Rethinking the dispersal of Homo sapiens out of Africa

An excellent review which -among its other graces- demolishes the view that mtDNA haplogroup L3 provides a terminus post quem of 70 thousand years for the Out-of-Africa expansion, a question I've discussed in this blog before.

I think the evidence is overwhelming at this point that there were modern humans outside Africa before 100,000 years ago. The argument that they were a  failed expansion is shoddy and is based, as far as I can tell on things like the age of L3, the assumption that Y-chromosome haplogroup E is native to Africa and not derived from back-to-Africa migrants, the assumption that Out-of-Africa coincided with the Upper Paleolithic cultural efflorescence (disproven by the earlier dating of Neandertal admixture), or the failed hypothesis of a coastal route Out of Africa 60 thousand years ago that seems to be repeated in inverse proportion to the evidence for it. The halving of the human autosomal mutation rate relative to what was inferred before has certainly not helped either.

Evolutionary Anthropology: Issues, News, and Reviews Volume 24, Issue 4, pages 149–164, July/August 2015

Rethinking the dispersal of Homo sapiens out of Africa

Huw S. Groucutt, Michael D. Petraglia, Geoff Bailey, Eleanor M. L. Scerri, Ash Parton, Laine Clark-Balzan, Richard P. Jennings, Laura Lewis, James Blinkhorn, Nick A. Drake, Paul S. Breeze, Robyn H. Inglis, Maud H. Devès, Matthew Meredith-Williams, Nicole Boivin, Mark G. Thomas andAylwyn Scally

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.

Link and here

Complex demographic history of Western Central African Pygmies

bioRxiv doi: http://dx.doi.org/10.1101/022194

Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

PingHsun Hsieh et al.

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

Link

More Y-chromosome super-fathers

The time estimates are based on a mutation rate of 1x10-9 mutations/bp/year which is ~1/3 higher than mutation rate of Karmin et al.  So the values on the table may be a little lower.

There may be additional founders with recent time depths than shown in the table, e.g., a very shallow clusters within E-M35 (probably E-V13?) and a couple of shallow clusters within I-P215

Also of interest is the fact that Greeks and Anatolian Turks do not show evidence of the recent Y-chromosomal bottleneck:

The plots are consistent with patterns seen in the relative numbers of singletons, described above, in that the Saami and Palestinians show markedly different demographic histories compared with the rest, featuring very recent reductions, while the Turks and Greeks show evidence of general expansion, with increased growth rate around 14 KYA. A different pattern is seen in the remaining majority (13/17) of populations, which share remarkably similar histories featuring a minimum effective population size ~2.1–4.2 KYA (considering the 95% confidence intervals (CIs) reported in Supplementary Table 4), followed by expansion to the present.

Related:

• Y chromosome super-fathers 
• Bottleneck in human Y-chromosomes in the last 10,000 years

Nature Communications 6, Article number: 7152 doi:10.1038/ncomms8152

Large-scale recent expansion of European patrilineages shown by population resequencing

Chiara Batini, Pille Hallast et al.

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Link

Ice age Europeans on the brink of extinction

Ice-age Europeans roamed in small bands of fewer than 30, on brink of extinction (Horizon magazine)

In some cases, small bands of potentially as few as 20 to 30 people could have been moving over very large areas, over the whole of Europe as a single territory, according to Professor Ron Pinhasi, principal investigator on the EU-funded ADNABIOARC project.

This demographic model is based on new evidence that suggests populations were much smaller than is generally thought to be a stable size for healthy reproduction, usually around 500 people. Such small groupings may have led to reduced fitness and even extinctions.

‘As an archaeologist and anthropologist, I was quite shocked to see how limited, how small the population numbers were. You know, shockingly small,’ said Prof. Pinhasi, based at University College Dublin, Ireland.

...

Prof. Pinhasi’s team has found that the genomes sequenced from hunter-gatherers from Hungary and Switzerland between 14 000 to 7 500 years ago are very close to specimens from Denmark or Sweden from the same period.

These findings suggest that genetic diversity between inhabitants of most of western and central Europe after the ice age was very limited, indicating a major demographic bottleneck triggered by human isolation and extinction during the ice age.

‘We’re starting to be able to reconstruct the actual dynamics of migrations and colonisation of the continent by modern humans and that’s never been done before the genomic era,’ explained Prof. Pinhasi.

He believes that early humans crossed the continent in small groups that were cut off while the ice was at its peak, then successively dispersed and regrouped over thousands of years, with dwindling northern populations invigorated by humans arriving from the south, where the climate was better.

‘You see a real reduction in population numbers and diversity, so you see the few lineages that probably split or separated before the ice age, and then stayed isolated during the ice age,’ he said. ‘Some time after the ice age, they kind of re-emerge, or disperse, and get together, as we see new contributions to European lineages from Asia and in particular the Near East.’

The last couple of statements are interesting because they hint at post-glacial recolonization of Europe after the Ice Age. So far, we are in the dark about what happened in Europe between the time of Kostenki and 8kya. Hopefully another interesting study is on its way to throw some light into the lattter part of this time interval.

MSMC preprint (Schiffels and Durbin)

From the paper:

In particular, the early beginning of the drop would be consistent with an initial formation of distinct populations prior to 150kya, while the late end of the decline would be consistent with a final split around 50kya. This suggests a long period of partial divergence with ongoing genetic exchange between Yoruban and Non-African ancestors that began beyond 150kya, with population structure within Africa, and lasted for over 100,000 years, with a median point around 60-80kya at which time there was still substantial genetic exchange, with half the coalescences between populations and half within (see Discussion). We also observe that the rate of genetic divergence is not uniform but can be roughly divided into two phases. First, up until about 100kya, the two populations separated more slowly, while after 100kya genetic exchange dropped faster.

