Kevin Lewis

February 23, 2014

A Genetic Atlas of Human Admixture History

Garrett Hellenthal et al.
Science, 14 February 2014, Pages 747-751

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.


Neanderthal Demographic Estimates

Jean-Pierre Bocquet-Appel & Anna Degioanni
Current Anthropology, December 2013, Pages S202-S213

This article offers a critical review of population estimates for the Neanderthal metapopulation based on (paleo-) biological, archaeological, climatic, and genetic data. What do these data tell us about putative Neanderthal demography? Biological data suggest a similar demographic frame (life-history traits, such as potential maximum longevity, age at menarche, and duration of gestation) between Neanderthals and modern humans. Archaeological data have revealed a contradiction between the mortality pattern corresponding to 45+ yr in Neanderthals and the longevity displayed by the manifest continuum of extant mammals, including primates. Paleoclimatic data suggest that the demography of Neanderthals, living as they did under highly fluctuating climatic conditions, was subject to frequent bottlenecks. This demographic instability combined with the fragmentation of geographical areas and variations in their distribution and extent could account for the fact that potential for technical creativity in the Neanderthal metapopulation would have been limited precisely because of its small numbers, leading it into what is known as a “Boserupian trap” in macrodemographic theory. Finally, genetic literature reports different — but always very low — estimations of the effective size (Ne) of the Neanderthal metapopulation. It is not easy to relate Ne to the census size of a population, but by combining different demographic values, this study produced nine different scenarios that were used to obtain an order of magnitude ranging from 5,000 to 70,000 individuals. The cause of the cultural limitation of the Neanderthal metapopulation, compared with that of modern humans, may well have resided in its small numbers alone.


The Pre-History of Urban Scaling

Scott Ortman et al.
PLoS ONE, February 2014

Cities are increasingly the fundamental socio-economic units of human societies worldwide, but we still lack a unified characterization of urbanization that captures the social processes realized by cities across time and space. This is especially important for understanding the role of cities in the history of human civilization and for determining whether studies of ancient cities are relevant for contemporary science and policy. As a step in this direction, we develop a theory of settlement scaling in archaeology, deriving the relationship between population and settled area from a consideration of the interplay between social and infrastructural networks. We then test these models on settlement data from the Pre-Hispanic Basin of Mexico to show that this ancient settlement system displays spatial scaling properties analogous to those observed in modern cities. Our data derive from over 1,500 settlements occupied over two millennia and spanning four major cultural periods characterized by different levels of agricultural productivity, political centralization and market development. We show that, in agreement with theory, total settlement area increases with population size, on average, according to a scale invariant relation with an exponent in the range 2/3 ≤ α ≤ 5/6. As a consequence, we are able to infer aggregate socio-economic properties of ancient societies from archaeological measures of settlement organization. Our findings, from an urban settlement system that evolved independently from its old-world counterparts, suggest that principles of settlement organization are very general and may apply to the entire range of human history.


The genome of a Late Pleistocene human from a Clovis burial site in western Montana

Morten Rasmussen et al.
Nature, 13 February 2014, Pages 225–229

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14C years before present (BP) (13,000 to 12,600 calendar years BP). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 14C years BP (approximately 12,707–12,556 calendar years BP) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal’ta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years BP. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.


Convergent evolution in European and Rroma populations reveals pressure exerted by plague on Toll-like receptors

Hafid Laayouni et al.
Proceedings of the National Academy of Sciences, 18 February 2014, Pages 2668–2673

Recent historical periods in Europe have been characterized by severe epidemic events such as plague, smallpox, or influenza that shaped the immune system of modern populations. This study aims to identify signals of convergent evolution of the immune system, based on the peculiar demographic history in which two populations with different genetic ancestry, Europeans and Rroma (Gypsies), have lived in the same geographic area and have been exposed to similar environments, including infections, during the last millennium. We identified several genes under evolutionary pressure in European/Romanian and Rroma/Gipsy populations, but not in a Northwest Indian population, the geographic origin of the Rroma. Genes in the immune system were highly represented among those under strong evolutionary pressures in Europeans, and infections are likely to have played an important role. For example, Toll-like receptor 1 (TLR1)/TLR6/TLR10 gene cluster showed a strong signal of adaptive selection. Their gene products are functional receptors for Yersinia pestis, the agent of plague, as shown by overexpression studies showing induction of proinflammatory cytokines such as TNF, IL-1β, and IL-6 as one possible infection that may have exerted evolutionary pressures. Immunogenetic analysis showed that TLR1, TLR6, and TLR10 single-nucleotide polymorphisms modulate Y. pestis–induced cytokine responses. Other infections may also have played an important role. Thus, reconstruction of evolutionary history of European populations has identified several immune pathways, among them TLR1/TLR6/TLR10, as being shaped by convergent evolution in two human populations with different origins under the same infectious environment.


