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.
January 01, 2016
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
November 26, 2015
Neolithic farmers from Greece and Anatolia
A couple of new papers appeared this week. First, an article in Nature on natural selection in ancient Europe includes a sample of Anatolian Neolithic farmers and concludes that the European Neolithic farmers were descended from them with a bit of extra European hunter-gatherer admixture. Second, a new preprint on the bioRxiv includes Neolithic samples from northern Greece and finds that they too resemble the Anatolian and European farmers. I think it is time to declare the problem of "Neolithization of Europe" done. It took less than 4 years to solve it with ancient DNA. Here is a (non-exhaustive) list of papers in historical review:
Nature (2015) doi:10.1038/nature16152
Genome-wide patterns of selection in 230 ancient Eurasians
Iain Mathieson et al.
Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 BC, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe’s first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 BC, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.
Link
bioRxiv http://dx.doi.org/10.1101/032763
Early farmers from across Europe directly descended from Neolithic Aegeans
Zuzana Hofmanová, Susanne Kreutzer et al.
Farming and sedentism first appear in southwest Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion and admixture with local foragers in the early Neolithisation of Europe. Here we present paleogenomic data for five Neolithic individuals from northwestern Turkey and northern Greece, spanning the time and region of the earliest spread of farming into Europe. We observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.
Link
- Keller et al. (2012): Iceman (5kya) looks Sardinian! Was this a fluke?
- Skoglund et al. (2012): No, because... Swedish farmer (5kya) looked Sardinian too! When did these "Sardinians" come to Europe?
- Lazaridis et al. (2014): No later than an LBK farmer from Germany (7kya) but what about western Europe?
- Haak, Lazaridis et al. (2015): Spanish early farmers from northern Spain looked Sardinian too
- Olalde, Schroeder et al. (2015): Ditto for Mediterranean Spain! So where did they all come from?
- Mathieson et al. (2015): Anatolia!
- Hofmanová, Kreutzer et al. (2015): via Greece!
Genome-wide patterns of selection in 230 ancient Eurasians
Iain Mathieson et al.
Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 BC, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe’s first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 BC, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.
Link
Early farmers from across Europe directly descended from Neolithic Aegeans
Zuzana Hofmanová, Susanne Kreutzer et al.
Farming and sedentism first appear in southwest Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion and admixture with local foragers in the early Neolithisation of Europe. Here we present paleogenomic data for five Neolithic individuals from northwestern Turkey and northern Greece, spanning the time and region of the earliest spread of farming into Europe. We observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.
Link
November 18, 2015
Two more Denisovans (Sawyer, Renaud et al. 2015)
PNAS doi: 10.1073/pnas.1519905112
Nuclear and mitochondrial DNA sequences from two Denisovan individuals
Susanna Sawyer, Gabriel Renaud et al.
Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.
Link
Nuclear and mitochondrial DNA sequences from two Denisovan individuals
Susanna Sawyer, Gabriel Renaud et al.
Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.
Link
November 16, 2015
West_Asian in the flesh (hunter-gatherers from Georgia) (Jones et al. 2015)
Earlier this year, the study by Haak et al. showed that steppe invaders after 5kya brought into Europe a 50/50 mix of "Eastern European Hunter-Gatherer" (EHG) ancestry/An unknown population from the Near East/Caucasus. The "unknown population" was most similar to Caucasians/Near Easterners like Armenians but did not correspond to any ancient sample.
