PNAS DOI: doi: 10.1073/pnas.1523158113
A high-precision chronological model for the decorated Upper Paleolithic cave of Chauvet-Pont d’Arc, Ardèche, France
Anita Quiles et al.
Radiocarbon dates for the ancient drawings in the Chauvet-Pont d’Arc Cave revealed ages much older than expected. These early ages and nature of this Paleolithic art make this United Nations Educational, Scientific and Cultural Organization (UNESCO) site indisputably unique. A large, multidisciplinary dating program has recently mapped the anthropological evolution associated with the cave. More than 350 dates (by 14C, U-Th, TL and 36Cl) were obtained over the last 15 y. They include 259 radiocarbon dates, mainly related to the rock art and human activity in the cave. We present here more than 80 previously unpublished dates. All of the dates were integrated into a high-precision Bayesian model based on archaeological evidence to securely reconstruct the complete history of the Chauvet-Pont d’Arc Cave on an absolute timescale. It shows that there were two distinct periods of human activity in the cave, one from 37 to 33,500 y ago, and the other from 31 to 28,000 y ago. Cave bears also took refuge in the cave until 33,000 y ago.
Link
April 14, 2016
April 10, 2016
Nubian assemblages from the Negev
Nubian assemblages from the Levant are quite important because they provide an intermediate link (along land routes) between those from Africa and Arabia. It's also more difficult now to consider the Arabian finds as a limited event without broader implications about modern human dispersals.
From the paper:
“Diffusion with modifications”: Nubian assemblages in the central Negev highlands of Israel and their implications for Middle Paleolithic inter-regional interactions
Mae Goder-Goldberger, Natalia Gubenko, Erella Hovers
Nubian Levallois cores, now known from sites in eastern Africa, the Nile Valley and Arabia, have been used as a material culture marker for Upper Pleistocene dispersals of hominins out of Africa. The Levantine corridor, being the only land route connecting Africa to Eurasia, has been viewed as a possible dispersal route. We report here on lithic assemblages from the Negev highlands of Israel that contain both Levallois centripetal and Nubian-type cores. Wetter conditions over the Sahara and Negev deserts during MIS 6a–5e provided a generally continuous environmental corridor into the Levant that enabled the dispersal of hominin groups bearing the Nubian variant of prepared core technologies. The Negev assemblages draw renewed attention to the place of the Levant as one of the dispersal routes out of Africa during the Late Pleistocene and could suggest that processes of human dispersals and cultural diffusion resulted in the spread of Nubian technology across eastern Africa, the western Sahara and the Nile Valley, the southern Levant and Arabia.
Link
Mapping the earliest dated sites that contain a Nubian component does not permit an unequivocal identification of a region of origin for the Nubian Technology.Quaternary International doi:10.1016/j.quaint.2016.02.008
“Diffusion with modifications”: Nubian assemblages in the central Negev highlands of Israel and their implications for Middle Paleolithic inter-regional interactions
Mae Goder-Goldberger, Natalia Gubenko, Erella Hovers
Nubian Levallois cores, now known from sites in eastern Africa, the Nile Valley and Arabia, have been used as a material culture marker for Upper Pleistocene dispersals of hominins out of Africa. The Levantine corridor, being the only land route connecting Africa to Eurasia, has been viewed as a possible dispersal route. We report here on lithic assemblages from the Negev highlands of Israel that contain both Levallois centripetal and Nubian-type cores. Wetter conditions over the Sahara and Negev deserts during MIS 6a–5e provided a generally continuous environmental corridor into the Levant that enabled the dispersal of hominin groups bearing the Nubian variant of prepared core technologies. The Negev assemblages draw renewed attention to the place of the Levant as one of the dispersal routes out of Africa during the Late Pleistocene and could suggest that processes of human dispersals and cultural diffusion resulted in the spread of Nubian technology across eastern Africa, the western Sahara and the Nile Valley, the southern Levant and Arabia.
