Inverse European Latitudinal Cline at the timeless Locus of Drosophila melanogaster Reveals Selection on a Clock Gene: Population Genetics of ls-tim

The spread of adaptive genetic variants in populations is a cornerstone of evolutionary theory but with relatively few biologically well-understood examples. Previous work on the ls-tim variant of timeless, which encodes the light-sensitive circadian regulator in Drosophila melanogaster, suggests that it may have originated in southeastern Italy. Flies characterized by the new allele show photoperiod-related phenotypes likely to be adaptive in seasonal environments. ls-tim may be spreading from its point of origin in Italy by directional selection, but there are alternative explanations for its observed clinal geographical distribution, including balancing selection and demography. From population analyses of ls-tim frequencies collected on the eastern side of the Iberian Peninsula, we show that ls-tim frequencies are inverted compared with those in Italy. This pattern is consistent with a scenario of directional selection rather than latitude-associated balancing selection. Neutrality tests further reveal the signature of directional selection at the ls-tim site, which is reduced a few kb pairs either side of ls-tim. A reanalysis of allele frequencies from a large number of microsatellite loci do not demonstrate any frequent ls-tim-like spatial patterns, so a general demographic effect or population expansion from southeastern Italy cannot readily explain current ls-tim frequencies. Finally, a revised estimate of the age of ls-tim allele using linkage disequilibrium and coalescent-based approaches reveals that it may be only 300 to 3000 years old, perhaps explaining why it has not yet gone to fixation. ls-tim thus provides a rare temporal snapshot of a new allele that has come under selection before it reaches equilibrium.

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species

Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation.

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence in Four Endangered Notopterygium Herbs

Mountain uplift and climatic fluctuations are important driving forces that have affected the geographic distribution and population dynamics history of organisms. However, it is unclear how geological and climatic events might have affected the phylogeographic history and species divergence in high-alpine herbal plants. In this study, we analyzed the population demographic history and species differentiation of four endangered Notopterygium herbs on the high-altitude Qinghai-Tibetan Plateau (QTP) and adjacent areas. We combined phylogeographic analysis with species distribution modeling to detect the genetic variations in four Notopterygium species (N. incisum, N. franchetii, N. oviforme, and N. forrestii). In total, 559 individuals from 74 populations of the four species were analyzed based on three maternally inherited chloroplast fragments (matK, rbcL, and trnS-trnG) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-five chloroplast DNA (cpDNA) and 48 ITS haplotypes were identified in the four species. All of the cpDNA and ITS haplotypes were species-specific, except N. franchetii and N. oviforme shared one cpDNA haplotype, H32. Phylogenetic analysis suggested that all four species formed a monophyletic clade with high bootstrap support, where N. franchetii and N. oviforme were sisters. In addition, each Notopterygium species generated an individual clade that corresponded to their respective species in the ITS tree. Population dynamics analyses and species distribution modeling showed that the two widely distributed herbs N. incisum and N. franchetii exhibited obvious demographic expansions during the Pleistocene ice ages. Molecular dating suggested that the divergence of the four Notopterygium species occurred approximately between 3.6 and 1.2 Mya, and it was significantly associated with recent extensive uplifts of the QTP. Our results support the hypothesis that mountain uplift and Quaternary climatic oscillations profoundly shaped the population genetic divergence and demographic dynamics of Notopterygium species. The findings of this and previous studies provide important insights into the effects of QTP uplifts and climatic changes on phylogeography and species differentiation in high altitude mountainous areas. Our results may also facilitate the conservation of endangered herbaceous medicinal plants in the genus Notopterygium.

Harnessing ancient genomes to study the history of human adaptation

The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.

A parsimonious neutral model suggests Neanderthal replacement was determined by migration and random species drift

Most hypotheses in the heated debate about the Neanderthals’ replacement by modern humans highlight the role of environmental pressures or attribute the Neanderthals’ demise to competition with modern humans, who occupied the same ecological niche. The latter assume that modern humans benefited from some selective advantage over Neanderthals, which led to the their extinction. Here we show that a scenario of migration and selectively neutral species drift predicts the Neanderthals’ replacement. Our model offers a parsimonious alternative to those that invoke external factors or selective advantage, and represents a null hypothesis for assessing such alternatives. For a wide range of parameters, this hypothesis cannot be rejected. Moreover, we suggest that although selection and environmental factors may or may not have played a role in the inter-species dynamics of Neanderthals and modern humans, the eventual replacement of the Neanderthals was determined by the repeated migration of modern humans from Africa into Eurasia.

The replacement of Neanderthals by modern humans is thought to have been due to environmental factors, a selective advantage of modern humans, or both. Here, Kolodny and Feldman develop a neutral model of species drift showing that rapid Neanderthal replacement can be explained parsimoniously by simple migration dynamics.