A new paper in Nature Communications by Jones et al. finds this "missing link" in the flesh in Upper Paleolithic/Mesolithic hunter-gatherers from Georgia which they call "Caucasus Hunter-Gatherers" (CHG). From the paper:
The separation between CHG and both EF and WHG ended during the Early Bronze Age when a major ancestral component linked to CHG was carried west by migrating herders from the Eurasian Steppe. The foundation group for this seismic change was the Yamnaya, who we estimate to owe half of their ancestry to CHG-linked sources.The authors also make the connection to South Asia:
In modern populations, the impact of CHG also stretches beyond Europe to the east. Central and South Asian populations received genetic influx from CHG (or a population close to them), as shown by a prominent CHG component in ADMIXTURE (Supplementary Fig. 5; Supplementary Note 9) and admixture f3-statistics, which show many samples as a mix of CHG and another South Asian population (Fig. 4b; Supplementary Table 9).Also of interest:
Both Georgian hunter-gatherer samples were assigned to haplogroup J with Kotias belonging to the subhaplogroup J2a (see methods).The paper is open access, so go ahead and read it for other details.
Nature Communications 6, Article number: 8912 doi:10.1038/ncomms9912
Upper Palaeolithic genomes reveal deep roots of modern Eurasians
Eppie R. Jones et al.
We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.
Link
November 11, 2015
Genetic structure of 1,272 Italians
The distribution of the pairwise Fst distances between all population pairs is shown in Supplementary Table S3. The genetic distance between Southern and Northern Italians (Fst=0.0013) is comparable to that between individuals living in different political units (ie, Iberians-Romanians Fst=0.0011; British-French Fst=0.0007), and, interestingly, in >50% of all the possible pairwise comparisons within Europe (Supplementary Figure S7).European Journal of Human Genetics advance online publication 11 November 2015; doi: 10.1038/ejhg.2015.233
The Italian genome reflects the history of Europe and the Mediterranean basin
Giovanni Fiorito et al.
Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population’s ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., ‘barbarian invasion’ of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe.
Link
November 04, 2015
Selection against Neandertal deleterious alleles
Sampled Neandertals (from Europe, the Caucasus, and Siberia) certainly had lower effective population size than living humans, but I wonder what the comparison would be between ancient tribes of modern humans and Neandertals in the Near East where admixture presumably took place.
doi: http://dx.doi.org/10.1101/030387
The Genetic Cost of Neanderthal Introgression
Kelley Harris, Rasmus Nielsen
Approximately 2-4% of the human genome is in non-Africans comprised of DNA intro- gressed from Neanderthals. Recent studies have shown that there is a paucity of introgressed DNA around functional regions, presumably caused by selection after introgression. This observation has been suggested to be a possible consequence of the accumulation of a large amount of Dobzhansky-Muller incompatibilities, i.e. epistatic effects between human and Neanderthal specific mutations, since the divergence of humans and Neanderthals approx. 400-600 kya. However, using previously published estimates of inbreeding in Neanderthals, and of the distribution of fitness effects from human protein coding genes, we show that the average Neanderthal would have had at least 40% lower fitness than the average human due to higher levels of inbreeding and an increased mutational load, regardless of the dominance coefficients of new mutations. Using simulations, we show that under the assumption of additive dominance effects, early Neanderthal/human hybrids would have experienced strong negative selection, though not so strong that it would prevent Neanderthal DNA from entering the human population. In fact, the increased mutational load in Neanderthals predicts the observed reduction in Neanderthal introgressed segments around protein coding genes, without any need to invoke epistasis. The simulations also predict that there is a residual Neanderthal derived mutational load in non-African humans, leading to an average fitness reduction of at least 0.5%. Although there has been much previous debate about the effects of the out-of-Africa bottleneck on mutational loads in non-Africans, the significant deleterious effects of Neanderthal introgression have hitherto been left out of this discussion, but might be just as important for understanding fitness differences among human populations. We also show that if deleterious mutations are recessive, the Neanderthal admixture fraction would gradually increase over time due to selection for Neanderthal haplotypes that mask human deleterious mutations in the heterozygous state. This effect of dominance heterosis might partially explain why adaptive introgression appears to be widespread in nature.
Link
doi: http://dx.doi.org/10.1101/030148
The Strength of Selection Against Neanderthal Introgression
Ivan Juric, Simon Aeschbacher, Graham Coop
Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that there are systematically lower levels of initial introgression on the X chromosome, a finding consistent with a strong sex bias in the initial matings between the populations. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.