Hominin Footprints from Early Pleistocene Deposits at Happisburgh, UK

Nick Ashton et al.
PLoS ONE, February 2014

Investigations at Happisburgh, UK, have revealed the oldest known hominin footprint surface outside Africa at between ca. 1 million and 0.78 million years ago. The site has long been recognised for the preservation of sediments containing Early Pleistocene fauna and flora, but since 2005 has also yielded humanly made flint artefacts, extending the record of human occupation of northern Europe by at least 350,000 years. The sediments consist of sands, gravels and laminated silts laid down by a large river within the upper reaches of its estuary. In May 2013 extensive areas of the laminated sediments were exposed on the foreshore. On the surface of one of the laminated silt horizons a series of hollows was revealed in an area of ca. 12 m2. The surface was recorded using multi-image photogrammetry which showed that the hollows are distinctly elongated and the majority fall within the range of juvenile to adult hominin foot sizes. In many cases the arch and front/back of the foot can be identified and in one case the impression of toes can be seen. Using foot length to stature ratios, the hominins are estimated to have been between ca. 0.93 and 1.73 m in height, suggestive of a group of mixed ages. The orientation of the prints indicates movement in a southerly direction on mud-flats along the river edge. Early Pleistocene human fossils are extremely rare in Europe, with no evidence from the UK. The only known species in western Europe of a similar age is Homo antecessor, whose fossil remains have been found at Atapuerca, Spain. The foot sizes and estimated stature of the hominins from Happisburgh fall within the range derived from the fossil evidence of Homo antecessor.


Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

Iñigo Olalde et al.
Nature, forthcoming

Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.


Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

Benjamin Vernot & Joshua Akey
Science, forthcoming

Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering over 15 Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR = 5%). Analyses of surviving archaic lineages suggests that there were fitness costs to hybridization, admixture occurred both before and subsequent to divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups even in the absence of fossilized remains.


The complete genome sequence of a Neanderthal from the Altai Mountains

Kay Prüfer et al.
Nature, 2 January 2014, Pages 43–49

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.


The Invisible Cliff: Abrupt Imposition of Malthusian Equilibrium in a Natural-Fertility, Agrarian Society

Cedric Puleston, Shripad Tuljapurkar & Bruce Winterhalder
PLoS ONE, January 2014

Analysis of a natural fertility agrarian society with a multi-variate model of population ecology isolates three distinct phases of population growth following settlement of a new habitat: (1) a sometimes lengthy copial phase of surplus food production and constant vital rates; (2) a brief transition phase in which food shortages rapidly cause increased mortality and lessened fertility; and (3) a Malthusian phase of indefinite length in which vital rates and quality of life are depressed, sometimes strikingly so. Copial phase duration declines with increases in the size of the founding group, maximum life expectancy and fertility; it increases with habitat area and yield per hectare; and, it is unaffected by the sensitivity of vital rates to hunger. Transition phase duration is unaffected by size of founding population and area of settlement; it declines with yield, life expectancy, fertility and the sensitivity of vital rates to hunger. We characterize the transition phase as the Malthusian transition interval (MTI), in order to highlight how little time populations generally have to adjust. Under food-limited density dependence, the copial phase passes quickly to an equilibrium of grim Malthusian constraints, in the manner of a runner dashing over an invisible cliff. The three-phase pattern diverges from widely held intuitions based on standard Lotka-Verhulst approaches to population regulation, with implications for the analysis of socio-cultural evolution, agricultural intensification, bioarchaeological interpretation of food stress in prehistoric societies, and state-level collapse.


Immediate replacement of fishing with dairying by the earliest farmers of the northeast Atlantic archipelagos

Lucy Cramp et al.
Proceedings of the Royal Society: Biological Sciences, 7 April 2014

The appearance of farming, from its inception in the Near East around 12 000 years ago, finally reached the northwestern extremes of Europe by the fourth millennium BC or shortly thereafter. Various models have been invoked to explain the Neolithization of northern Europe; however, resolving these different scenarios has proved problematic due to poor faunal preservation and the lack of specificity achievable for commonly applied proxies. Here, we present new multi-proxy evidence, which qualitatively and quantitatively maps subsistence change in the northeast Atlantic archipelagos from the Late Mesolithic into the Neolithic and beyond. A model involving significant retention of hunter–gatherer–fisher influences was tested against one of the dominant adoptions of farming using a novel suite of lipid biomarkers, including dihydroxy fatty acids, ω-(o-alkylphenyl)alkanoic acids and stable carbon isotope signatures of individual fatty acids preserved in cooking vessels. These new findings, together with archaeozoological and human skeletal collagen bulk stable carbon isotope proxies, unequivocally confirm rejection of marine resources by early farmers coinciding with the adoption of intensive dairy farming. This pattern of Neolithization contrasts markedly to that occurring contemporaneously in the Baltic, suggesting that geographically distinct ecological and cultural influences dictated the evolution of subsistence practices at this critical phase of European prehistory.


Helminths and human ancestral immune ecology: What is the evidence for high helminth loads among foragers?

Douglas London & Daniel Hruschka
American Journal of Human Biology, March/April 2014, Pages 124–129

Objectives: Recent theories of human immune ecology have invoked high helminth loads as an important selection factor among early humans. However, few studies have assessed this assumption among extant human foragers.

Methods: We review the current evidence for high helminth loads in documented forager populations and present new data from members of a Kawymeno Waorani forager group in Amazonian Ecuador (n = 16) compared with neighboring Kichwa subsistence farmers (n = 63).

Results: Stool samples indicated a near absence of helminths among the Kawymeno foraging group (6.25% with Ascaris lumbricoides and 0% with Ancylostoma duodenale or Trichuris trichiura). In contrast neighboring, isolated Kichwa subsistence farmers in a similar ecosystem had abundant helminth infestations (76.1% with Ascaris lumbricoides, 11.1% with Ancylostoma duodenale, and 1.5% with Trichuris trichiura). The presence of helminths among the Waorani and Kichwa was triangulated across multiple data sources, including presence in stool samples, medical exams, and 3 years of participant observation.

Conclusions: These findings, coupled with the modern forager literature, raise questions as to whether helminths were prevalent enough in Paleolithic humans to be a unique evolutionary selective force in human physiology.


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