The origin and evolution of Homo sapiens

If we restrict the use of Homo sapiens in the fossil record to specimens which share a significant number of derived features in the skeleton with extant H. sapiens, the origin of our species would be placed in the African late middle Pleistocene, based on fossils such as Omo Kibish 1, Herto 1 and 2, and the Levantine material from Skhul and Qafzeh. However, genetic data suggest that we and our sister species Homo neanderthalensis shared a last common ancestor in the middle Pleistocene approximately 400-700 ka, which is at least 200 000 years earlier than the species origin indicated from the fossils already mentioned. Thus, it is likely that the African fossil record will document early members of the sapiens lineage showing only some of the derived features of late members of the lineage. On that basis, I argue that human fossils such as those from Jebel Irhoud, Florisbad, Eliye Springs and Omo Kibish 2 do represent early members of the species, but variation across the African later middle Pleistocene/early Middle Stone Age fossils shows that there was not a simple linear progression towards later sapiens morphology, and there was chronological overlap between different 'archaic' and 'modern' morphs. Even in the late Pleistocene within and outside Africa, we find H. sapiens specimens which are clearly outside the range of Holocene members of the species, showing the complexity of recent human evolution. The impact on species recognition of late Pleistocene gene flow between the lineages of modern humans, Neanderthals and Denisovans is also discussed, and finally, I reconsider the nature of the middle Pleistocene ancestor of these lineages, based on recent morphological and genetic data.This article is part of the themed issue 'Major transitions in human evolution'.

A call for action: Why anthropologists can (and should) join the discussion on climate change through education

Anthropologists, human biologists, and researchers in related fields have been investigating the human-environment interaction and its effects on health for decades. While there have been numerous studies from the medical- and health-sectors pointing to the connection between climate change and health needs, as well as studies advocating for the incorporation of appropriate curricula addressing these needs in medical schools and health-professional programs, this connection is not being systematically taught to our future healthcare professionals. Here, we first briefly summarize research highlighting the interaction between environment and health; we follow this with discussion about why this interaction is important for current and future medical professionals to understand, particularly in light of the current issues of climate change. We specifically address how anthropologists and human biologists have contributed to the literature on marginal environments and climate change, and how anthropological research may be incorporated in health-oriented and medical classrooms to aid in this discussion. Through interdisciplinary collaboration between anthropologists, human biologists, medical-health professionals, and researchers in other fields, we can learn from our past and play a part in piecing together our future health care issues and needs.

The role of hydrophobicity in tuberculosis evolution and pathogenicity

The evolution of tubercle bacilli parallels a route from environmental Mycobacterium kansasii, through intermediate "Mycobacterium canettii", to the modern Mycobacterium tuberculosis complex. Cell envelope outer membrane lipids change systematically from hydrophilic lipooligosaccharides and phenolic glycolipids to hydrophobic phthiocerol dimycocerosates, di- and pentaacyl trehaloses and sulfoglycolipids. Such lipid changes point to a hydrophobic phenotype for M. tuberculosis sensu stricto. Using Congo Red staining and hexadecane-aqueous buffer partitioning, the hydrophobicity of rough morphology M. tuberculosis and Mycobacterium bovis strains was greater than smooth "M. canettii" and M. kansasii. Killed mycobacteria maintained differential hydrophobicity but defatted cells were similar, indicating that outer membrane lipids govern overall hydrophobicity. A rough M. tuberculosis H37Rv ΔpapA1 sulfoglycolipid-deficient mutant had significantly diminished Congo Red uptake though hexadecane-aqueous buffer partitioning was similar to H37Rv. An M. kansasii, ΔMKAN27435 partially lipooligosaccharide-deficient mutant absorbed marginally more Congo Red dye than the parent strain but was comparable in partition experiments. In evolving from ancestral mycobacteria, related to "M. canettii" and M. kansasii, modern M. tuberculosis probably became more hydrophobic by increasing the proportion of less polar lipids in the outer membrane. Importantly, such a change would enhance the capability for aerosol transmission, affecting virulence and pathogenicity.

Robust and scalable inference of population history from hundreds of unphased whole genomes

It has recently been demonstrated that inference methods based on genealogical processes with recombination can uncover past population history in unprecedented detail. However, these methods scale poorly with sample size, limiting resolution in the recent past, and they require phased genomes, which contain switch errors that can catastrophically distort the inferred history. Here we present SMC++, a new statistical tool capable of analyzing orders of magnitude more samples than existing methods while requiring only unphased genomes (its results are independent of phasing). SMC++ can jointly infer population size histories and split times in diverged populations, and it employs a novel spline regularization scheme that greatly reduces estimation error. We apply SMC++ to analyze sequence data from over a thousand human genomes in Africa and Eurasia, hundreds of genomes from a Drosophila melanogaster population in Africa, and tens of genomes from zebra finch and long-tailed finch populations in Australia.