Link
doi: http://dx.doi.org/10.1101/030387
The Genetic Cost of Neanderthal Introgression
Kelley Harris, Rasmus Nielsen
Approximately 2-4% of the human genome is in non-Africans comprised of DNA intro- gressed from Neanderthals. Recent studies have shown that there is a paucity of introgressed DNA around functional regions, presumably caused by selection after introgression. This observation has been suggested to be a possible consequence of the accumulation of a large amount of Dobzhansky-Muller incompatibilities, i.e. epistatic effects between human and Neanderthal specific mutations, since the divergence of humans and Neanderthals approx. 400-600 kya. However, using previously published estimates of inbreeding in Neanderthals, and of the distribution of fitness effects from human protein coding genes, we show that the average Neanderthal would have had at least 40% lower fitness than the average human due to higher levels of inbreeding and an increased mutational load, regardless of the dominance coefficients of new mutations. Using simulations, we show that under the assumption of additive dominance effects, early Neanderthal/human hybrids would have experienced strong negative selection, though not so strong that it would prevent Neanderthal DNA from entering the human population. In fact, the increased mutational load in Neanderthals predicts the observed reduction in Neanderthal introgressed segments around protein coding genes, without any need to invoke epistasis. The simulations also predict that there is a residual Neanderthal derived mutational load in non-African humans, leading to an average fitness reduction of at least 0.5%. Although there has been much previous debate about the effects of the out-of-Africa bottleneck on mutational loads in non-Africans, the significant deleterious effects of Neanderthal introgression have hitherto been left out of this discussion, but might be just as important for understanding fitness differences among human populations. We also show that if deleterious mutations are recessive, the Neanderthal admixture fraction would gradually increase over time due to selection for Neanderthal haplotypes that mask human deleterious mutations in the heterozygous state. This effect of dominance heterosis might partially explain why adaptive introgression appears to be widespread in nature.
Link
doi: http://dx.doi.org/10.1101/030148
The Strength of Selection Against Neanderthal Introgression
Ivan Juric, Simon Aeschbacher, Graham Coop
Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that there are systematically lower levels of initial introgression on the X chromosome, a finding consistent with a strong sex bias in the initial matings between the populations. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.
Link
October 28, 2015
October 22, 2015
Bronze Age Plague
The result: 2,800-5,000 year old Yersinia pestis from Europe to the Altai. It will be cool to look at even older remains than the Bronze Age, but this already pushes the date for plague by a couple thousand years, and implicates steppe people in its earliest spread.
Cell Volume 163, Issue 3, p571–582, 22 October 2015
Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
Simon Rasmussen18, Morten Erik Allentoft18, Kasper Nielsen, Ludovic Orlando, Martin Sikora, Karl-Göran Sjögren, Anders Gorm Pedersen, Mikkel Schubert, Alex Van Dam, Christian Moliin Outzen Kapel, Henrik Bjørn Nielsen, Søren Brunak, Pavel Avetisyan, Andrey Epimakhov, Mikhail Viktorovich Khalyapin, Artak Gnuni, Aivar Kriiska, Irena Lasak, Mait Metspalu, Vyacheslav Moiseyev, Andrei Gromov, Dalia Pokutta, Lehti Saag, Liivi Varul, Levon Yepiskoposyan, Thomas Sicheritz-Pontén, Robert A. Foley, Marta Mirazón Lahr, Rasmus Nielsen, Kristian Kristiansen, Eske Willerslev
The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.
Link
October 15, 2015
Modern humans in China ~80,000 years ago (?)
Another (?)-worthy paper has just appeared in Nature in the heels of the African ancient genome paper. Time will tell how these worldview-altering discoveries will change the story of Mankind, and a degree of skepticism is warranted. In the view I've held for a few years, modern humans expanded to Arabia before 100 thousand years ago, started leaving it 70 thousand years ago as the ecological situation worsened due to desertification and broke through the "Neandertal barrier" between 70-50 thousand years ago when they developed the skills and technology to overcome them.
