhonov et al.
Archaeological evidence for human dispersal through northern Eurasia before 40,000 years ago is rare. In west Siberia, the northernmost find of that age is located at 57°N. Elsewhere, the earliest presence of humans in the Arctic is commonly thought to be circa 35,000 to 30,000 years before the present. A mammoth kill site in the central Siberian Arctic, dated to 45,000 years before the present, expands the populated area to almost 72°N. The advancement of mammoth hunting probably allowed people to survive and spread widely across northernmost Arctic Siberia.
Link
Science 15 Jan 2016:
Vol. 351, Issue 6270, pp. 260-263
Early human presence in the Arctic: Evidence from 45,000-year-old mammoth remains
Vladimir V. Pitulko, Alexei N. Tikhonov et al.
Archaeological evidence for human dispersal through northern Eurasia before 40,000 years ago is rare. In west Siberia, the northernmost find of that age is located at 57°N. Elsewhere, the earliest presence of humans in the Arctic is commonly thought to be circa 35,000 to 30,000 years before the present. A mammoth kill site in the central Siberian Arctic, dated to 45,000 years before the present, expands the populated area to almost 72°N. The advancement of mammoth hunting probably allowed people to survive and spread widely across northernmost Arctic Siberia.
Link
January 08, 2016
Helicobacter pylori in the Iceman
Science 8 January 2016:
Vol. 351 no. 6269 pp. 162-165
The 5300-year-old Helicobacter pylori genome of the Iceman
Frank Maixner1,*,†, Ben Krause-Kyora2,†, Dmitrij Turaev3,†, Alexander Herbig4,5, et al.
The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The “Iceman” H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.
Link
Vol. 351 no. 6269 pp. 162-165
The 5300-year-old Helicobacter pylori genome of the Iceman
Frank Maixner1,*,†, Ben Krause-Kyora2,†, Dmitrij Turaev3,†, Alexander Herbig4,5, et al.
The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The “Iceman” H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.
Link
January 06, 2016
Even more Anatolian Neolithic genomes
Recently I proclaimed the problem of "Neolithization of Europe" to be "done", but it doesn't hurt to have more confirmation as this new paper does. The Anatolian data is from a different site than those used by Mathieson et al. and Hofmanová, Kreutzer et al. albeit still in the extreme northwest of Asia Minor. Nonetheless, the individual from Kumtepe doesn't seem to carry any major surprises, so "Neolithization of Europe" remains "done".
Current Biology http://dx.doi.org/10.1016/j.cub.2015.12.019
Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool
Ayça Omrak et al.
Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [ 1–5 ]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [ 6–9 ]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [ 10 ]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia’s central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.
Link
Current Biology http://dx.doi.org/10.1016/j.cub.2015.12.019
Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool
Ayça Omrak et al.
Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [ 1–5 ]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [ 6–9 ]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [ 10 ]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia’s central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.
Link
January 01, 2016
Happy New Year 2016
Last year I wished for ancient African DNA and I got my wish.
This year I wish for some ancient East Asian DNA. It's quite an embarrassment that hundreds of ancient European genomes have been published, but only a single Chromosome 21 from East Asia.
This year I wish for some ancient East Asian DNA. It's quite an embarrassment that hundreds of ancient European genomes have been published, but only a single Chromosome 21 from East Asia.
December 29, 2015
Bronze Age people from Ireland had steppe ancestry and R1b
We were able to deduce that Neolithic Ballynahatty had a dark hair shade (99.5% probability), most likely black (86.1% probability), and brown eyes (97.3% probability) (46). Bronze Age Rathlin1 probably had a light hair shade (61.4%) and brown eyes (64.3%). However, each Rathlin genome possessed indication of at least one copy of a haplotype associated with blue eye color in the HERC2/OCA2 region.and:
Third, we followed the methods described in Haak et al. (9), which use a collection of outgroup populations, to estimate the mixture proportions of three different sources, Linearbandkeramik (Early Neolithic; 35 ± 6%), Loschbour (WHG; 26 ± 12%), and Yamnaya (39 ± 8%), in the total Irish Bronze Age group. These three approaches give an overlapping estimate of ∼32% Yamnaya ancestry.PNAS doi: 10.1073/pnas.1518445113
Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome
Lara M. Cassidy, Rui Martiniano et al.