Across the Gap: Geochronological and Sedimentological Analyses from the Late Pleistocene-Holocene Sequence of Goda Buticha, Southeastern Ethiopia

Goda Buticha is a cave site near Dire Dawa in southeastern Ethiopia that contains an archaeological sequence sampling the late Pleistocene and Holocene of the region. The sedimentary sequence displays complex cultural, chronological and sedimentological histories that seem incongruent with one another. A first set of radiocarbon ages suggested a long sedimentological gap from the end of Marine Isotopic Stage (MIS) 3 to the mid-Holocene. Macroscopic observations suggest that the main sedimentological change does not coincide with the chronostratigraphic hiatus. The cultural sequence shows technological continuity with a late persistence of artifacts that are usually attributed to the Middle Stone Age into the younger parts of the stratigraphic sequence, yet become increasingly associated with lithic artifacts typically related to the Later Stone Age. While not a unique case, this combination of features is unusual in the Horn of Africa. In order to evaluate the possible implications of these observations, sedimentological analyses combined with optically stimulated luminescence (OSL) were conducted. The OSL data now extend the radiocarbon chronology up to 63 ± 7 ka; they also confirm the existence of the chronological gap between 24.8 ± 2.6 ka and 7.5 ± 0.3 ka. The sedimentological analyses suggest that the origin and mode of deposition were largely similar throughout the whole sequence, although the anthropic and faunal activities increased in the younger levels. Regional climatic records are used to support the sedimentological observations and interpretations. We discuss the implications of the sedimentological and dating analyses for understanding cultural processes in the region.

Mapping Post-Glacial expansions: The Peopling of Southwest Asia

Archaeological, palaeontological and geological evidence shows that post-glacial warming released human populations from their various climate-bound refugia. Yet specific connections between these refugia and the timing and routes of post-glacial migrations that ultimately established modern patterns of genetic variation remain elusive. Here, we use Y-chromosome markers combined with autosomal data to reconstruct population expansions from regional refugia in Southwest Asia. Populations from three regions in particular possess distinctive autosomal genetic signatures indicative of likely refugia: one, in the north, centered around the eastern coast of the Black Sea, the second, with a more Levantine focus, and the third in the southern Arabian Peninsula. Modern populations from these three regions carry the widest diversity and may indeed represent the most likely descendants of the populations responsible for the Neolithic cultures of Southwest Asia. We reveal the distinct and datable expansion routes of populations from these three refugia throughout Southwest Asia and into Europe and North Africa and discuss the possible correlations of these migrations to various cultural and climatic events evident in the archaeological record of the past 15,000 years.

Can a linguistic serial founder effect originating in Africa explain the worldwide phonemic cline?

It has been proposed that a serial founder effect could have caused the present observed pattern of global phonemic diversity. Here we present a model that simulates the human range expansion out of Africa and the subsequent spatial linguistic dynamics until today. It does not assume copying errors, Darwinian competition, reduced contrastive possibilities or any other specific linguistic mechanism. We show that the decrease of linguistic diversity with distance (from the presumed origin of the expansion) arises under three assumptions, previously introduced by other authors: (i) an accumulation rate for phonemes; (ii) small phonemic inventories for the languages spoken before the out-of-Africa dispersal; (iii) an increase in the phonemic accumulation rate with the number of speakers per unit area. Numerical simulations show that the predictions of the model agree with the observed decrease of linguistic diversity with increasing distance from the most likely origin of the out-of-Africa dispersal. Thus, the proposal that a serial founder effect could have caused the present observed pattern of global phonemic diversity is viable, if three strong assumptions are satisfied.

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3-5]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [6-9]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [3-5, 8, 9]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China

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.

Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia

Most previous attempts at reconstructing the past history of human populations did not explicitly take geography into account or considered very simple scenarios of migration and ignored environmental information. However, it is likely that the last glacial maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite data set genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion or due to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations.

Co-evolution of Mycobacterium tuberculosis and Homo sapiens

The causative agent of human tuberculosis (TB), Mycobacterium tuberculosis, is an obligate pathogen that evolved to exclusively persist in human populations. For M. tuberculosis to transmit from person to person, it has to cause pulmonary disease. Therefore, M. tuberculosis virulence has likely been a significant determinant of the association between M. tuberculosis and humans. Indeed, the evolutionary success of some M. tuberculosis genotypes seems at least partially attributable to their increased virulence. The latter possibly evolved as a consequence of human demographic expansions. If co-evolution occurred, humans would have counteracted to minimize the deleterious effects of M. tuberculosis virulence. The fact that human resistance to infection has a strong genetic basis is a likely consequence of such a counter-response. The genetic architecture underlying human resistance to M. tuberculosis remains largely elusive. However, interactions between human genetic polymorphisms and M. tuberculosis genotypes have been reported. Such interactions are consistent with local adaptation and allow for a better understanding of protective immunity in TB. Future 'genome-to-genome' studies, in which locally associated human and M. tuberculosis genotypes are interrogated in conjunction, will help identify new protective antigens for the development of better TB vaccines.