The new paper claims that modern humans were in China 80 thousand years ago and came to Europe much later because Neandertal represented a barrier to successful entry to Europe. This begs the question of how they reached China without encountering Neandertals, as Neandertals were also in West Asia where -presumably- they passed through to get to China. A coastal route to south China would explain away this problem, but the coastal migration is usually envisioned much later, at around 60 thousand years ago. On top of that, how did Chinese end up having equal (or more) levels of Neandertals admixture if modern humans first went to China and later moved west and successfully outcompeted the Neandertals. How were they able to do so eventually? (There is no evidence that the kind of advantages associated with behavioral modernity first emerged in East Asia). It's possible that there were 80 thousand year-old modern humans in China (just as there were 100 thousand year-old modern humans in Israel), but that the later East Asians are not descended from them.
One would think that science would present an increasingly reasonable and consistent picture of the past, but it seems that we're a very long way from the point where the dust settles and the puzzle pieces start falling into place.
Nature (2015) doi:10.1038/nature15696
The earliest unequivocally modern humans in southern China
Wu Liu, María Martinón-Torres, Yan-jun Cai, Song Xing, Hao-wen Tong, Shu-wen Pei, Mark Jan Sier, Xiao-hong Wu, R. Lawrence Edwards, Hai Cheng, Yi-yuan Li, Xiong-xin Yang, José María Bermúdez de Castro & Xiu-jie Wu
The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ~45,000 years that can be unequivocally attributed to Homo sapiens are lacking1, 2, 3, 4. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000–70,000 years earlier than in the Levant and Europe5, 6, 7. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals’ extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ~80,000 years ago, there is no evidence that they entered Europe before ~45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started.
Link
The new paper claims that modern humans were in China 80 thousand years ago and came to Europe much later because Neandertal represented a barrier to successful entry to Europe. This begs the question of how they reached China without encountering Neandertals, as Neandertals were also in West Asia where -presumably- they passed through to get to China. A coastal route to south China would explain away this problem, but the coastal migration is usually envisioned much later, at around 60 thousand years ago. On top of that, how did Chinese end up having equal (or more) levels of Neandertals admixture if modern humans first went to China and later moved west and successfully outcompeted the Neandertals. How were they able to do so eventually? (There is no evidence that the kind of advantages associated with behavioral modernity first emerged in East Asia). It's possible that there were 80 thousand year-old modern humans in China (just as there were 100 thousand year-old modern humans in Israel), but that the later East Asians are not descended from them.
One would think that science would present an increasingly reasonable and consistent picture of the past, but it seems that we're a very long way from the point where the dust settles and the puzzle pieces start falling into place.
Nature (2015) doi:10.1038/nature15696
The earliest unequivocally modern humans in southern China
Wu Liu, María Martinón-Torres, Yan-jun Cai, Song Xing, Hao-wen Tong, Shu-wen Pei, Mark Jan Sier, Xiao-hong Wu, R. Lawrence Edwards, Hai Cheng, Yi-yuan Li, Xiong-xin Yang, José María Bermúdez de Castro & Xiu-jie Wu
The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ~45,000 years that can be unequivocally attributed to Homo sapiens are lacking1, 2, 3, 4. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000–70,000 years earlier than in the Levant and Europe5, 6, 7. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals’ extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ~80,000 years ago, there is no evidence that they entered Europe before ~45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started.
Link
October 08, 2015
West Eurasian admixture throughout Africa (?)
In 2012, I wrote:
UPDATE (1/26/2016). An erratum has now appeared that rejects the claim for Eurasian admixture in all Africans which was the result of the bioinformatic error. I continue to think that there was Eurasian back-migration into Africa, but it was a long shot that this had happened in the last 4,500 years (hence the ? in the title of this entry). A time series of African DNA may show whether the null model of Sub-Saharan Africans receiving virtually no admixture from Eurasia for the entirety of the existence of H. sapiens can remain valid.