Link
April 07, 2016
Neandertal Y-chromosome (finally)
It's been six years since the publication of the draft Neandertal genome, and one piece of the puzzle that's always been missing is the Neandertal Y-chromosome (unfortunately most of the Neandertals yielding data were female). But, the wait is finally over, with the first publication of Neandertal Y-chromosome data.
AJHG Volume 98, Issue 4, p728–734, 7 April 2016
The Divergence of Neandertal and Modern Human Y Chromosomes
Fernando L. Mendez, G. David Poznik, Sergi Castellano, Carlos D. Bustamante
Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.
Link
AJHG Volume 98, Issue 4, p728–734, 7 April 2016
The Divergence of Neandertal and Modern Human Y Chromosomes
Fernando L. Mendez, G. David Poznik, Sergi Castellano, Carlos D. Bustamante
Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.
Link
April 01, 2016
Zhiren cave human remains: 116-106 ka old
Quaternary International doi:10.1016/j.quaint.2015.12.088
The age of human remains and associated fauna from Zhiren Cave in Guangxi, southern China
Yanjun Cai et al.
Zhiren Cave in southern China is an important site for the study of the origin and the environmental background of early modern humans. The combination of Elephas kiangnanensis, Elephas maximus, and Megatapirus augustus, indicates an early representative of the typical Asian elephant fauna. Previous U-series dating of flowstone calcite has pinpointed an upper age limit for the fossils of about 100 ka. In order to achieve a better comprehension of the chronology of the modern human and contemporaneous faunal assemblage, paleomagnetic, stratigraphic, and optically stimulated luminescence (OSL) dating methods have been applied to the cave sediments. Paleomagnetic analyses reveal that there is a reversed polarity excursion below the fossiliferous layer. This excursion can be regarded as the Blake excursion event, given the U-series ages of the overlying flowstone calcite, the OSL measurements, the virtual geomagnetic pole (VGP) path of the excursion, the two reverse polarity zones within this excursion event, and the characteristic of the fauna assemblage. The human remains and mammalian fauna assemblage can be bracketed to 116–106 ka. Application of OSL dating leads to erroneous ages, largely due to the uncertainty associated with the estimation on the dose rates.
Link
The age of human remains and associated fauna from Zhiren Cave in Guangxi, southern China
Yanjun Cai et al.
Zhiren Cave in southern China is an important site for the study of the origin and the environmental background of early modern humans. The combination of Elephas kiangnanensis, Elephas maximus, and Megatapirus augustus, indicates an early representative of the typical Asian elephant fauna. Previous U-series dating of flowstone calcite has pinpointed an upper age limit for the fossils of about 100 ka. In order to achieve a better comprehension of the chronology of the modern human and contemporaneous faunal assemblage, paleomagnetic, stratigraphic, and optically stimulated luminescence (OSL) dating methods have been applied to the cave sediments. Paleomagnetic analyses reveal that there is a reversed polarity excursion below the fossiliferous layer. This excursion can be regarded as the Blake excursion event, given the U-series ages of the overlying flowstone calcite, the OSL measurements, the virtual geomagnetic pole (VGP) path of the excursion, the two reverse polarity zones within this excursion event, and the characteristic of the fauna assemblage. The human remains and mammalian fauna assemblage can be bracketed to 116–106 ka. Application of OSL dating leads to erroneous ages, largely due to the uncertainty associated with the estimation on the dose rates.
Link
March 31, 2016
Denisovan ancestry in Oceanians (and some in South Asians)
Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2016.03.037
The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans
Sriram Sankararaman et al.
Some present-day humans derive up to ∼5% [ 1 ] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [ 2 ]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [ 3 ]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.
Link
The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans
Sriram Sankararaman et al.
Some present-day humans derive up to ∼5% [ 1 ] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [ 2 ]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [ 3 ]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.
