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The Australian lungfish is a primitive and endangered representative of the subclass Dipnoi. The distribution of this species is limited to south-east Queensland, with some populations considered endemic and others possibly descending from translocations in the late nineteenth century shortly after European discovery. Attempts to resolve the historical distribution for this species have met with conflicting results based on descriptive genetic studies. Understanding if all populations are endemic or some are the result of, or influenced by, translocation events, has implications for conservation management. In this work, we analysed the genetic variation at three types of markers (mtDNA genomes, 11 STRs, and 5,196 nuclear SNPs) using the Approximate Bayesian Computation algorithm to compare several demographic models. We postulated different contributions of Mary River and Burnett River gene pools into the Brisbane River and North Pine River populations, related to documented translocation events. We ran the analysis for each marker separately, and we also estimated the posterior probabilities of the models combining the markers. Nuclear SNPs have the highest power to correctly identify the true model amongst the simulated datasets (where the model was known), but different markers typically provided similar answers. The most supported demographic model able to explain the real dataset implies that an endemic gene pool is present in the Brisbane and North Pine Rivers where past translocations are documented. These results will inform ongoing conservation efforts for this endangered and iconic species and warrant careful consideration of future genetic management of the Australian lungfish populations.

A clearer understanding of the structure of pest populations in newly invaded areas is a key step towards their effective management. Here, we use Drosophila suzukii as a model to highlight how populations from separate geographical regions differ in their genetic and phenotypic traits, including those associated with their invasiveness. New X-linked data indicate the presence of at most three D. suzukii genetic clusters in Europe, while North American populations are characterised by a larger genetic diversity. We found a likely new colonisation event from America to Italy and demonstrate that reference genomes from Italian and Californian populations lay in highly distant clusters. Comparative genomics indicate that these two genomes bear the traces of distinct evolutionary forces and are genetically distant, having diversified long ago in their native Asian range. Phenotypic studies further indicate that European and North American populations have differences in hatch rate, generation time, and parasitoid susceptibility. The observed genotypic and phenotypic differences likely represent a small fraction of the features unique to each of the two populations. The results provide some new insights towards both fundamental and management studies on invasive pests, particularly when findings are transferred across populations found in different geographical regions.

Funder: Wellcome Trust, The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.

Objectives Genetic drift and admixture are driving forces in human evolution, but their concerted impact to population evolution in historical times and at a micro‐geographic scale is poorly assessed. In this study we test a demographic model encompassing both admixture and drift to the case of social‐cultural isolates such as the so‐called “Commons.” Materials and methods Commons are peculiar institutions of medieval origins whose key feature is the tight relationship between population and territory, mediated by the collective property of shared resources. Here, we analyze the Y‐chromosomal genetic structure of four Commons (for a total of 366 samples) from the Central and Eastern Padana plain in Northern Italy. Results Our results reveal that all these groups exhibit patterns of significant diversity reduction, peripheral/outlier position within the Italian/European genetic space and high frequency of Common‐specific haplogroups. By explicitly testing different drift‐admixture models, we show that a drift‐only model is more probable for Central Padana Commons, while additional admixture (~20%) from external population around the same time of their foundation cannot be excluded for the Eastern ones. Discussion Building on these results, we suggest central Middle Ages as the most probable age of foundation for three of the considered Commons, the remaining one pointing to late antiquity. We conclude that an admixture‐drift model is particularly useful for interpreting the genetic structure and recent demographic history of small‐scale populations in which social‐cultural features play a significant role.

There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question whether AMH left Africa through a single process, dispersing almost simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Australo-Melanesia, and later through a northern route crossing the Levant. The development of new methodologies for inferring population history and the availability of worldwide high-coverage whole-genome sequences did not resolve this debate. In this work, we test the two main out-of-Africa hypotheses through an Approximate Bayesian Computation approach, based on the Random-Forest algorithm. We evaluated the ability of the method to discriminate between the alternative models of AMH out-of-Africa, using simulated data. Once assessed that the models are distinguishable, we compared simulated data with real genomic variation, from modern and archaic populations. This analysis showed that a model of multiple dispersals is four-fold as likely as the alternative single-dispersal model. According to our estimates, the two dispersal processes may be placed, respectively, around 74,000 and around 46,000 years ago.