Science DOI: 10.1126/science.aad2879
Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent
M. Gallego Llorente et al
Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.
Link
It is no longer tenable to view West Eurasian back-migrations as limited events that affected only North and East Africa: their effects are clearly evident throughout Africa, having affected different populations to a different extent.A new paper in Science seems to confirm West Eurasian admixture related to Early Neolithic farmers throughout Africa, including the Yoruba, and Mbuti. I haven't read the paper yet, but it would be a striking discovery if confirmed.
UPDATE (1/26/2016). An erratum has now appeared that rejects the claim for Eurasian admixture in all Africans which was the result of the bioinformatic error. I continue to think that there was Eurasian back-migration into Africa, but it was a long shot that this had happened in the last 4,500 years (hence the ? in the title of this entry). A time series of African DNA may show whether the null model of Sub-Saharan Africans receiving virtually no admixture from Eurasia for the entirety of the existence of H. sapiens can remain valid.
Science DOI: 10.1126/science.aad2879
Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent
M. Gallego Llorente et al
Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.
Link
September 19, 2015
Recent admixture in contemporary West Eurasians
After applying Globetrotter to the world and to the British, a new study in Current Biology applies to the intermediately-sized region of West Eurasia. This is an open-access article, so go ahead and read it.
Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2015.08.007
The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape
George B.J. Busby et al.
Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [ 1–7 ]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [ 8–11 ]. Here, using recently described haplotype-based techniques [ 11 ], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia.
Link
September 18, 2015
Political (non) diversity in social psychology
Behavioral and Brain Sciences / Volume 38 / January 2015, e130 (13 pages)
Political diversity will improve social psychological science
José L. Duartea1, Jarret T. Crawforda2, Charlotta Sterna3, Jonathan Haidta4, Lee Jussima5 and Philip E. Tetlocka6
Psychologists have demonstrated the value of diversity – particularly diversity of viewpoints – for enhancing creativity, discovery, and problem solving. But one key type of viewpoint diversity is lacking in academic psychology in general and social psychology in particular: political diversity. This article reviews the available evidence and finds support for four claims: (1) Academic psychology once had considerable political diversity, but has lost nearly all of it in the last 50 years. (2) This lack of political diversity can undermine the validity of social psychological science via mechanisms such as the embedding of liberal values into research questions and methods, steering researchers away from important but politically unpalatable research topics, and producing conclusions that mischaracterize liberals and conservatives alike. (3) Increased political diversity would improve social psychological science by reducing the impact of bias mechanisms such as confirmation bias, and by empowering dissenting minorities to improve the quality of the majority's thinking. (4) The underrepresentation of non-liberals in social psychology is most likely due to a combination of self-selection, hostile climate, and discrimination. We close with recommendations for increasing political diversity in social psychology.
Link
Political diversity will improve social psychological science
José L. Duartea1, Jarret T. Crawforda2, Charlotta Sterna3, Jonathan Haidta4, Lee Jussima5 and Philip E. Tetlocka6
Psychologists have demonstrated the value of diversity – particularly diversity of viewpoints – for enhancing creativity, discovery, and problem solving. But one key type of viewpoint diversity is lacking in academic psychology in general and social psychology in particular: political diversity. This article reviews the available evidence and finds support for four claims: (1) Academic psychology once had considerable political diversity, but has lost nearly all of it in the last 50 years. (2) This lack of political diversity can undermine the validity of social psychological science via mechanisms such as the embedding of liberal values into research questions and methods, steering researchers away from important but politically unpalatable research topics, and producing conclusions that mischaracterize liberals and conservatives alike. (3) Increased political diversity would improve social psychological science by reducing the impact of bias mechanisms such as confirmation bias, and by empowering dissenting minorities to improve the quality of the majority's thinking. (4) The underrepresentation of non-liberals in social psychology is most likely due to a combination of self-selection, hostile climate, and discrimination. We close with recommendations for increasing political diversity in social psychology.
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