Link
Middle (not Upper) Paleolithic hobbits
Nature (2016) doi:10.1038/nature17179
Revised stratigraphy and chronology for Homo floresiensis at Liang Bua in Indonesia
Thomas Sutikna, Matthew W. Tocheri, Michael J. Morwood, E. Wahyu Saptomo, Jatmiko, Rokus Due Awe, Sri Wasisto, Kira E. Westaway, Maxime Aubert, Bo Li, Jian-xin Zhao, Michael Storey, Brent V. Alloway, Mike W. Morley, Hanneke J. M. Meijer, Gerrit D. van den Bergh, Rainer Grün, Anthony Dosseto, Adam Brumm, William L. Jungers & Richard G. Roberts
Homo floresiensis, a primitive hominin species discovered in Late Pleistocene sediments at Liang Bua (Flores, Indonesia)1, 2, 3, has generated wide interest and scientific debate. A major reason this taxon is controversial is because the H. floresiensis-bearing deposits, which include associated stone artefacts2, 3, 4 and remains of other extinct endemic fauna5, 6, were dated to between about 95 and 12 thousand calendar years (kyr) ago2, 3, 7. These ages suggested that H. floresiensis survived until long after modern humans reached Australia by ~50 kyr ago8, 9, 10. Here we report new stratigraphic and chronological evidence from Liang Bua that does not support the ages inferred previously for the H. floresiensis holotype (LB1), ~18 thousand calibrated radiocarbon years before present (kyr cal. BP), or the time of last appearance of this species (about 17 or 13–11 kyr cal. BP)1, 2, 3, 7, 11. Instead, the skeletal remains of H. floresiensis and the deposits containing them are dated to between about 100 and 60 kyr ago, whereas stone artefacts attributable to this species range from about 190 to 50 kyr in age. Whether H. floresiensis survived after 50 kyr ago—potentially encountering modern humans on Flores or other hominins dispersing through southeast Asia, such as Denisovans12, 13—is an open question.
Link
Revised stratigraphy and chronology for Homo floresiensis at Liang Bua in Indonesia
Thomas Sutikna, Matthew W. Tocheri, Michael J. Morwood, E. Wahyu Saptomo, Jatmiko, Rokus Due Awe, Sri Wasisto, Kira E. Westaway, Maxime Aubert, Bo Li, Jian-xin Zhao, Michael Storey, Brent V. Alloway, Mike W. Morley, Hanneke J. M. Meijer, Gerrit D. van den Bergh, Rainer Grün, Anthony Dosseto, Adam Brumm, William L. Jungers & Richard G. Roberts
Homo floresiensis, a primitive hominin species discovered in Late Pleistocene sediments at Liang Bua (Flores, Indonesia)1, 2, 3, has generated wide interest and scientific debate. A major reason this taxon is controversial is because the H. floresiensis-bearing deposits, which include associated stone artefacts2, 3, 4 and remains of other extinct endemic fauna5, 6, were dated to between about 95 and 12 thousand calendar years (kyr) ago2, 3, 7. These ages suggested that H. floresiensis survived until long after modern humans reached Australia by ~50 kyr ago8, 9, 10. Here we report new stratigraphic and chronological evidence from Liang Bua that does not support the ages inferred previously for the H. floresiensis holotype (LB1), ~18 thousand calibrated radiocarbon years before present (kyr cal. BP), or the time of last appearance of this species (about 17 or 13–11 kyr cal. BP)1, 2, 3, 7, 11. Instead, the skeletal remains of H. floresiensis and the deposits containing them are dated to between about 100 and 60 kyr ago, whereas stone artefacts attributable to this species range from about 190 to 50 kyr in age. Whether H. floresiensis survived after 50 kyr ago—potentially encountering modern humans on Flores or other hominins dispersing through southeast Asia, such as Denisovans12, 13—is an open question.
Link
March 25, 2016
Bronze Age war in northern Germany
Slaughter at the bridge: Uncovering a colossal Bronze Age battle
About 3200 years ago, two armies clashed at a river crossing near the Baltic Sea. The confrontation can’t be found in any history books—the written word didn’t become common in these parts for another 2000 years—but this was no skirmish between local clans. Thousands of warriors came together in a brutal struggle, perhaps fought on a single day, using weapons crafted from wood, flint, and bronze, a metal that was then the height of military technology.