If divergence between Yoruba and non-Africans began 150kya, then I wonder when divergence between Bushmen or the non-farmer ancestors of Pygmies and the Yoruba started. These dates are well within the time period when anatomical modernity was already in existence, but well before the time period when behavioral modernity first appears. This is important, as some people imagine that humans lived together for most of the time period since their first appearance ~200kya and only split recently at ~50kya, but this is obviously wrong. ~50kya seems to be the time for cessation of gene flow, with 100ky more of impeded gene flow.

Also:

As expected, the oldest split amongst out-of-Africa populations is between European and East Asian (CHB and MXL) populations, most of which occurs between 20-40kya (Figure 4b). Intriguingly there may be a small component (10% or less) of this separation extending much further back towards 100kya, not compatible with a single out-of-Africa event around 50kya.

This is the most intriguing part of this preprint as it suggests that European/East Asian genetic differentiation may not only be due to the their post-UP divergence, but also to older strands of ancestry. Such deep differentiation may be related to the ~100kya settlement of the Near East (but not East Asia) by anatomically modern humans and the recent evidence for a deep "Basal Eurasian" lineage in Europeans but not East Asians.

bioRxiv, doi: http://dx.doi.org/10.1101/005348

Inferring human population size and separation history from multiple genome sequences

Stephan Schiffels, Richard Durbin

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.

Link

Neandertal populations were small (+ differences along the Neandertal/sapiens evolutionary lineages)

PNAS doi: 10.1073/pnas.1405138111

Patterns of coding variation in the complete exomes of three Neandertals

Sergi Castellano et al.

We present the DNA sequence of 17,367 protein-coding genes in two Neandertals from Spain and Croatia and analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia. Comparisons with present-day humans from Africa, Europe, and Asia reveal that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans. Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans. We also identify amino acid substitutions in Neandertals and present-day humans that may underlie phenotypic differences between the two groups. We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in behavior and pigmentation have changed more on the modern human lineage.

Link

Paternal and maternal demographic histories (Lippold et al. 2014)

A new preprint on the bioRxiv on the different male/female demographic history of humans.

Red=female, blue=male.

This is probably related to the new paper on selection on the Y chromosome which interprets reduced diversity as evidence for selection.

doi: 10.1101/001792

Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences 

Sebastian Lippold et al.

To investigate in detail the paternal and maternal demographic histories of humans, we obtained ~500 kb of non-recombining Y chromosome (NRY) sequences and complete mtDNA genome sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). Our results: confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA; suggest very small ancestral effective population sizes (less than 100) for the out-of-Africa migration as well as for many human populations; and indicate that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf. However, we also find substantial differences in patterns of mtDNA vs. NRY variation in different regional groups; thus, global patterns of variation are not necessarily representative of specific geographic regions.

Link

Neolithic boom followed by later collapse (Shennan et al. 2013)

From the paper:

It is particularly important to note that the bust following the initial farming boom is found in two historically separate agricultural expansions, the first into Central Europe c. 7,500 years ago and the second into Northwest Europe 1,500 years later. It is possible that some of these regional declines represent out-migration to neighbouring areas rather than a real decline in numbers, for example, from the Paris Basin into Britain, but, in some cases, for example, Ireland, Scotland and Wessex, it is very clear that the rising and falling trends are roughly synchronous with one another—there is little indication of one going up as the others go down. On present evidence the decline in the initially raised population levels following the introduction of agriculture does not seem to be climate-related, but of course this still leaves open a variety of possible causes that remain to be explored in the future. One possibility is disease, as the reference to the Black Death above implies, although this would have to be occurring on multiple occasions at different times in different places, given the patterns shown. It is perhaps more likely that it arose from endogenous causes; for example, rapid population growth driven by farming to unsustainable levels, soil depletion or erosion arising from early farming practices, or simply the risk arising from relying on a small number of exploitable species32. However, these suggestions remain speculative and an autocorrelation analysis of the demographic data did not find evidence of a cyclical pattern, which would be one indicator of the operation of endogenous processes (Supplementary Fig. S7). Regardless of the cause, collapsing Neolithic populations must have had a major impact on social, economic and cultural processes.

Nature Communications 4, Article number: 2486 doi:10.1038/ncomms3486

Regional population collapse followed initial agriculture booms in mid-Holocene Europe

Stephen Shennan et al.

Following its initial arrival in SE Europe 8,500 years ago agriculture spread throughout the continent, changing food production and consumption patterns and increasing population densities. Here we show that, in contrast to the steady population growth usually assumed, the introduction of agriculture into Europe was followed by a boom-and-bust pattern in the density of regional populations. We demonstrate that summed calibrated radiocarbon date distributions and simulation can be used to test the significance of these demographic booms and busts in the context of uncertainty in the radiocarbon date calibration curve and archaeological sampling. We report these results for Central and Northwest Europe between 8,000 and 4,000 cal. BP and investigate the relationship between these patterns and climate. However, we find no evidence to support a relationship. Our results thus suggest that the demographic patterns may have arisen from endogenous causes, although this remains speculative.

Link

Pre-farming population expansions (Aimé et al. 2013)

Mol Biol Evol (2013) doi: 10.1093/molbev/mst156

Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming.

C. Aimé et al.

Demographic changes are known to leave footprints on genetic polymorphism. Together with the increased availability of large polymorphism datasets, coalescent-based methods allow inferring the past demography of populations from their present-day patterns of genetic diversity. Here, we analyzed both nuclear (20 non-coding regions) and mitochondrial (HVS-I) re-sequencing data to infer the demographic history of 66 African and Eurasian human populations presenting contrasting life-styles (nomadic hunter-gatherers, nomadic herders and sedentary farmers). This allowed us to investigate the relationship between life-style and demography, and to address the long-standing debate about the chronology of demographic expansions and the Neolithic transition. In Africa, we inferred expansion events for farmers, but constant population sizes or contraction events for hunter-gatherers. In Eurasia, we inferred higher expansion rates for farmers than herders with HVS-I data, except in Central Asia and Korea. Although isolation and admixture processes could have impacted our demographic inferences, these processes alone seem unlikely to explain the contrasted demographic histories inferred in populations with different life-styles. The small expansion rates or constant population sizes inferred for herders and hunter-gatherers may thus result from constraints linked to nomadism. However, autosomal data revealed contraction events for two sedentary populations in Eurasia, which may be caused by founder effects. Finally, the inferred expansions likely predated the emergence of agriculture and herding. This suggests that human populations could have started to expand in Paleolithic times, and that strong Paleolithic expansions in some populations may have ultimately favored their shift towards agriculture during the Neolithic.