A Human Deciduous Tooth and New 40Ar/39Ar Dating Results from the Middle Pleistocene Archaeological Site of Isernia La Pineta, Southern Italy

Isernia La Pineta (south-central Italy, Molise) is one of the most important archaeological localities of the Middle Pleistocene in Western Europe. It is an extensive open-air site with abundant lithic industry and faunal remains distributed across four stratified archaeosurfaces that have been found in two sectors of the excavation (3c, 3a, 3s10 in sect. I; 3a in sect. II). The prehistoric attendance was close to a wet environment, with a series of small waterfalls and lakes associated to calcareous tufa deposits. An isolated human deciduous incisor (labelled IS42) was discovered in 2014 within the archaeological level 3 coll (overlying layer 3a) that, according to new ⁴⁰Ar/³⁹Ar measurements, is dated to about 583–561 ka, i.e. to the end of marine isotope stage (MIS) 15. Thus, the tooth is currently the oldest human fossil specimen in Italy; it is an important addition to the scanty European fossil record of the Middle Pleistocene, being associated with a lithic assemblage of local raw materials (flint and limestone) characterized by the absence of handaxes and reduction strategies primarily aimed at the production of small/medium-sized flakes. The faunal assemblage is dominated by ungulates often bearing cut marks. Combining chronology with the archaeological evidence, Isernia La Pineta exhibits a delay in the appearance of handaxes with respect to other European Palaeolithic sites of the Middle Pleistocene. Interestingly, this observation matches the persistence of archaic morphological features shown by the human calvarium from the Middle Pleistocene site of Ceprano, not far from Isernia (south-central Italy, Latium). In this perspective, our analysis is aimed to evaluate morphological features occurring in IS42.

Human Leukocyte Antigen Diversity: A Southern African Perspective

Despite the increasingly well-documented evidence of high genetic, ethnic, and linguistic diversity amongst African populations, there is limited data on human leukocyte antigen (HLA) diversity in these populations. HLA is part of the host defense mechanism mediated through antigen presentation to effector cells of the immune system. With the high disease burden in southern Africa, HLA diversity data is increasingly important in the design of population-specific vaccines and the improvement of transplantation therapeutic interventions. This review highlights the paucity of HLA diversity data amongst southern African populations and defines a need for information of this kind. This information will support disease association studies, provide guidance in vaccine design, and improve transplantation outcomes.

Genetic evidence for contribution of human dispersal to the genetic diversity of EBA-175 in Plasmodium falciparum

Background

The 175-kDa erythrocyte binding antigen (EBA-175) of Plasmodium falciparum plays a crucial role in merozoite invasion into human erythrocytes. EBA-175 is believed to have been under diversifying selection; however, there have been no studies investigating the effect of dispersal of humans out of Africa on the genetic variation of EBA-175 in P. falciparum.

Methods

The PCR-direct sequencing was performed for a part of the eba-175 gene (regions II and III) using DNA samples obtained from Thai patients infected with P. falciparum. The divergence times for the P. falciparum eba-175 alleles were estimated assuming that P. falciparum/Plasmodium reichenowi divergence occurred 6 million years ago (MYA). To examine the possibility of diversifying selection, nonsynonymous and synonymous substitution rates for Plasmodium species were also estimated.

Results

A total of 32 eba-175 alleles were identified from 131 Thai P. falciparum isolates. Their estimated divergence time was 0.13–0.14 MYA, before the exodus of humans from Africa. A phylogenetic tree for a large sequence dataset of P. falciparumeba-175 alleles from across the world showed the presence of a basal Asian-specific cluster for all P. falciparum sequences. A markedly more nonsynonymous substitutions than synonymous substitutions in region II in P. falciparum was also detected, but not within Plasmodium species parasitizing African apes, suggesting that diversifying selection has acted specifically on P. falciparumeba-175.

Conclusions

Plasmodium falciparumeba-175 genetic diversity appeared to increase following the exodus of Asian ancestors from Africa. Diversifying selection may have played an important role in the diversification of eba-175 allelic lineages. The present results suggest that the dispersals of humans out of Africa influenced significantly the molecular evolution of P. falciparum EBA-175.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-015-0820-2) contains supplementary material, which is available to authorized users.