...
In 1996, an amateur archaeologist found a single upper arm bone sticking out of the steep riverbank—the first clue that the Tollense Valley, about 120 kilometers north of Berlin, concealed a gruesome secret. A flint arrowhead was firmly embedded in one end of the bone, prompting archaeologists to dig a small test excavation that yielded more bones, a bashed-in skull, and a 73-centimeter club resembling a baseball bat. The artifacts all were radiocarbon-dated to about 1250 B.C.E., suggesting they stemmed from a single episode during Europe’s Bronze Age.
...
Northern Europe in the Bronze Age was long dismissed as a backwater, overshadowed by more sophisticated civilizations in the Near East and Greece. Bronze itself, created in the Near East around 3200 B.C.E., took 1000 years to arrive here. But Tollense’s scale suggests more organization—and more violence—than once thought. “We had considered scenarios of raids, with small groups of young men killing and stealing food, but to imagine such a big battle with thousands of people is very surprising,” says Svend Hansen, head of the German Archaeological Institute’s (DAI’s) Eurasia Department in Berlin. The well-preserved bones and artifacts add detail to this picture of Bronze Age sophistication, pointing to the existence of a trained warrior class and suggesting that people from across Europe joined the bloody fray.
...
There was reason for skepticism. Before Tollense, direct evidence of large-scale violence in the Bronze Age was scanty, especially in this region. Historical accounts from the Near East and Greece described epic battles, but few artifacts remained to corroborate these boastful accounts. “Even in Egypt, despite hearing many tales of war, we never find such substantial archaeological evidence of its participants and victims,” UCD’s Molloy says.
...
Ancient DNA could potentially reveal much more: When compared to other Bronze Age samples from around Europe at this time, it could point to the homelands of the warriors as well as such traits as eye and hair color. Genetic analysis is just beginning, but so far it supports the notion of far-flung origins. DNA from teeth suggests some warriors are related to modern southern Europeans and others to people living in modern-day Poland and Scandinavia. “This is not a bunch of local idiots,” says University of Mainz geneticist Joachim Burger. “It’s a highly diverse population.”
March 20, 2016
Neandertal and Denisovan DNA from Melanesians
Admixture models are out of control these days, with 4 inferred archaic introgressions into three groups of Eurasians (Europeans, East Asians, Melanesians). The model on the left has to be a simplification/incomplete/wrong in some way (Melanesians are not an outgroup to Europeans and East Asians; Europeans have "Basal Eurasian" ancestry via Early European Farmers; Denisovans have some kind of weird archaic ancestry that Neandertals don't, and according to a recent study, the Altai Neandertal also has some kind of weird Proto-Modern Human lineage). In any case, this may not matter much for the problem at hand which is excavating archaic DNA from Melanesian genomes.
But, if you combined all the admixtures inferred in the literature, you'd probably need something like 8 admixtures to model 5 populations. Time and data will show which of them are real, and reveal news ones (e.g., in Africans, who remain blissfully simple in the absence of archaic African genomes).
Science DOI: 10.1126/science.aad9416
Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
Benjamin Vernot et al.
Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 new Island Melanesian genomes. In aggregate, we recovered 1.34 Gb and 303 Mb of the Neandertal and Denisovan genome, respectively. We leverage these maps of archaic sequence to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequence, and identify signatures of adaptive introgression.
Link
Adaptation in the light of ancient genomes
Nature Communications 7, Article number: 10775 doi:10.1038/ncomms10775
Human adaptation and population differentiation in the light of ancient genomes
Felix M. Key, Qiaomei Fu, Frédéric Romagné, Michael Lachmann and Aida M. Andrés
The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation.
Link
Human adaptation and population differentiation in the light of ancient genomes
Felix M. Key, Qiaomei Fu, Frédéric Romagné, Michael Lachmann and Aida M. Andrés
The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation.
Link
March 15, 2016
Preprint revolution in biology
A very nice article by Amy Harmon in the NY Times.
