Maker's mark
Hominids adapted to metabolize ethanol long before human-directed fermentation
Matthew Carrigan et al.
Proceedings of the National Academy of Sciences, forthcoming
Abstract:
Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate–ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol.
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Michael Vendetti & Silvia Bunge
Neuron, 3 December 2014, Pages 906–917
Abstract:
Relational thinking, or the ability to represent the relations between items, is widespread in the animal kingdom. However, humans are unparalleled in their ability to engage in the higher-order relational thinking required for reasoning and other forms of abstract thought. Here we propose that the versatile reasoning skills observed in humans can be traced back to developmental and evolutionary changes in the lateral frontoparietal network (LFPN). We first identify the regions within the LFPN that are most strongly linked to relational thinking, and show that stronger communication between these regions over the course of development supports improvements in relational reasoning. We then explore differences in the LFPN between humans and other primate species that could explain species differences in the capacity for relational reasoning. We conclude that fairly small neuroanatomical changes in specific regions of the LFPN and their connections have led to big ontogenetic and phylogenetic changes in cognition.
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Probabilistic cognition in two indigenous Mayan groups
Laura Fontanari et al.
Proceedings of the National Academy of Sciences, 2 December 2014, Pages 17075–17080
Abstract:
Is there a sense of chance shared by all individuals, regardless of their schooling or culture? To test whether the ability to make correct probabilistic evaluations depends on educational and cultural guidance, we investigated probabilistic cognition in preliterate and prenumerate Kaqchikel and K’iche’, two indigenous Mayan groups, living in remote areas of Guatemala. Although the tested individuals had no formal education, they performed correctly in tasks in which they had to consider prior and posterior information, proportions and combinations of possibilities. Their performance was indistinguishable from that of Mayan school children and Western controls. Our results provide evidence for the universal nature of probabilistic cognition.
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Genomic structure in Europeans dating back at least 36,200 years
Andaine Seguin-Orlando et al.
Science, 28 November 2014, Pages 1113-1118
Abstract:
The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.
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Genome sequence of a 45,000-year-old modern human from western Siberia
Qiaomei Fu et al.
Nature, 23 October 2014, Pages 445–449
Abstract:
We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before — or simultaneously with — the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.
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Homo erectus at Trinil on Java used shells for tool production and engraving
Josephine Joordens et al.
Nature, forthcoming
Abstract:
The manufacture of geometric engravings is generally interpreted as indicative of modern cognition and behaviour. Key questions in the debate on the origin of such behaviour are whether this innovation is restricted to Homo sapiens, and whether it has a uniquely African origin. Here we report on a fossil freshwater shell assemblage from the Hauptknochenschicht (‘main bone layer’) of Trinil (Java, Indonesia), the type locality of Homo erectus discovered by Eugène Dubois in 1891. In the Dubois collection (in the Naturalis museum, Leiden, The Netherlands) we found evidence for freshwater shellfish consumption by hominins, one unambiguous shell tool, and a shell with a geometric engraving. We dated sediment contained in the shells with 40Ar/39Ar and luminescence dating methods, obtaining a maximum age of 0.54 ± 0.10 million years and a minimum age of 0.43 ± 0.05 million years. This implies that the Trinil Hauptknochenschicht is younger than previously estimated. Together, our data indicate that the engraving was made by Homo erectus, and that it is considerably older than the oldest geometric engravings described so far. Although it is at present not possible to assess the function or meaning of the engraved shell, this discovery suggests that engraving abstract patterns was in the realm of Asian Homo erectus cognition and neuromotor control.
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Hie Lim Kim et al.
Nature Communications, December 2014
Abstract:
The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/’hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100–150 kyr ago. In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80–100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations.
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Right for the Wrong Reasons: Reflections on Modern Human Origins in the Post-Neanderthal Genome Era
Trenton Holliday, Joanna Gautney & Lukáš Friedl
Current Anthropology, December 2014, Pages 696-724
Abstract:
The sequencing of the Neanderthal genome answered once and for all the question of whether these hominins played a role in the origins of modern humans — they did, and a majority of humans alive today retain a small portion of Neanderthal genes. This finding rejects the strictest versions of the Recent African Origin model and has been celebrated by supporters of Multiregional Evolution (MRE). However, we argue that MRE can also be rejected and that other, intermediate, models of modern human origins better represent the means by which modern humans became the only extant human species. We argue this because we reject one of the major tenets of MRE: global gene flow that prevents cladogenesis from occurring. First, using reconstructions of Pleistocene hominin census size, we maintain that populations were neither large nor dense enough to result in such high levels of gene flow across the Old World. Second, we use mammalian divergence and hybridization data to show that the emergence of Homo is recent enough that member species of this genus were unlikely to have been reproductively isolated from each other, even in the absence of the high levels of global gene flow postulated by MRE supporters.
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Rapid climate change did not cause population collapse at the end of the European Bronze Age
Ian Armit et al.
Proceedings of the National Academy of Sciences, 2 December 2014, Pages 17045–17049
Abstract:
The impact of rapid climate change on contemporary human populations is of global concern. To contextualize our understanding of human responses to rapid climate change it is necessary to examine the archeological record during past climate transitions. One episode of abrupt climate change has been correlated with societal collapse at the end of the northwestern European Bronze Age. We apply new methods to interrogate archeological and paleoclimate data for this transition in Ireland at a higher level of precision than has previously been possible. We analyze archeological 14C dates to demonstrate dramatic population collapse and present high-precision proxy climate data, analyzed through Bayesian methods, to provide evidence for a rapid climatic transition at ca. 750 calibrated years B.C. Our results demonstrate that this climatic downturn did not initiate population collapse and highlight the nondeterministic nature of human responses to past climate change.
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Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 BP
F.H. Chen et al.
Science, forthcoming
Abstract:
Our understanding of when and how humans adapted to living at altitudes above 2000 to 3000 meters of the Tibetan Plateau has been constrained by a paucity of archaeological data. Here we report data sets from the northeastern Tibetan Plateau indicating that the first villages were established only by 5200 years ago. Since 3600 calendar years before the present, a novel agropastoral economy facilitated year-round living at higher altitudes. This successful subsistence strategy facilitated the adaptation of farmers-herders to the challenges of global temperature decline during the late Holocene.
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A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations
Florian Clemente et al.
American Journal of Human Genetics, 6 November 2014, Pages 584–589
Abstract:
Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6–23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.
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Genome flux and stasis in a five millennium transect of European prehistory
Cristina Gamba et al.
Nature Communications, October 2014
Abstract:
The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.