Diagnosing Homo sapiens in the fossil record

BACKGROUND

Diagnosing Homo sapiens is a critical question in the study of human evolution. Although what constitutes living members of our own species is straightforward, in the fossil record this is still a matter of much debate. The issue is complicated by questions of species diagnoses and ideas about the mode by which a new species is born, by the arguments surrounding the behavioural and cognitive separateness of the species, by the increasing appreciation of variation in the early African H. sapiens record and by new DNA evidence of hybridization with extinct species.

METHODS AND RESULTS

This study synthesizes thinking on the fossils, archaeology and underlying evolutionary models of the last several decades with recent DNA results from both H. sapiens and fossil species.

CONCLUSION

It is concluded that, although it may not be possible or even desirable to cleanly partition out a homogenous morphological description of recent H. sapiens in the fossil record, there are key, distinguishing morphological traits in the cranium, dentition and pelvis that can be usefully employed to diagnose the H. sapiens lineage. Increasing advances in retrieving and understanding relevant genetic data provide a complementary and perhaps potentially even more fruitful means of characterizing the differences between H. sapiens and its close relatives.

Extra-long interglacial in Northern Hemisphere during MISs 15-13 arising from limited extent of Arctic ice sheets in glacial MIS 14

Knowledge of the behavior of Northern Hemisphere (NH) ice sheets over the past million years is crucial for understanding the role of orbitally driven insolation changes on glacial/interglacial cycles. Here, based on the demonstrable link between changes in Chinese loess grain-size and NH ice-sheet extent, we use loess grain-size records to confirm that northern ice-sheets were restricted during marine oxygen isotope stage (MIS) 14. Thus, an unusually long NH interglacial climate of over 100 kyr persisted during MISs 15−13, much longer than expected from marine oxygen isotope records. Taking a global view of the paleoclimate records, MIS 14 inception seems to be a response to changes in Antarctic ice-sheets rather than to NH cooling. Orbital configuration in the two Polar regions shows that the onset of MIS 14 was forced by austral insolation changes, rather than by boreal summer insolation, as Milankovitch theory proposes. Our analysis of MIS 14 raises the possibility that southern insolation forcing may have played an important role in the inception of several other glacials. We suggest that the extra-long NH interglacial climate during MISs 15−13 provided favorable conditions for the second major dispersal episode of African hominins into Eurasia.

Pleistocene aridification cycles shaped the contemporary genetic architecture of Southern African baboons

Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa’s faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons (Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes, are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Nef) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region’s biodiversity.

Global late Quaternary megafauna extinctions linked to humans, not climate change

The late Quaternary megafauna extinction was a severe global-scale event. Two factors, climate change and modern humans, have received broad support as the primary drivers, but their absolute and relative importance remains controversial. To date, focus has been on the extinction chronology of individual or small groups of species, specific geographical regions or macroscale studies at very coarse geographical and taxonomic resolution, limiting the possibility of adequately testing the proposed hypotheses. We present, to our knowledge, the first global analysis of this extinction based on comprehensive country-level data on the geographical distribution of all large mammal species (more than or equal to 10 kg) that have gone globally or continentally extinct between the beginning of the Last Interglacial at 132 000 years BP and the late Holocene 1000 years BP, testing the relative roles played by glacial–interglacial climate change and humans. We show that the severity of extinction is strongly tied to hominin palaeobiogeography, with at most a weak, Eurasia-specific link to climate change. This first species-level macroscale analysis at relatively high geographical resolution provides strong support for modern humans as the primary driver of the worldwide megafauna losses during the late Quaternary.

Ancient genomics

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

Apparent variation in Neanderthal admixture among African populations is consistent with gene flow from Non-African populations

Recent studies have found evidence of introgression from Neanderthals into modern humans outside of sub-Saharan Africa. Given the geographic range of Neanderthals, the findings have been interpreted as evidence of gene exchange between Neanderthals and modern humans descended from the Out-of-Africa (OOA) migration. Here, we examine an alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African modern humans who were the ancestors of those involved in the OOA migration. Under the alternative model, if the population structure among present-day Africans predates the OOA migration, we might find some African populations show a signal of Neanderthal introgression whereas others do not. To test this alternative model, we compiled a whole-genome data set including 38 sub-Saharan Africans from eight populations and 25 non-African individuals from five populations. We assessed differences in the amount of Neanderthal-like single-nucleotide polymorphism alleles among these populations and observed up to 1.5% difference in the number of Neanderthal-like alleles among African populations. Further analyses suggest that these differences are likely due to recent non-African admixture in these populations. After accounting for recent non-African admixture, our results do not support the alternative model of older (e.g., >100 kya) admixture between modern humans and Neanderthal-like hominids within Africa.