Handful of Biologists Went Rogue and Published Directly to Internet
Handful of Biologists Went Rogue and Published Directly to Internet
On Feb. 29, Carol Greider of Johns Hopkins University became the third Nobel Prize laureate biologist in a month to do something long considered taboo among biomedical researchers: She posted a report of her recent discoveries to a publicly accessible website, bioRxiv, before submitting it to a scholarly journal to review for “official’’ publication.
...
And many #ASAPbio supporters retweeted John Hawks, a paleoanthropologist from the University of Wisconsin, who found himself recently at an African university where a paper on African genomes was unavailable because it could not pay the fee for the journal where it was published, and no preprint was available. He expressed his frustration with a profanity.
...
Preprint advocates counter that scientists care too much about their reputations to publish shoddy work, and posts to bioRxiv are clearly marked to indicate that they may contain information that “has not yet been accepted or endorsed in any way by the scientific or medical community.’’ Others note that plenty of peer-reviewed papers in high-profile journals have proved to be wrong, and some argue that carrying out peer review after a paper is published would provide a more rigorous and fair vetting of papers, anyway.
March 14, 2016
The dysgenic effects of modern civilization
I hope that strong AI and practical gene editing becomes a reality before this bleak future kicks in.
GENETICS March 7, 2016 vol. 202 no. 3 869-875; DOI: 10.1534/genetics.115.180471
Mutation and Human Exceptionalism: Our Future Genetic Load
Michael Lynch
Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
Link
GENETICS March 7, 2016 vol. 202 no. 3 869-875; DOI: 10.1534/genetics.115.180471
Mutation and Human Exceptionalism: Our Future Genetic Load
Michael Lynch
Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
Link
Sima de los Huesos hominins were Proto-Neandertals
Nature (2016) doi:10.1038/nature17405
Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
Matthias Meyer, Juan-Luis Arsuaga, Cesare de Filippo, Sarah Nagel, Ayinuer Aximu-Petri, Birgit Nickel, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell, Bence Viola, Janet Kelso, Kay Prüfer & Svante Pääbo
A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago1. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals2. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.
Link
Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
Matthias Meyer, Juan-Luis Arsuaga, Cesare de Filippo, Sarah Nagel, Ayinuer Aximu-Petri, Birgit Nickel, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell, Bence Viola, Janet Kelso, Kay Prüfer & Svante Pääbo
A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago1. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals2. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.
Link
March 09, 2016
Stature/body mass index and socioeconomic status
BMJ 2016; 352 doi: http://dx.doi.org/10.1136/bmj.i582 (Published 08 March 2016)
Height, body mass index, and socioeconomic status: mendelian randomisation study in UK Biobank
Jessica Tyrrell, research fellow1 2, Samuel E Jones, associate research fellow1, Robin Beaumont, associate research fellow1, Christina M Astley, research fellow3 4, Rebecca Lovell, research fellow2, Hanieh Yaghootkar, research fellow1, Marcus Tuke, associate research fellow1, Katherine S Ruth, associate research fellow1, Rachel M Freathy, senior research fellow1, Joel N Hirschhorn, professor2 3 5, Andrew R Wood, research fellow1, Anna Murray, senior lecturer1, Michael N Weedon, associate professor1, Timothy M Frayling, professor1
Abstract
Objective To determine whether height and body mass index (BMI) have a causal role in five measures of socioeconomic status.
Design Mendelian randomisation study to test for causal effects of differences in stature and BMI on five measures of socioeconomic status. Mendelian randomisation exploits the fact that genotypes are randomly assigned at conception and thus not confounded by non-genetic factors.
Setting UK Biobank.
Participants 119 669 men and women of British ancestry, aged between 37 and 73 years.
Main outcome measures Age completed full time education, degree level education, job class, annual household income, and Townsend deprivation index.