Inferring past demographic histories is crucial in population genetics, and the amount of complete genomes now available should in principle facilitate this inference. In practice, however, the available inferential methods suffer from severe limitations. Although hundreds complete genomes can be simultaneously analysed, complex demographic processes can easily exceed computational constraints, and the procedures to evaluate the reliability of the estimates contribute to increase the computational effort. Here we present an approximate Bayesian computation framework based on the random forest algorithm (ABC-RF), to infer complex past population processes using complete genomes. To this aim, we propose to summarize the data by the full genomic distribution of the four mutually exclusive categories of segregating sites (FDSS), a statistic fast to compute from unphased genome data and that does not require the ancestral state of alleles to be known. We constructed an efficient ABC pipeline and tested how accurately it allows one to recognize the true model among models of increasing complexity, using simulated data and taking into account different sampling strategies in terms of number of individuals analysed, number and size of the genetic loci considered. We also compared the FDSS with the unfolded and folded site frequency spectrum (SFS), and for these statistics we highlighted the experimental conditions maximizing the inferential power of the ABC-RF procedure. We finally analysed real data sets, testing models on the dispersal of anatomically modern humans out of Africa and exploring the evolutionary relationships of the three species of Orangutan inhabiting Borneo and Sumatra.

OBJECTIVES With the advent of ancient DNA analyses, it has been possible to disentangle the contribution of ancient populations to the genetic pool of the modern inhabitants of many regions. Reconstructing the maternal ancestry has often highlighted genetic continuity over several millennia, but almost always in isolated areas. Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast. MATERIALS AND METHODS We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present-day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups. RESULTS Our analyses always favor continuity over discontinuity for all groups considered, with the Etruscans being part of the genealogy. Moreover, the posterior distributions of the parameters support very small female effective population sizes. CONCLUSIONS The observed signals of long-term genetic continuity and isolation are in contrast with the history of the region, conquered several times (Etruscans, Romans, Lombards, and French). While the Etruscans appear as a local population, intermediate between the prehistoric and the other samples, we suggest that the other conquerors-arriving from far-had a consistent social or sex bias, hence only marginally affecting the maternal lineages. At the same time, our results show that long-term genealogical continuity is not necessarily linked to geographical isolation.

Tai-Kadai (TK) is one of the major language families in Mainland Southeast Asia (MSEA), with a concentration in the area of Thailand and Laos. Our previous study of 1,234 mtDNA genome sequences supported a demic diffusion scenario in the spread of TK languages from southern China to Laos as well as northern and northeastern Thailand. Here we add an additional 560 mtDNA sequences from 22 groups, with a focus on the TK-speaking central Thai people and the Sino-Tibetan speaking Karen. We find extensive diversity, including 62 haplogroups not reported previously from this region. Demic diffusion is still a preferable scenario for central Thais, emphasizing the extension and expansion of TK people through MSEA, although there is also some support for an admixture model. We also tested competing models concerning the genetic relationships of groups from the major MSEA languages, and found support for an ancestral relationship of TK and Austronesian-speaking groups.

The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4–5 ka) and the Bronze/Iron Age (∼2.0–2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.

Inferring past demographic histories is crucial in population genetics, and the amount of complete genomes now available should in principle facilitate this inference. In practice, however, the available inferential methods suffer from severe limitations. Although hundreds complete genomes can be simultaneously analyzed, complex demographic processes can easily exceed computational constraints, and the procedures to evaluate the reliability of the estimates contribute to increase the computational effort. Here we present an Approximate Bayesian Computation (ABC) framework, based on the Random Forest algorithm, to infer complex past population processes using complete genomes. To do this, we propose to summarize the data by the full genomic distribution of the four mutually exclusive categories of segregating sites (FDSS), a statistic fast to compute from unphased genome data. We constructed an efficient ABC pipeline and tested how accurately it allows one to recognize the true model among models of increasing complexity, using simulated data and taking into account different sampling strategies in terms of number of individuals analyzed, number and size of the genetic loci considered. We tested the power of theFDSSto be informative about even complex evolutionary histories and compared the results with those obtained summarizing the data through the unfolded Site Frequency Spectrum, thus highlighting for both statistics the experimental conditions maximizing the inferential power. Finally, we analyzed two datasets, testing models (a) on the dispersal of anatomically modern humans out of Africa and (b) the evolutionary relationships of the three species of Orangutan inhabiting Borneo and Sumatra.