The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.
Link
December 25, 2015
December 22, 2015
Refining Y-chromosome phylogeny with South African sequences
bioRxiv http://dx.doi.org/10.1101/034983
Refining the Y chromosome phylogeny with southern African sequences
Chiara Barbieri, Alexander Hübner, Enrico Macholdt, Shengyu Ni, Sebastian Lippold, Roland Schröder, Sununguko Wata Mpoloka, Josephine Purps, Lutz Roewer, Mark Stoneking, Brigitte Pakendorf
The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We find new branches within haplogroups A2 and A3b1 and suggest that the prehistory of haplogroup B2a is more complex than previously suspected; this haplogroup is likely to have existed in Khoisan groups before the arrival of Bantu-speakers, who brought additional B2a lineages to southern Africa. Furthermore, we estimate older dates than obtained previously for both the A2-T node within the human Y chromosome phylogeny and for some individual haplogroups. Finally, there is pronounced variation in branch length between major haplogroups; haplogroups associated with Bantu-speakers have significantly longer branches. This likely reflects a combination of biases in the SNP calling process and demographic factors, such as an older average paternal age (hence a higher mutation rate), a higher effective population size, and/or a stronger effect of population expansion for Bantu-speakers than for Khoisan groups.
Link
Refining the Y chromosome phylogeny with southern African sequences
Chiara Barbieri, Alexander Hübner, Enrico Macholdt, Shengyu Ni, Sebastian Lippold, Roland Schröder, Sununguko Wata Mpoloka, Josephine Purps, Lutz Roewer, Mark Stoneking, Brigitte Pakendorf
The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We find new branches within haplogroups A2 and A3b1 and suggest that the prehistory of haplogroup B2a is more complex than previously suspected; this haplogroup is likely to have existed in Khoisan groups before the arrival of Bantu-speakers, who brought additional B2a lineages to southern Africa. Furthermore, we estimate older dates than obtained previously for both the A2-T node within the human Y chromosome phylogeny and for some individual haplogroups. Finally, there is pronounced variation in branch length between major haplogroups; haplogroups associated with Bantu-speakers have significantly longer branches. This likely reflects a combination of biases in the SNP calling process and demographic factors, such as an older average paternal age (hence a higher mutation rate), a higher effective population size, and/or a stronger effect of population expansion for Bantu-speakers than for Khoisan groups.
Link
December 18, 2015
Archaic femur from Maludong, China
PLoS ONE 10(12): e0143332. doi:10.1371/journal.pone.0143332
A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China
Darren Curnoe et al.
The number of Late Pleistocene hominin species and the timing of their extinction are issues receiving renewed attention following genomic evidence for interbreeding between the ancestors of some living humans and archaic taxa. Yet, major gaps in the fossil record and uncertainties surrounding the age of key fossils have meant that these questions remain poorly understood. Here we describe and compare a highly unusual femur from Late Pleistocene sediments at Maludong (Yunnan), Southwest China, recovered along with cranial remains that exhibit a mixture of anatomically modern human and archaic traits. Our studies show that the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora. However, the scarcity of later Middle and Late Pleistocene archaic remains in East Asia makes an assessment of systematically relevant character states difficult, warranting caution in assigning the specimen to a species at this time. The Maludong fossil probably samples an archaic population that survived until around 14,000 years ago in the biogeographically complex region of Southwest China.
Link
A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China
Darren Curnoe et al.
The number of Late Pleistocene hominin species and the timing of their extinction are issues receiving renewed attention following genomic evidence for interbreeding between the ancestors of some living humans and archaic taxa. Yet, major gaps in the fossil record and uncertainties surrounding the age of key fossils have meant that these questions remain poorly understood. Here we describe and compare a highly unusual femur from Late Pleistocene sediments at Maludong (Yunnan), Southwest China, recovered along with cranial remains that exhibit a mixture of anatomically modern human and archaic traits. Our studies show that the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora. However, the scarcity of later Middle and Late Pleistocene archaic remains in East Asia makes an assessment of systematically relevant character states difficult, warranting caution in assigning the specimen to a species at this time. The Maludong fossil probably samples an archaic population that survived until around 14,000 years ago in the biogeographically complex region of Southwest China.
Link
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