Link

Population growth and deleterious mutations

Genetics doi: 10.1534/genetics.113.153973

Population Growth Inflates the Per-Individual Number of Deleterious Mutations and Reduces Their Mean Effect

Elodie Gazave et al.

This study addresses the question of how purifying selection operates during recent rapid population growth such as has been experienced by human populations. This is not a straightforward problem because the human population is not at equilibrium: population genetics predicts that, on the one hand, the efficacy of natural selection increases as population size increases, eliminating ever more weakly deleterious variants; on the other hand, a larger number of deleterious mutations will be introduced into the population and will be more likely to increase in their number of copies as the population grows. To understand how patterns of human genetic variation have been shaped by the interaction of natural selection and population growth, we examined the trajectories of mutations with varying selection coefficients using computer simulations. We observed that while population growth dramatically increases the number of deleterious segregating sites in the population, it only mildly increases the number carried by each individual. Our simulations also show an increased efficacy of natural selection, reflected in a higher fraction of deleterious mutations eliminated at each generation, and a more efficient elimination of the most deleterious ones. As a consequence, while each individual carries a larger number of deleterious alleles than expected in the absence of growth, the average selection coefficient of each segregating allele is less deleterious. Combined, our results suggest that the genetic risk of complex diseases might be distributed across a larger number of more weakly deleterious rare variants.

Link

Population growth and the linkage disequilibrium curve

The concluding paragraph:

The European LD curve is steeper than either of the equilibrium curves in Fig. 10, suggesting a history of population expansion. This might re- flect the spread of modern humans into Europe, the spread of farmers during the Neolithic, or the spread of Indo-European speakers. I evaluate these alternatives in a separate publication

arXiv:1308.1984 [q-bio.PE]

How Population Growth Affects Linkage Disequilibrium

Alan R. Rogers

Linkage disequilibrium (LD) is often summarized using the "LD curve," which relates the LD between pairs of sites to the distance that separates them along the chromosome. This paper shows how the LD curve responds to changes in population size. An expansion of population size generates an LD curve that declines steeply, especially if that expansion has followed a bottleneck. A reduction in size generates an LD curve that is high but relatively flat. In European data, the curve is steep, suggesting a history of population expansion. These conclusions emerge from the study of $\sigma_d^2$, a measure of LD that has never played a central role. It has been seen merely as an approximation to another measure, $r^2$. Yet $\sigma_d^2$ has different dynamical behavior and provides deeper time depth. Furthermore, it is easily estimated from data and can be predicted from population history using a fast, deterministic algorithm.

Link

SMBE 2013 abstracts

Some abstracts from the SMBE 2013 conference that will take place next week. 

Legacy of Early Migrants in Neolithic East Asian Hunter-Gatherer from Fukushima, Japan

K.K. Hideaki et al.   

Clarifying the genetic relationship between Neolithic East Asian Hunter-Gatherer, Jomon people, and modern human populations is one of the Keystones to understand the controversial history of modern East Asian populations. Jomon people inhabited in the Japanese archipelago from 16,000 years ago, and their origin and the relationship with modern humans have been debated for a long time. To solve these questions, we obtained 20 million base pairs of genomic DNA from a ~4,000-year-old Jomon male tooth, excavated in Sanganji shell mound, Fukushima, Japan. We compared his genetic components with the data of modern worldwide populations. Our major findings are: (1) Sanganji Jomon was very similar with modern East Asians when we compared the worldwide populations in the PCA plot; (2) when only East Asians were compared, Sanganji Jomon was distant from both modern Northeast and Southeast Asians, indicating that Sanganji Jomon people were already isolated from other continental populations for a long time; (3) the Sanganji Jomon male shared more SNP alleles with southern and northern minorities in China than geographically close Han Chinese, implying a complex history of people in China after the divergence between Jomon ancestors and Eurasian continent people; (4) Sanganji Jomon is genetically closer to modern mainland Japanese than continental populations, indicating that some of their components were transmitted to modern Japanese; (5) within Japanese archipelago, Ainu and Ryukyuan (the populations of northern and southern edges of the Japanese archipelago) have more Jomon components than mainland Japanese, indicating that the genetic effect of agricultural people who migrated from the Eurasian continent in and after the Yayoi period is stronger in Mainland Japanese than Ainu and Ryukyuan.

Extensive Gene Gain in Human Brain Evolution

Yong E. Zhang et al.
The genetic changes contributing to the evolution of the human brain have always attracted wide interest. A emerging consensus view is that while there have been no major patterns of genome-wide changes to the coding regions of brain-related genes, cis-regulatory changes of these genes have played a key role. Here, motivated by anecdotal studies of primate-specific genes implicated in brain function, we identified thousands of lineage-specific (primate-specific or rodent-specific) genes by mining syntenic vertebrate genomic alignments and examined the expression profile of these genes in both fetal and adult brains of human and mouse across different transcriptome profiling platforms. We found that an excess of lineage-specific genes are expressed in the early (fetal or infant) developing human brain compared with those in mouse brain. Expression data covering numerous subregions of the developing brain further demonstrate that these young genes are mainly transcribed in the neocortex. They originated in the evolutionary period during which the neocortex was expanding, suggesting the functional association of new genes with this newly evolving brain structure. Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination and also via evolution of regulatory networks, as hinted by the enrichment of primate-specific transcriptional regulators in our dataset. More than that, these ?ndings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach based on functional and evolutionary genomic methods to better annotate these non-conserved genes.