Objectives In modern humans, the significant correlation between neutral genetic loci and cranial anatomy suggests that the cranium preserves a population history signature. However, there is disagreement on whether certain parts of the cranium preserve this signature to a greater degree than other parts. It is also unclear how different quantitative measures of phenotype affect the association of genetic variation and anatomy. Here, we revisit these matters by testing the correlation of genetic distances and various phenotypic distances for ten modern human populations. Materials and Methods Geometric morphometric shape data from the crania of adult individuals (n = 224) are used to calculate phenotypic PST, Procrustes, and Mahalanobis distances. We calculate their correlation to neutral genetic distances, FST, derived from single nucleotide polymorphisms (SNPs). We subset the cranial data into landmark configurations that include the neurocranium, the face, and the temporal bone in order to evaluate whether these cranial regions are differentially correlated to neutral genetic variation. Results Our results show that PST, Mahalanobis, and Procrustes distances are correlated with FST distances to varying degrees. They indicate that overall cranial shape is significantly correlated with neutral genetic variation. Of the component parts examined, PST distances for both the temporal bone and the face have a stronger association with FST distances than the neurocranium. When controlling for population divergence time, only the whole cranium and the temporal bone have a statistically significant association with FST distances. Discussion Our results confirm that the cranium, as a whole, and the temporal bone can be used to reconstruct modern human population history.

Circadian clocks give rise to daily oscillations in behavior and physiological functions that often anticipate upcoming environmental changes generated by the Earth rotation. In model organisms a relationship exists between several genes affecting the circadian rhythms and latitude. We investigated the allele distributions at 116 000 single-nucleotide polymorphisms (SNPs) of 25 human clock and clock-related genes from the 1000Genomes Project, and at a reference data set of putatively neutral polymorphisms. The global genetic structure at the clock genes did not differ from that observed at the reference data set. We then tested for evidence of local adaptation searching for FST outliers under both an island and a hierarchical model, and for significant association between allele frequencies and environmental variables by a Bayesian approach. A total of 230 SNPs in 23 genes, or 84 SNPs in 19 genes, depending on the significance thresholds chosen, showed signs of local adaptation, whereas a maximum of 190 SNPs in 23 genes had significant covariance with one or more environmental variables. Only two SNPs from two genes (NPAS2 and AANAT) exhibit both elevated population differentiation and covariance with at least one environmental variable. We then checked whether the SNPs emerging from these analyses fall within a set of candidate SNPs associated with different chronotypes or sleep disorders. Correlation of five such SNPs with environmental variables supports a selective role of latitude or photoperiod, but certainly not a major one.

Balancing selection is an important evolutionary force that maintains genetic and phenotypic diversity in populations. Most studies in humans have focused on long-standing balancing selection, which persists over long periods of time and is generally shared across populations. But balanced polymorphisms can also promote fast adaptation, especially when the environment changes. To better understand the role of previously balanced alleles in novel adaptations, we analyzed in detail four loci as case examples of this mechanism. These loci show hallmark signatures of long-term balancing selection in African populations, but not in Eurasian populations. The disparity between populations is due to changes in allele frequencies, with intermediate frequency alleles in Africans (likely due to balancing selection) segregating instead at low- or high-derived allele frequency in Eurasia. We explicitly tested the support for different evolutionary models with an approximate Bayesian computation approach and show that the patterns in PKDREJ, SDR39U1, and ZNF473 are best explained by recent changes in selective pressure in certain populations. Specifically, we infer that alleles previously under long-term balancing selection, or alleles linked to them, were recently targeted by positive selection in Eurasian populations. Balancing selection thus likely served as a source of functional alleles that mediated subsequent adaptations to novel environments.