Were Upper Pleistocene human/non-human predator occupations at the Témara caves (El Harhoura 2 and El Mnasra, Morocco) influenced by climate change?

The influence of climate change on human settlements in coastal areas is a central question for archaeologists. This paper addresses this issue by focusing on the Témara region in Morocco. The study area was selected for two main reasons. First, it contains numerous caves with Upper Pleistocene deposits, which have yielded remains of anatomically modern humans in association with Aterian and Iberomaurusian artifacts. Second, these caves are currently located on the shore, thus this region is particularly sensitive to major climate change and sea level fluctuations. Diachronic taphonomic study of faunal remains from two sites in the region, El Harhoura 2 and El Mnasra caves, shows alternating human/non-human predator occupations. The lower layers of El Mnasra Cave dating to Oxygen Isotope Stage (OIS) 5 have yielded diverse ungulate remains with significant anthropogenic impact marks, together with numerous mollusk shells, Nassarius shell beads, hearths, lithics, some bone tools and used pigments. Faunal remains from the upper layers dating to OIS 4, 3 and 2 of El Harhoura 2 and El Mnasra caves, largely dominated by gazelles, provide evidence of carnivore activities, such as tooth marks, numerous semi-digested bones and coprolites alongside some anthropogenic signatures (cut marks and burnt bones). Non-human predators appear to be the main agents responsible for faunal modifications and accumulations. The 'non-intensive' nature of human occupation is confirmed by analyses of the lithic industry at El Harhoura 2. The 'intensive' human occupations date to OIS 5 and could have taken place during wet periods in connection with high sea levels, which allowed the exploitation of shellfish in this area. 'Non-intensive' human occupations generally correspond to arid periods and lower sea levels, during which the Témara area was further inland and may have been less attractive to humans.

Iwo Eleru's place among Late Pleistocene and Early Holocene populations of North and East Africa

The Iwo Eleru site in Nigeria preserves the only terminal Pleistocene fossil from tropical West Africa. The peoples of this region contributed to significant population movements throughout the continent during the Holocene. As such, characterizing the phenotype of Late Pleistocene West African populations is critical for disentangling the evolutionary signatures of a highly complex African population history and structure. Previous research approached the calvaria's morphology from a paleoanthropological perspective, noting its mosaic of archaic and modern neurocranial features and distinctiveness from Pleistocene fossil taxa and contemporary modern human samples. In this paper, I compare Iwo Eleru with contemporary Late Pleistocene Africans and also consider the specimen's affinities with Holocene populations of the central and western Sahara, Nile Valley, and East Africa. Craniometric data were recorded for 22 neurocranial dimensions and subjected to principal components analysis and Mahalanobis distance estimation. Multidimensional scaling of distances indicated that Iwo Eleru fell outside the observed range of variation of other terminal Pleistocene supra-equatorial African populations, confirming previous results that documented its divergence from Neanderthals, Upper Paleolithic Europeans, and modern Africans. The calvaria was also distinct from Holocene Saharan, Nile Valley, and East African populations, which suggests limited West African input into the Sahara during the African Humid Period. Results presented here bolster previous research that suggested Iwo Eleru's anatomy reflected either admixture with archaic humans or the long-term survival of populations with more archaic neurocranial anatomy until the end of the Pleistocene.

A re-examination of the human fossil specimen from Bački Petrovac (Serbia)

A fragmented human calotte was discovered during the early 1950s near Bački Petrovac (Serbia), in association with Palaeolithic stone tools. After its initial publication, the fossil specimen remained largely unknown outside of the Serbian academe and no detailed comparative study has ever been carried out. Since the whereabouts of the fossil itself are currently unknown, and given its potential significance for the Pleistocene human evolution, we re-examine the data published by Živanović (1966, 1975). Using the original measurements, mostly taken on the frontal bone, and a wide comparative sample of 68 fossil specimens, the fossil was compared and analyzed by statistical multivariate methods. We also conducted a visual examination of the morphology based on the available photographic material. Our analysis reveals phenetic similarity with Middle Pleistocene archaic Homo from Africa and anatomically modern Homo sapiens. However, the absence of primitive cranial traits in Bački Petrovac indicates a clear modern Homo sapiens designation. Although lost at the moment, there is a chance for the re-discovery of the fossil in the years to come. This would give us an opportunity to acquire absolute dates and to study the specimen in a more detailed manner.