Recent Human Demography Impacts the Architecture of Genetic Disease in Populations but Not Individual Genetic Load

Yuval Simons et al.
Human populations have undergone dramatic changes in population sizes in the past 100,000 years, including a severe bottleneck of non-African populations and recent explosive population growth. There is currently great interest in how these demographic events may have affected the burden of deleterious mutations in individuals and the allele frequency spectrum of disease mutations in populations. Here we use population genetic models to show that--contrary to previous conjectures--recent human demography likely had very little impact on the average burden of deleterious mutations carried by individuals. This prediction is supported by exome sequence data showing that African American and European American individuals carry very similar burdens of damaging mutations. We next considered whether recent population growth has increased the importance of very rare mutations in disease. Our analysis predicts that, even given recent growth, it is unlikely that very rare mutations contribute a large fraction of disease heritability except for diseases that are largely due to strongly deleterious mutations. In summary, demographic history has dramatically impacted patterns of variation in different human populations, but these changes likely had little impact on either genetic load or on the importance of rare variants in most complex traits.

Functional and Population Genetic Analyses of a High-Coverage Neandertal Genome

Fernando Racimo et al.
We have sequenced the genome of a Neandertal from the Altai mountains in Siberia at 50-fold coverage. This Neandertal was located in the same cave as the Denisovan individual, but is phylogenetically closer to Neandertals from Western Eurasia. To avoid confusion, we call this individual the Altai Neandertal. Here we show an assessment of genome data quality and functional and population genetic comparisons with the Denisovan genome and a set of 25 high-coverage modern human genomes. We present an analysis of genes with recent changes in either the modern human lineage or the archaic human lineage (Neandertal+Denisova). We find enrichment for nonsynonymous changes in genes associated with melanosomes in the modern human lineage, and genes associated with particular muscoskeletal morphologies in the archaic human lineage. We utilize a compound deleteriousness scoring that allows us to combine a variety of conservation, regulatory and expression data to rank all modern and archaic-specific single-nucleotide changes and InDels across the genome, and predict which are those that could have been most disruptive in our evolutionary history. Furthermore, we overlap the modern-specific catalog with the top regions of a screen for selective sweeps exclusive to the modern human lineage, and observe enrichments for changes in genes related to ion channel activity, muscle contraction and membrane transport. Finally, we note an excess of ancestral alleles in the Denisovan individual relative to the Altai Neandertal individual, which is strongest at sites where modern humans are fixed derived. We develop an approximate Bayesian computation approach that allows us to test different models, and conclude that gene flow between the Denisovan individual and a more anciently diverged human lineage is most consistent with the patterns observed.

Multiple Episodes of Population Mixture in Southern African History

Joseph K. Pickrell et al.
The history of southern Africa involved interactions between indigenous hunter-gatherers and a range of populations that moved temporarily or permanently into the region. The influence of these interactions on the genetic structure of current populations remains unclear. Here, using patterns of linkage disequilibrium, we show that there are at least two admixture events in the genetic history of southern African hunter-gatherers and pastoralists: one involving populations related to Niger-Congo-speaking African populations, and one which introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We estimate that at least a few percent of ancestry in the Khoisan is derived from this latter admixture event, which occurred on average 1,200-1,800 years ago. We show that a similar signal of west Eurasian ancestry is present throughout eastern Africa; in particular, we also find evidence for two admixture events in the genetic history of several Kenyan, Tanzanian, and Somali populations, the earliest of which involved populations related to southern Europeans and which we date to approximately 2700 - 3300 years ago. We thus suggest that west Eurasian ancestry entered southern Africa indirectly through eastern Africa. These results demonstrate how large-scale genomic datasets can inform complex models of population movements, and highlight the genomic impact of largely uncharacterized back-to-Africa migrations in human history.

Mechanistic Models of Admixture and Approximate-Approximate-Bayesian Computation 

Noah Rosenberg et al.   

Investigations of the history of migrations that underlie admixed populations often use nonmechanistic admixture models rather than a modeling perspective that incorporates a population-genetic history of admixture built from first principles. We build a general model of admixture that mechanistically accounts for complex admixture processes, considering two source populations that contribute to the ancestry of a hybrid population, potentially with variable contributions across generations. For a random individual in the hybrid population at a given point in time, we study the fraction of admixture originating from a specific one of the source populations. Quite different admixture processes can produce identical mean admixture across individuals, but such processes typically produce different values for the variance of admixture. Interestingly, even without considering sex chromosomes, the variance of admixture for autosomes captures information about sex-specific migration in the contributions of the source populations to the admixed group. To perform inference under the model, we use approximate-approximate-Bayesian computation (AABC), a modification of approximateBayesian computation well-suited to estimation under complex mechanistic models that are computationally intensive to simulate. The model and inference method can contribute to an understanding of the theory and analysis of the history of admixed populations.

Inferring Human Population History and Migration Patterns from Multiple Genome Sequences

Stephan Schiffels, Richard Durbin
The availability of human genomes from populations across the world has given rise to new inference methods that exploit high-coverage sequence data. Among the most influential recent developments is the Pairwise Sequentially Markovian Coalescenct (PSMC) by Li and Durbin, 2011. While PSMC infers the demographic history for times between 20kya and 2mya with high resolution, neither the more recent evolutionary history nor migration patterns across populations can be adressed. Here we present a new method that overcomes both of these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) infers the recent evolutionary history within and across populations only a few thousand years ago and younger. MSMC models the pattern of mutations in multiple genome sequences under the coalescent with recombination. It fits local genealogical trees to the observed pattern, focussing on the first coalescence among any two individuals. We apply our method to the genome sequences from several family trios from the 1000 Genomes project with African, European, Asian and SouthAmerican ancestry. We infer population sizes and migration rates as a function of time with high resolution. In particular, our method resolves the more recent evolutionary history of non-African populations after the out-of-Africa event, such as the peopling of the Americas.

Genetic load accumulation during range expansions

arXiv:1306.1652 [q-bio.PE]

On the accumulation of deleterious mutations during range expansions

Stephan Peischl et al.