From the first century AD, Europe has been interested by population movements, commonly known as Barbarian migrations. Among these processes, the one involving the Longobard culture interested a vast region, but its dynamics and demographic impact remains largely unknown. Here we report 87 new complete mitochondrial sequences coming from nine early-medieval cemeteries located along the area interested by the Longobard migration (Czech Republic, Hungary and Italy). From the same areas, we sampled necropoleis characterized by cultural markers associated with the Longobard culture (LC) and coeval burials where no such markers were found, or with a chronology slightly preceding the presumed arrival of the Longobards in that region (NLC). Population genetics analysis and demographic modeling highlighted a similarity between LC individuals, as reflected by the sharing of quite rare haplogroups and by the degree of genetic resemblance between Hungarian and Italian LC necropoleis estimated via a Bayesian approach, ABC. The demographic model receiving the strongest statistical support also postulates a contact between LC and NLC communities, thus indicating a complex dynamics of admixture in medieval Europe.

Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern Italy., The Longobards invaded and conquered much of Italy after the fall of the Western Roman Empire. Here, the authors sequence and analyze ancient genomic DNA from 63 samples from two cemeteries associated with the Longobards and identify kinship networks and two distinct genetic and cultural groups in each.

The Tai–Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity across the region, with 212 different haplogroups, and significant genetic differentiation among different samples from the same ethnolinguistic group. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion. Electronic supplementary material The online version of this article (doi:10.1007/s00439-016-1742-y) contains supplementary material, which is available to authorized users.

Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where it originated, as well as its subsequent dynamics. We found that R1b-DF27 is present in frequencies ~40% in Iberian populations and up to 70% in Basques, but it drops quickly to 6–20% in France. Overall, the age of R1b-DF27 is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of W Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates; NE Iberia is the most likely place of origin of DF27. Subhaplogroup frequencies within R1b-DF27 are geographically structured, and show domains that are reminiscent of the pre-Roman Celtic/Iberian division, or of the medieval Christian kingdoms. Funding was provided by the Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grants CGL2013-44351-P, CGL2016-75389-P), by Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866, and by the Basque Government (IT-424-07). FT was supported by the ERC Advanced Grant Agreement No 295733, ‘LanGeLin’ project SI

Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times.

About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes., Financial support for the collection of the samples was provided by Vodafone Greece and the Vodafone Group Foundation. Fondo Ateneo Ricerca (FAR) grants from the University of Ferrara supported the study. P.M.D. was funded by Agence Nationale de la Recherche Demochips Grant ANR-12-BSV7-0012.

It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.

Understanding how and why humans are biologically different is indispensable to get oriented in the ever-growing body of genomic data. Here we discuss the evidence based on which we can confidently state that humans are the least genetically variable primate, both when individuals and when populations are compared, and that each individual genome can be regarded as a mosaic of fragments of different origins. Each population is somewhat different from any other population, and there are geographical patterns in that variation. These patterns clearly indicate an African origin for our species, and keep a record of the main demographic changes accompanying the peopling of the whole planet. However, only a minimal fraction of alleles, and a small fraction of combinations of alleles along the chromosome, is restricted to a single geographical region (and even less so to a single population), and diversity between members of the same population is very large. The small genomic differences between populations and the extensive allele sharing across continents explain why historical attempts to identify, once and for good, major biological groups in humans have always failed. Nevertheless, racial categorization is all but gone, especially in clinical studies. We argue that racial labels may not only obscure important differences between patients but also that they have become positively useless now that cheap and reliable methods for genotyping are making it possible to pursue the development of truly personalized medicine.