Craniometric analysis of European Upper Palaeolithic and Mesolithic samples supports discontinuity at the Last Glacial Maximum

The Last Glacial Maximum (LGM) represents the most significant climatic event since the emergence of anatomically modern humans (AMH). In Europe, the LGM may have played a role in changing morphological features as a result of adaptive and stochastic processes. We use craniometric data to examine morphological diversity in pre- and post-LGM specimens. Craniometric variation is assessed across four periods--pre-LGM, late glacial, Early Holocene and Middle Holocene--using a large, well-dated, data set. Our results show significant differences across the four periods, using a MANOVA on size-adjusted cranial measurements. A discriminant function analysis shows separation between pre-LGM and later groups. Analyses repeated on a subsample, controlled for time and location, yield similar results. The results are largely influenced by facial measurements and are most consistent with neutral demographic processes. These findings suggest that the LGM had a major impact on AMH populations in Europe prior to the Neolithic.

Coral reefs in the Anthropocene: persistence or the end of the line?

Tropical coastal ecosystems such as coral reefs have provided food, income and resources to humans for millennia. The first interactions that people had with coral reef ecosystems left little signature or impact, most probably due to the restricted access, as well as the challenges and ephemeral technologies that people used to exploit these important ecosystems. As human populations expanded along tropical coastal areas, however, the influence of coastal people on coral reefs grew rapidly. Deforestation and coastal agriculture reduced coastal water quality, with many fringing coral reefs disappearing as impacts grew. Increasing numbers of fishers with increasingly advanced technologies exploited tropical coastal fisheries so that many marine species declined dramatically. These activities have removed some functional groups to the point where ecological transformations away from coral-dominated communities increasingly occurred. Shipping and marine pollution, as well as ocean warming and acidification from the burning of fossil fuels, have added further stress on tropical marine ecosystems. The latter represents a major threat with even small amounts of change potentially driving the ecological extinction of coral reefs and other marine ecosystems. Given inaction on the core drivers of these changes, the future does not look bright for coral reef ecosystems as we move into the critical phase of the Anthropocene Epoch.

The role of spatial foresight in models of hominin dispersal

Increasingly sophisticated hominin cognition is assumed to play an important role in major dispersal events but it is unclear what that role is. We present an agent-based model showing that there is a close relationship between level of foresight, environmental heterogeneity, and population dispersibility. We explore the dynamics between these three factors and discuss how they may affect the capacity of a hominin population to disperse. Generally, we find that high levels of environmental heterogeneity select for increased foresight and that high levels of foresight tend to reduce dispersibility. This suggests that cognitively complex hominins in heterogeneous environments have low dispersibility relative to cognitively less complex organisms in more homogeneous environments. The model predicts that the environments leading up to major episodes of dispersal, such as the initial hominin dispersal into Eurasia, were likely relatively low in spatial heterogeneity and that the dispersing hominins had relatively low foresight.

The impact of whole-genome sequencing on the reconstruction of human population history

Examining patterns of molecular genetic variation in both modern-day and ancient humans has proved to be a powerful approach to learn about our origins. Rapid advances in DNA sequencing technology have allowed us to characterize increasing amounts of genomic information. Although this clearly provides unprecedented power for inference, it also introduces more complexity into the way we use and interpret such data. Here, we review ongoing debates that have been influenced by improvements in our ability to sequence DNA and discuss some of the analytical challenges that need to be overcome in order to fully exploit the rich historical information that is contained in the entirety of the human genome.

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

Tuberculosis caused 20% of all human deaths in the Western world between the seventeenth and nineteenth centuries and remains a cause of high mortality in developing countries. In analogy to other crowd diseases, the origin of human tuberculosis has been associated with the Neolithic Demographic Transition, but recent studies point to a much earlier origin. We analyzed the whole genomes of 259 M. tuberculosis complex (MTBC) strains and used this data set to characterize global diversity and to reconstruct the evolutionary history of this pathogen. Coalescent analyses indicate that MTBC emerged about 70,000 years ago, accompanied migrations of anatomically modern humans out of Africa and expanded as a consequence of increases in human population density during the Neolithic period. This long coevolutionary history is consistent with MTBC displaying characteristics indicative of adaptation to both low and high host densities.

Possible interbreeding in late Italian Neanderthals? New data from the Mezzena jaw (Monti Lessini, Verona, Italy)

In this article we examine the mandible of Riparo Mezzena a Middle Paleolithic rockshelter in the Monti Lessini (NE Italy, Verona) found in 1957 in association with Charentian Mousterian lithic assemblages. Mitochondrial DNA analysis performed on this jaw and on other cranial fragments found at the same stratigraphic level has led to the identification of the only genetically typed Neanderthal of the Italian peninsula and has confirmed through direct dating that it belongs to a late Neanderthal. Our aim here is to re-evaluate the taxonomic affinities of the Mezzena mandible in a wide comparative framework using both comparative morphology and geometric morphometrics. The comparative sample includes mid-Pleistocene fossils, Neanderthals and anatomically modern humans. This study of the Mezzena jaw shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, La Ferrassie, Saint-Césaire). In our view, this change in morphology among late Neanderthals supports the hypothesis of anatomical change of late Neanderthals and the hypothesis of a certain degree of interbreeding with AMHs that, as the dating shows, was already present in the European territory. Our observations on the chin of the Mezzena mandible lead us to support a non abrupt phylogenetic transition for this period in Europe.