We investigate the effect of spatial range expansions on the evolution of fitness when beneficial and deleterious mutations co-segregate. We perform individual-based simulations of a uniform linear habitat and complement them with analytical approximations for the evolution of mean fitness at the edge of the expansion. We find that deleterious mutations accumulate steadily on the wave front during range expansions, thus creating an expansion load. Reduced fitness due to the expansion load is not restricted to the wave front but occurs over a large proportion of newly colonized habitats. The expansion load can persist and represent a major fraction of the total mutation load thousands of generations after the expansion. Our results extend qualitatively and quantitatively to two-dimensional expansions. The phenomenon of expansion load may explain growing evidence that populations that have recently expanded, including humans, show an excess of deleterious mutations. To test the predictions of our model, we analyze patterns of neutral and non-neutral genetic diversity in humans and find an excellent fit between theory and data.

Link

Demographic history from distribution of shared IBS lengths

An interesting new paper has appeared in PLoS Genetics, with what appears to be a nice new method for inferring demographic history from genome-scale data. The authors observe that segments inherited from common ancestors are "broken up" by mutation as time goes by: initially there are long identical tracts, but these are "split" whenever a new mutation appears, so they study the distribution of lengths of the pieces between mutations that remain identical by state.

A practical application of the new technique is applied to European-African history:

We estimate that the European-African divergence occurred 55 kya and that gene flow continued until 13 kya. About 5.8% of European genetic material is derived from a ghost population that diverged 420 kya from the ancestors of modern humans. The out-of-Africa bottleneck period, where the European effective population size is only 1,530, lasts until 5.9 kya.

The authors use the "old" 2.5x10-8 mutation derived from a paleontological calibration of the human-chimp split, which renders their calculations comparable to many past papers on human demographic history, but at odds with many of the newer rates that are approximately twice slower. There is lingering controversy about the appropriateness of different rates.

The authors estimate that perhaps a 1.75x increase in their estimates will be effected if the slower rates are used; this is not 2x as one might expect from a 2x slower rate, because their age estimates depend on both the mutation rate (for which there is controversy) and the recombination rate. By applying the 1.75x correction factor, we may obtain a time for European-African split at 96 thousand years and a continuation of gene flow between Europeans and Africans down to 23 thousand years.

I suppose that things might be complicated by the occurrence of Amerindian-like admixture in some West Eurasians in the past, as well as the occurrence of intra-African admixture (which I've called "Palaeoafrican") in the ancestry of Yoruba, both of which do not appear to be modeled here: the former might have infused an "African-less" component of ancestry at a time when the authors suggest that there was continuing gene flow between West Eurasia and African; the latter would inflate the effective population size of the Yoruba and make the appear earlier diverged from non-Africans.

In any case, this is a useful addition to our understanding of human history and may tie in to some of my arguments about Eurasian back-migration into Africa (although the authors consider bidrectional gene flow in their model). The lack of non-M,N mitochondria in non-Africans makes the post-OoA gene flow from Africa->Eurasia difficult to stomach, while the opposing migration of Y-haplogroup E bearers into Africa (as I have suggested) seems too instantaneous to account for the authors' evidence for protracted gene flow.


PLoS Genet 9(6): e1003521. doi:10.1371/journal.pgen.1003521

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

Kelley Harris, Rasmus Nielsen

There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.

Link

Variance of IBD sharing (Carmi et al. 2012)

Genetics doi: 10.1534/genetics.112.147215

The Variance of Identity-by-Descent Sharing in the Wright-Fisher Model

Shai Carmi et al.

Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced recent genetic drift. Detection of these IBD segments has recently become feasible, enabling a wide range of applications from phasing and imputation to demographic inference. Here, we study the distribution of IBD sharing in the Wright-Fisher model. Specifically, using coalescent theory, we calculate the variance of the total sharing between random pairs of individuals. We then investigate the cohort-averaged sharing: the average total sharing between one individual and the rest of the cohort. We find that for large cohorts, the cohort-averaged sharing is distributed approximately normally and surprisingly, the variance of this distribution does not vanish large even for large cohorts, implying the existence of "hyper-sharing" individuals. The presence of such individuals has consequences for the design of sequencing studies, since, if they are selected for whole-genome sequencing, a larger fraction of the cohort can be subsequently imputed. We calculate the expected gain in power of imputation by IBD, and subsequently, in power to detect an association, when individuals are either randomly selected or are specifically chosen to be the hyper-sharing individuals. Using our framework, we also compute the variance of an estimator of the population size that is based on the mean IBD sharing and the variance in the sharing between inbred siblings. Finally, we study IBD sharing in an admixture pulse model, and show that in the Ashkenazi Jewish population the admixture fraction is correlated with the cohort-averaged sharing.

Link

Recent origin of protein-coding variants in humans (Fu et al. 2012)

From the paper:

We estimated the age of all 1,146,401 SNVs using 6 different demographic models 5,6,8–11, 3 of which considered recent explosive population growth5,6,8 (Supplementary Table 2). Estimates of allele age were generally robust across different demographic models, with the largest discrepancies resulting in a twofold difference in average age across all SNVs (Supplementary Table 3 and Supplementary Fig. 8a). However, because most SNVs arose recently (see below), differences among demographic models were highly concordant (Supplementary Information). Accordingly, we report results based on a modified Out-of-Africa model9 in which accelerated population growth began 5,115 years ago with a per-generation growth rate of 1.95% and 1.66% for European Americans and African Americans, respectively6. 

The six models considered are:

None of them are very satisfactory, because 5/6 place the Out-of-Africa event at 87.5kya or later, and it now seems likely that this event took place before 100kya. On the other hand, this parameter may not be as critical in this case, because it appears that while the earliest colonization of Eurasia by modern humans did indeed take place prior to 100kya, the Eurasian population stems from a post-70kya bottleneck. The OOA event may not have caused the Eurasian bottleneck; the latter may be a consequence of environmental deterioration in North Africa-Arabia belt c. 70kya.