The debate on the origins of Etruscans, documented in central Italy between the eighth century BC and the first century AD, dates back to antiquity. Herodotus described them as a group of immigrants from Lydia, in Western Anatolia, whereas for Dionysius of Halicarnassus they were an indigenous population. Dionysius' view is shared by most modern archeologists, but the observation of similarities between the (modern) mitochondrial DNAs (mtDNAs) of Turks and Tuscans was interpreted as supporting an Anatolian origin of the Etruscans. However, ancient DNA evidence shows that only some isolates, and not the bulk of the modern Tuscan population, are genetically related to the Etruscans. In this study, we tested alternative models of Etruscan origins by Approximate Bayesian Computation methods, comparing levels of genetic diversity in the mtDNAs of modern and ancient populations with those obtained by millions of computer simulations. The results show that the observed genetic similarities between modern Tuscans and Anatolians cannot be attributed to an immigration wave from the East leading to the onset of the Etruscan culture in Italy. Genetic links between Tuscany and Anatolia do exist, but date back to a remote stage of prehistory, possibly but not necessarily to the spread of farmers during the Neolithic period. Am J Phys Anthropol 152:11–18, 2013. © 2013 Wiley Periodicals, Inc.

The Tai-Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1,234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity, with 212 haplogroups. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion. Surprisingly, there is significant genetic differentiation within ethnolinguistic groups, calling into question the common assumption that there is genetic homogeneity within ethnolinguistic groups.

The migration of the Tai-Kadai speaking people from southern China to northern Thailand over the past hundreds of years has revealed numerous patterns that have likely been influenced by routes, purposes and periods of time. To study the effects of different migration patterns on Tai-Kadai maternal genetic structure, mitochondrial DNA hypervariable region I sequences from the Yong and the Lue people having well-documented histories in northern Thailand were analyzed. Although the Yong and Lue people were historically close relatives who shared Xishuangbanna Dai ancestors, significant genetic differences have been observed among them. The Yong people who have been known to practice mass migration have exhibited a closer genetic affinity to their Dai ancestors than have the Lue people. Genetic heterogeneity and a sudden reduced effective population size within the Lue group is likely a direct result of the circumstances of the founder effect.

Lobón, Irene et al., The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81–1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41–0.78] with further internal separations at 0.32 Mya [0.22–0.43] and 0.16 Mya [0.17–0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics., The authors thank Luca Betti for drawing the map of the Chimpanzees distribution, Stefania Rubbini for helping with the dataset management, T.M-B is supported by ICREA ( www.icrea.cat ), EMBO YIP ( www.embo.org ) 2013, MINECO BFU2014-55090-P (FEDER), BFU2015-7116-ERC and BFU2015-6215-ERCU01 MH106874 grant, Fundacio Zoo Barcelona and Secretaria d Universitats i Recerca del Departament d Economia i Coneixement de la Generalitat de Catalunya. S.T. was supported by the Young Researcher Fellowship (5×1000 Year 2010 and Unicredit 2013 Funds) from the University of Ferrara.

Common variants in the UMOD gene encoding uromodulin, associated with risk of hypertension and CKD in the general population, increase UMOD expression and urinary excretion of uromodulin, causing salt-sensitive hypertension and renal lesions. To determine the effect of selective pressure on variant frequency, we investigated the allelic frequency of the lead UMOD variant rs4293393 in 156 human populations, in eight ancient human genomes, and in primate genomes. The T allele of rs4293393, associated with CKD risk, has high frequency in most modern populations and was the one detected in primate genomes. In contrast, we identified only the derived, C allele in Denisovan and Neanderthal genomes. The distribution of the UMOD ancestral allele did not follow the ancestral susceptibility model observed for variants associated with salt-sensitive hypertension. Instead, the global frequencies of the UMOD alleles significantly correlated with pathogen diversity (bacteria, helminths) and prevalence of antibiotic-resistant urinary tract infections (UTIs). The inverse correlation found between urinary levels of uromodulin and markers of UTIs in the general population substantiates the link between UMOD variants and protection against UTIs. These data strongly suggest that the UMOD ancestral allele, driving higher urinary excretion of uromodulin, has been kept at a high frequency because of its protective effect against UTIs.

Background Anthropological and genetic data agree in indicating the African continent as the main place of origin for anatomically modern humans. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Oceania, and later through a northern route crossing the Levant. Results Here, we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of either hybridization with archaic human forms in Australo-Melanesia or back migration from Europe into Africa. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. Conclusions We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa Electronic supplementary material The online version of this article (doi:10.1186/s13323-015-0030-2) contains supplementary material, which is available to authorized users.