Hominin dispersal into the Nefud Desert and Middle palaeolithic settlement along the Jubbah Palaeolake, Northern Arabia

The Arabian Peninsula is a key region for understanding hominin dispersals and the effect of climate change on prehistoric demography, although little information on these topics is presently available owing to the poor preservation of archaeological sites in this desert environment. Here, we describe the discovery of three stratified and buried archaeological sites in the Nefud Desert, which includes the oldest dated occupation for the region. The stone tool assemblages are identified as a Middle Palaeolithic industry that includes Levallois manufacturing methods and the production of tools on flakes. Hominin occupations correspond with humid periods, particularly Marine Isotope Stages 7 and 5 of the Late Pleistocene. The Middle Palaeolithic occupations were situated along the Jubbah palaeolake-shores, in a grassland setting with some trees. Populations procured different raw materials across the lake region to manufacture stone tools, using the implements to process plants and animals. To reach the Jubbah palaeolake, Middle Palaeolithic populations travelled into the ameliorated Nefud Desert interior, possibly gaining access from multiple directions, either using routes from the north and west (the Levant and the Sinai), the north (the Mesopotamian plains and the Euphrates basin), or the east (the Persian Gulf). The Jubbah stone tool assemblages have their own suite of technological characters, but have types reminiscent of both African Middle Stone Age and Levantine Middle Palaeolithic industries. Comparative inter-regional analysis of core technology indicates morphological similarities with the Levantine Tabun C assemblage, associated with human fossils controversially identified as either Neanderthals or Homo sapiens.

Positive natural selection of TRIB2, a novel gene that influences visceral fat accumulation, in East Asia

Accumulation of visceral fat increases cardiovascular mortality in industrialized societies. However, during the evolution of the modern human, visceral fat may have acted as energy storage facility to survive in times of famine. Therefore, past natural selection might contribute to shaping the variation of visceral fat accumulation in present populations. Here, we report that the gene encoding tribbles homolog 2 (TRIB2) influenced visceral fat accumulation and was operated by recent positive natural selection in East Asians. Our candidate gene association analysis on 11 metabolic traits of 5,810 East Asians revealed that rs1057001, a T/A transversion polymorphism in 3'untranslated region (UTR) of TRIB2, was strongly associated with visceral fat area (VFA) and waist circumference adjusted for body mass index (P = 2.7 × 10(-6) and P = 9.0 × 10(-6), respectively). rs1057001 was in absolute linkage disequilibrium with a conserved insertion-deletion polymorphism in the 3'UTR and was associated with allelic imbalance of TRIB2 transcript levels in adipose tissues. rs1057001 showed high degree of interpopulation variation of the allele frequency; the low-VFA-associated A allele was found with high frequencies in East Asians. Haplotypes containing the rs1057001 A allele exhibited a signature of a selective sweep, which may have occurred 16,546-27,827 years ago in East Asians. Given the predominance of the thrifty gene hypothesis, it is surprising that the apparently non-thrifty allele was selectively favored in the evolution of modern humans. Environmental/physiological factors other than famine would be needed to explain the non-neutral evolution of TRIB2 in East Asians.

The great human expansion

Genetic and paleoanthropological evidence is in accord that today's human population is the result of a great demic (demographic and geographic) expansion that began approximately 45,000 to 60,000 y ago in Africa and rapidly resulted in human occupation of almost all of the Earth's habitable regions. Genomic data from contemporary humans suggest that this expansion was accompanied by a continuous loss of genetic diversity, a result of what is called the "serial founder effect." In addition to genomic data, the serial founder effect model is now supported by the genetics of human parasites, morphology, and linguistics. This particular population history gave rise to the two defining features of genetic variation in humans: genomes from the substructured populations of Africa retain an exceptional number of unique variants, and there is a dramatic reduction in genetic diversity within populations living outside of Africa. These two patterns are relevant for medical genetic studies mapping genotypes to phenotypes and for inferring the power of natural selection in human history. It should be appreciated that the initial expansion and subsequent serial founder effect were determined by demographic and sociocultural factors associated with hunter-gatherer populations. How do we reconcile this major demic expansion with the population stability that followed for thousands years until the inventions of agriculture? We review advances in understanding the genetic diversity within Africa and the great human expansion out of Africa and offer hypotheses that can help to establish a more synthetic view of modern human evolution.