The modified Out-of-Africa model used in the main paper is by Gravel et al. (2011). That model used a mutation rate of 2.38x10-8 mutations/bp/gen to convert into times in years, which is a little less than twice the slower mutation rate inferred recently with a variety of methods. Thus, its age estimates ought to be pushed back by a factor of two, and this would resolve the inferred 23ky differentiation between Europeans and Asians without invoking any special mechanism, simply as a consequence of the peopling of West and East Eurasia in the last 40-50 thousand years.

But, in the current paper (Fu et al.) a mutation rate of 1.5x10-8 has been used, which is a fairly slow one, albeit a little faster than the 1.2x10-8 reported in a number of studies. It's not entirely clear to me what the consequence would be of mixing a model (Gravel et al.'s) whose parameters have been inferred using a 2.38x10-8 mutation rate with a mutation rate of 1.5x10-9. Overall, I'd think that the main effect would be to bias age estimates downwards, although the analysis should probably be repeated.

Table S3 provides some idea of how different demographic models affect age estimates:

I took a look at Nelson et al. (which has the higher time estimates) in which a median mutation rate of 1.38x10-8 was inferred. Tennessen et al. estimate OOA at 51kya, so they are probably using the faster (and probably outdated) rate.

When did population growth (which meant more bodies, more mutations, higher chance of mildly deleterious mutations to survive) begin? One possibility is that this was a response to deglaciation and temperature rises after the end of the last Ice Age. Another is that it was a consequence of population growth facilitated by agriculture which increased the land's carrying capacity. Perhaps ancient DNA may inform this discussion by measuring the number of deleterious SNVs in individuals across the last 10 thousand years or so.


Nature (2012) doi:10.1038/nature11690

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

Wenqing Fu et al.

Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history1, 2 and will help to facilitate the development of new approaches for disease-gene discovery3. Large-scale surveys of human genetic variation have reported signatures of recent explosive population growth4, 5, 6, notable for an excess of rare genetic variants, suggesting that many mutations arose recently. To more quantitatively assess the distribution of mutation ages, we resequenced 15,336 genes in 6,515 individuals of European American and African American ancestry and inferred the age of 1,146,401 autosomal single nucleotide variants (SNVs). We estimate that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes. Furthermore, European Americans had an excess of deleterious variants in essential and Mendelian disease genes compared to African Americans, consistent with weaker purifying selection due to the Out-of-Africa dispersal. Our results better delimit the historical details of human protein-coding variation, show the profound effect of recent human history on the burden of deleterious SNVs segregating in contemporary populations, and provide important practical information that can be used to prioritize variants in disease-gene discovery.

Link

IBD length distribution and demographic history (Palamara)

Another interesting new paper in AJHG deals with the problem of inferring the demographic history of a population from the length distribution of IBD segments. I wonder how admixture (which is likely to have occurred in both chosen real-world examples used in the paper, the Ashkenazi Jews and the Maasai) may affect the accuracy of the reconstructed demographic history.

In any case, the conclusions are worth mentioning in themselves. For the Ashkenazi:

We obtained an improved fit for a population composed of ~2,300 ancestors 200 generations before the present; this population exponentially expanded to reach ~45,000 individuals 34 generations ago. After a severe founder event, the population was reduced to ~270 individuals, which then expanded rapidly during 33 generations (rate r ~ 0.29) and reached a modern population of ~4,300,000 individuals.

And, for the Maasai:

Optimizing a model of exponential expansion and contraction (Figure 1A), we obtained a good fit to the observed IBD frequency spectrum (Figure 6), suggesting that an ancestral population of ~23,500 individuals decreased to ~500 current individuals during the course of 23 generations (r ~ -0.17). We note that this result might not be driven by an actual gradual population contraction in the MKK individuals, but it most likely reflects the societal structure of this seminomadic population. ... We thus used the village model to analyze the MKK demography and relied on coalescent simulations to retrieve its parameters: migration rate, size, and number of villages that provide a good fit for the empirical distribution of IBD segments.We observed a compatible fit for this model, in which 44 villages of 485 individuals each intermix with a migration rate of 0.13 individuals per generation (Figure 6).

If I understand this correctly, it appears that Maasai (MKK) individuals share long IBD segments not because their population has contracted (and hence they're all descended from a limited number of founders, as is the case for Ashkenazi Jews), but rather because their social structure follows the "village model" in which people share shallow ancestry (and hence long IBD) with other people in their "village" and exchange genes with other "villages".

The American Journal of Human Genetics, 25 October 2012 doi:10.1016/j.ajhg.2012.08.030

Length Distributions of Identity by Descent Reveal Fine-Scale Demographic History

Pier Francesco Palamara et al.

Data-driven studies of identity by descent (IBD) were recently enabled by high-resolution genomic data from large cohorts and scalable algorithms for IBD detection. Yet, haplotype sharing currently represents an underutilized source of information for population-genetics research. We present analytical results on the relationship between haplotype sharing across purportedly unrelated individuals and a population’s demographic history. We express the distribution of IBD sharing across pairs of individuals for segments of arbitrary length as a function of the population’s demography, and we derive an inference procedure to reconstruct such demographic history. The accuracy of the proposed reconstruction methodology was extensively tested on simulated data. We applied this methodology to two densely typed data sets: 500 Ashkenazi Jewish (AJ) individuals and 56 Kenyan Maasai (MKK) individuals (HapMap 3 data set). Reconstructing the demographic history of the AJ cohort, we recovered two subsequent population expansions, separated by a severe founder event, consistent with previous analysis of lower-throughput genetic data and historical accounts of AJ history. In the MKK cohort, high levels of cryptic relatedness were detected. The spectrum of IBD sharing is consistent with a demographic model in which several small-sized demes intermix through high migration rates and result in enrichment of shared long-range haplotypes. This scenario of historically structured demographies might explain the unexpected abundance of runs of homozygosity within several populations.

Link

Neandertal-modern hybrid babies and their heads

A discussion in the comments of Gene Expression got me thinking about a potential scenario for modern-Neandertal interbreeding dynamics. That discussion dealt with difficulties in childbirth arising from population differences in birth canal/head size.