Results In the UK Biobank study, shorter stature and higher BMI were observationally associated with several measures of lower socioeconomic status. The associations between shorter stature and lower socioeconomic status tended to be stronger in men, and the associations between higher BMI and lower socioeconomic status tended to be stronger in women. For example, a 1 standard deviation (SD) higher BMI was associated with a £210 (€276; $300; 95% confidence interval £84 to £420; P=6×10−3) lower annual household income in men and a £1890 (£1680 to £2100; P=6×10−15) lower annual household income in women. Genetic analysis provided evidence that these associations were partly causal. A genetically determined 1 SD (6.3 cm) taller stature caused a 0.06 (0.02 to 0.09) year older age of completing full time education (P=0.01), a 1.12 (1.07 to 1.18) times higher odds of working in a skilled profession (P=6×10−7), and a £1130 (£680 to £1580) higher annual household income (P=4×10−8). Associations were stronger in men. A genetically determined 1 SD higher BMI (4.6 kg/m2) caused a £2940 (£1680 to £4200; P=1×10−5) lower annual household income and a 0.10 (0.04 to 0.16) SD (P=0.001) higher level of deprivation in women only.
Conclusions These data support evidence that height and BMI play an important partial role in determining several aspects of a person’s socioeconomic status, especially women’s BMI for income and deprivation and men’s height for education, income, and job class. These findings have important social and health implications, supporting evidence that overweight people, especially women, are at a disadvantage and that taller people, especially men, are at an advantage.
Link
Height, body mass index, and socioeconomic status: mendelian randomisation study in UK Biobank
Jessica Tyrrell, research fellow1 2, Samuel E Jones, associate research fellow1, Robin Beaumont, associate research fellow1, Christina M Astley, research fellow3 4, Rebecca Lovell, research fellow2, Hanieh Yaghootkar, research fellow1, Marcus Tuke, associate research fellow1, Katherine S Ruth, associate research fellow1, Rachel M Freathy, senior research fellow1, Joel N Hirschhorn, professor2 3 5, Andrew R Wood, research fellow1, Anna Murray, senior lecturer1, Michael N Weedon, associate professor1, Timothy M Frayling, professor1
Abstract
Objective To determine whether height and body mass index (BMI) have a causal role in five measures of socioeconomic status.
Design Mendelian randomisation study to test for causal effects of differences in stature and BMI on five measures of socioeconomic status. Mendelian randomisation exploits the fact that genotypes are randomly assigned at conception and thus not confounded by non-genetic factors.
Setting UK Biobank.
Participants 119 669 men and women of British ancestry, aged between 37 and 73 years.
Main outcome measures Age completed full time education, degree level education, job class, annual household income, and Townsend deprivation index.
Results In the UK Biobank study, shorter stature and higher BMI were observationally associated with several measures of lower socioeconomic status. The associations between shorter stature and lower socioeconomic status tended to be stronger in men, and the associations between higher BMI and lower socioeconomic status tended to be stronger in women. For example, a 1 standard deviation (SD) higher BMI was associated with a £210 (€276; $300; 95% confidence interval £84 to £420; P=6×10−3) lower annual household income in men and a £1890 (£1680 to £2100; P=6×10−15) lower annual household income in women. Genetic analysis provided evidence that these associations were partly causal. A genetically determined 1 SD (6.3 cm) taller stature caused a 0.06 (0.02 to 0.09) year older age of completing full time education (P=0.01), a 1.12 (1.07 to 1.18) times higher odds of working in a skilled profession (P=6×10−7), and a £1130 (£680 to £1580) higher annual household income (P=4×10−8). Associations were stronger in men. A genetically determined 1 SD higher BMI (4.6 kg/m2) caused a £2940 (£1680 to £4200; P=1×10−5) lower annual household income and a 0.10 (0.04 to 0.16) SD (P=0.001) higher level of deprivation in women only.
Conclusions These data support evidence that height and BMI play an important partial role in determining several aspects of a person’s socioeconomic status, especially women’s BMI for income and deprivation and men’s height for education, income, and job class. These findings have important social and health implications, supporting evidence that overweight people, especially women, are at a disadvantage and that taller people, especially men, are at an advantage.
Link
February 26, 2016
No Y-chromosomes of recent Indian origin in Australians
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
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 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.
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