The main idea is simple, and I will rephrase it as follows: offspring of a big man and small woman will tend to have bigger heads relative to the size of the woman's birth canal. On the other hand, offspring of a small man and big woman will not have that problem.

We have some information about differences between Neandertals and modern humans. The former were shorter and more "lateral" skeletally, while UP modern humans appear to have been more linear and taller. Headwise, modern humans had more globular head shapes, while Neandertals more linear ones, with no major differences in brain size between the two species.

If the above are correct, then male Neandertal-female modern human pairings would have a potential problem. Birth is a complex process, but at the end of the day, the most important factor is probably whether the diameter of the head can "fit" in the birth canal: the more it does not fit, the more likely it would seem that a mishap for both mother and offspring would occur.

Combine elongated Neandertal heads with narrow modern human pelves, and you have a potential problem. I am not 100% sure that modern humans and Neandertals differed in pelvis shape, although it would be a reasonable consequence of their overall build, but the same pattern would occur if they did not, simply on account of their different head shapes.

An additional factor involves sexual dimorphism, since male babies tend to be larger than female ones, and so any problems associated with "parental mismatch" might be particularly troublesome for male births.

So, all in all, we have 4 different cases:

1. Male H. n + Female H. s. => Male hybrid
2. Male H. n + Female H. s. => Female hybrid
3. Male H. s + Female H. n. => Male hybrid
4. Male H. s + Female H. n. => Female hybrid

It would appear, on the basis of the preceding discussion, that 1-2 would be more troublesome than 3-4, and 1 most troublesome of all. On the other hand, 4 seems to be the most advantageous case.

The most interesting thing about modern-Neandertal admixture is that it seems to have left no traces in uniparental markers, and, indeed, the lack of mtDNA lineages of Neandertal origin has been used to argue against the plausibility of estimated Neandertal admixture percentages. 

If my reasoning is correct, then case #4 is particularly worrying, since female hybrids with Neandertal mtDNA ought to be the most easy to bear, and would also be the ones who would contribute Neandertal mtDNA in a mixed population.

On the other hand, case #1 would explain the lack of Neandertal Y-chromosomes, since crossings between male Neandertals and female modern humans that produce male offspring might be particular troublesome, and they would also be the ones to introduce Neandertal Y-chromosomes in the population.

Of course, we don't know enough about the dynamics of the admixture process; it might be possible that other factors influence the abundance of the four cases, both biological and cultural. For example, if modern humans had a behavioral advantage, then modern males may contribute most admixture, and this would make the worrying case #4 even more difficult to explain. On the other hand, how did the admixture take place? bride-stealing vs. rape would result in potential offspring being raised in different groups (father's vs. mother's), and there may also have been unknown cultural taboos involving admixture and offpsring produced from it.

In any case, this brief excursus may be useful for anyone thinking of writing some palaeo-fiction set in the Upper Paleolithic, and I'd love to hear from people who have data at hand that might be pertinent to the above discussion.

Effects of ancestry and admixture on human variation (Kidd et al. 2012)

AJHG Volume 91, Issue 4, 5 October 2012, Pages 660–671

Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation

Jeffrey M. Kidd et al.

Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas—70% of the European ancestry in today’s African Americans dates back to European gene flow happening only 7–8 generations ago.

Link

ESHE 2012 abstracts

Some abstracts of interest from the European Society for the study of Human Evolution 2012 meeting (pdf). To avoid making this too long, I will just post the titles and the most relevant quotes. You can read the abstracts in the linked pdf for authors names and more information.

Neandertal and Denisovan Genomes from the Altai 

Susanna Sawyer  et al.

In 2010 a draft genome sequence was determined from a small finger bone found in Denisova Cave in southern Siberia. Its analysis revealed that it derives from an individual who belonged to a population related to, but distinct from, Neandertals. A molar has also been described from Denisova Cave and has shown to carry an mtDNA genome closely related to that of the finger bone.  We have recently determined the DNA sequence of the Denisova genome to a quality similar to present-day human genomes. We have also retrieved a complete mitochondrial genome and nuclear DNA sequences from an additional molar found in Denisova Cave. Furthermore, we have determined a high-quality nuclear genome from a pedal phalanx found in Denisova Cave in 2010. We show that the pedal phalanx derived from a Neandertal and thus that Neandertals as well as Denisovans have been present in the cave. We will discuss the genetic history of Denisovans as well as Neandertals in light of these new genome sequences. 

The discovery of a Neandertal genome from Denisova cave is certainly interesting. I have previously commented that:

If Vindija and Denisova, two caves less than 5,000km apart were home to people more divergent from each other than any two humans are today, it's strange to think that only "modern humans" inhabited Africa at the same time.

Now, it appears that Neandertals and Denisovans were present (when?) not only 5Mm apart, but literally on the same spot. Much later, during the Neolithic we see very differentiated humans co-existing in Europe. And, we get archaic hominins in Africa long after the appearance of anatomically modern humans there. I think the evidence is looking good for my hypothesis that regional human populations have recently gotten more similar over time through extensive admixture between divergent hominin groups, rather than that they became more dissimilar over time  through tree-like divergence.

On the same topic, here is more evidence for Neandertal presence in the Altai:

A Neanderthal mandible fragment from Chagyrskaya Cave (Altai Mountains, Russian Federation)

Both the mandible and the dentition preserve numerous derived Neanderthal traits: among else a posteriorly placed mandibular foramen, an oblique mylohyoid line, an asymmetrical P4 and continuous mid-trigonid crests on the M1 and M2. ... Ongoing ancient DNA analyses of the hominin remains from Chagyrskaya cave and absolute dates for the site will hopefully help to clarify the origin of the Altai Neanderthals, and their relationship with the Denisovans.

An hypothesis for the phylogenetic position of Homo floresiensis

Our cladistic analysis places H. floresiensis unequivocally as part of a clade with H. habilis

Who are you calling ”modern”? An assessment of the dental morphology and metrics of Homo sapiens

Although dental reduction has long been cited as a derived feature of H. sapiens, our data indicate this claim may be no longer tenable ... the single metrical assessment that groups all H. sapiens (early, Upper Paleolithic and recent) apart from other taxa is the ratio between mandibular:maxillary crown areas.  the results of our study are important for assessing recent claims of great antiquity for H. sapiens outside of Africa

Neanderthal in Malthusian demographic trap

It can be hypothesized that the demography of the Neanderthal metapopulation, living under conditions where extreme environmental instability with short periods was the norm, was primarily stagnant,

with frequent bottlenecks and episodes of decline.

 A New Framework for the Upper Paleolithic of Eastern Europe

The results of field and laboratory research during the past decade require a new classificatory framework for the Upper Paleolithic in Eastern Europe. It is now apparent that people making artifacts assigned to the Ahmarian industry occupied both the southern and northern slopes of the Caucasus Mountains (i.e., Ortvale Klde, Layer 4d; Mezmaiskaya Cave, Layer 1C). Their sites probably indicate a separate movement of anatomically modern humans (AMH) from the Near East directly into Eastern Europe, establishing an independent line of development during the earlier Upper Paleolithic that parallels the Proto-Aurignacian and Aurignacian sequence in Western and Central Europe. this East European industry is most fully represented at the Kostenki-Borshchevo sites on the Don River before 40,000 cal BP (e.g., Kostenki 14, Layer IVb). It is followed by a closely related industry, also characterized by bladelet production, that is dated to the interval between 40,000 and 30,000 cal BP in Crimea and the East European Plain. The proposed new framework reflects recognition of these distinctive East European entities and of two environmental events that had significant impacts on human settlement in Eastern Europe: (1) the Campanian Ignimbrite (CI) volcanic eruption (40,000 cal BP); and (2) the Last Glacial Maximum (LGM) ( 25,000 cal BP). It has been suggested that the early Upper Paleolithic (EUP) industry present in Eastern Europe before 40,000 cal BP should be labeled an eastern variant of the contemporaneous Proto-Aurignacian of Mediterranean Europe. However, given the separate movement of people from the Near East via the Caucasus Mountains, and independent development of the East European EUP, this industry is more appropriately termed “Proto-Gravettian.” The younger bladelet industry, which includes assemblages at Buran-Kaya III (Layer 6-1), Mira (Layer II/2), Kostenki 8 (Layer II), and probably Shlyakh (Layers 4C, 6), may be termed “Early Gravettian” to distinguish it from the classic Gravettian industry that dates to less than 30,000 cal BP (e.g., Avdeevo, Zaraisk).The upper temporal boundary of the Proto-Gravettian corresponds to the CI eruption (40,000 cal BP), while the classic Gravettian of the East European Plain appears to have been effectively terminated by the LGM ( 25,000 cal BP). Several sites that date to the 40,000–30,000 cal BP interval (e.g., Kostenki 1, Layer III) contain elements that suggest a connection with the Aurignacian technocomplex of Western-Central Europe. These assemblages may be placed into the category of “Eastern Aurignacian,” which reflects differences in content with the West and Central European sites. The apparent spread of this industry into Eastern Europe from Central Europe may be related to the impact of the CI eruption on portions of the East European Plain. 

 Conflicting dates for the Late Aterian

First at the huge Ifri n’Ammar sites, TL dates have indicated 80,000 years for the Late Middle Palaeolithic/Aterian levels. Our new C14 dates yield 35,000 BP for exactly the same levels. At the “grotte des Contrebandiers”, formerly dated at 28,000 BP by Debenath and his team, is now dated at 100,000 years by new TL dates. As starting points, this kind of methodological contradiction should be confronted, understood and resolved.

 The Rio Secco Cave in the North Adriatic Region, Italy. A new context for investigating the Neanderthal demise and the settllement of Anatomically Modern Humans

A sequence of several thin layers dated to 46.0–42.1ky Cal BP represents the final Mousterian.

The Dhofar Nubian Tradition: an enduring Middle Stone Age technocomplex in southern Arabia

Between 2010 and 2012, the Dhofar Archaeological Project has located and mapped 260 Nubian Complex occurrences across the Nejd Plateau of southern Oman. Diagnostic Nubian artifacts werefound cemented in fluvial sediments at the site of Aybut Al Auwal in Dhofar, with two OSL dates around 106 ka BP; hence, roughly contemporaneous with the African Nubian Complex (Rose et al. 2011). Many of these lithic assemblages, such as that from Aybut al Auwal, are technologically homologous to the Late Nubian Industry found in northeast Africa, sensu stricto, while others may represent local facies of the greater “Afro-Arabian Nubian Technocomplex.” This presentation describes the various reduction strategies encountered at a sample of Nubian Complex sites from Oman, explores inter-assemblage variability, and begins to articulate technological units within the “Dhofar Nubian Tradition.” To achieve this aim, we have developed an analytical scheme with which to describe technological variability among Nubian Levallois reduction strategies in both Africa and Arabia. Our analysis indicates at least two distinct Nubian industries. The first, which we refer to as the “Classic Dhofar Nubian,” is virtually identical to Late Nubian Industry from the Lower Nile Valley and Red Sea Hills in Egypt. Thee subsequent group of assemblages in Dhofar, called the “Mudayyan,” exhibits a technological shift toward diminutive Nubian Levallois cores and that, recurrent bidirectional cores with opposed, faceted striking platforms. We interpret this evidence to indicate an enduring, local Nubian tradition in Dhofar that is ultimately rooted in the African Nubian Complex. 

From Late Mousterian to Evolved Aurignacian: New evidence for the Middle-to-Upper Paleolithic transition in Mediterranean Spain

Combined, the evidence from CA and FDM indicates that, in chronostratigraphic terms, the Middle-to-Upper Paleolithic transition in Murcia consists of the replacement of a Late Mousterian by an Evolved Aurignacian and occurred some time during the 38th millennium cal BP