Neandertals, the archaic human form documented in Eurasia until 29,000 years ago, share no mitochondrial haplotype with modern Europeans. Whether this means that the two groups were reproduc- tively isolated is controversial, and indeed nuclear data have been interpreted as suggesting that they admixed. We explored the range of demographic parameters that may have generated the observed mitochondrial diversity, simulating 3.0 million genealogies under six models differing as for the relationships among contemporary Europeans, Neandertals, and Upper Palaeolithic Euro- pean early modern humans (EEMH), who coexisted with Neandertals for millennia. We compared by Approximate Bayesian Computations the simulation results with mito- chondrial diversity in 7 Neandertals, 3 EEMH, and 150 opportunely chosen modern Europeans. A model of genealogical continuity between EEMH and contemporary Europeans, with no Neandertal contribution, received overwhelming support from the analyses. The maximum degree of Neandertal admixture, under the model of gene flow supported by nuclear data, was estimated at 1.5%, but this model proved 20-32 times less likely than a model without any gene flow. Nuclear and mitochondrial evi- dence might be reconciled if smaller population sizes led to faster lineage sorting for mitochondrial DNA, and Nean- dertals shared a longer period of common ancestry with the non-African's than with the African's ancestors. Am J Phys Anthropol 146:242-252, 2011. V

The ancient inhabitants of a region are often regarded as ancestral, and hence genetically related, to the modern dwellers (for instance, in studies of admixture), but so far, this assumption has not been tested empirically using ancient DNA data. We studied mitochondrial DNA (mtDNA) variation in Sardinia, across a time span of 2,500 years, comparing 23 Bronze-Age (nuragic) mtDNA sequences with those of 254 modern individuals from two regions, Ogliastra (a likely genetic isolate) and Gallura, and considering the possible impact of gene flow from mainland Italy. To understand the genealogical relationships between past and present populations, we developed seven explicit demographic models; we tested whether these models can account for the levels and patterns of genetic diversity in the data and which one does it best. Extensive simulation based on a serial coalescent algorithm allowed us to compare the posterior probability of each model and estimate the relevant evolutionary (mutation and migration rates) and demographic (effective population sizes, times since population splits) parameters, by approximate Bayesian computations. We then validated the analyses by investigating how well parameters estimated from the simulated data can reproduce the observed data set. We show that a direct genealogical continuity between Bronze-Age Sardinians and the current people of Ogliastra, but not Gallura, has a much higher probability than any alternative scenarios and that genetic diversity in Gallura evolved largely independently, owing in part to gene flow from the mainland.

While South Americans are underrepresented in human genomic diversity studies, Brazil has been a classical model for population genetics studies on admixture. We present the results of the EPIGEN Brazil Initiative, the most comprehensive up-to-date genomic analysis of any Latin-American population. A population-based genome-wide analysis of 6,487 individuals was performed in the context of worldwide genomic diversity to elucidate how ancestry, kinship, and inbreeding interact in three populations with different histories from the Northeast (African ancestry: 50%), Southeast, and South (both with European ancestry >70%) of Brazil. We showed that ancestry-positive assortative mating permeated Brazilian history. We traced European ancestry in the Southeast/South to a wider European/Middle Eastern region with respect to the Northeast, where ancestry seems restricted to Iberia. By developing an approximate Bayesian computation framework, we infer more recent European immigration to the Southeast/South than to the Northeast. Also, the observed low Native-American ancestry (6–8%) was mostly introduced in different regions of Brazil soon after the European Conquest. We broadened our understanding of the African diaspora, the major destination of which was Brazil, by revealing that Brazilians display two within-Africa ancestry components: one associated with non-Bantu/western Africans (more evident in the Northeast and African Americans) and one associated with Bantu/eastern Africans (more present in the Southeast/South). Furthermore, the whole-genome analysis of 30 individuals (42-fold deep coverage) shows that continental admixture rather than local post-Columbian history is the main and complex determinant of the individual amount of deleterious genotypes.

Objectives: The notion that patterns of linguistic and biological variation may cast light on each other and on population histories dates back to Darwin's times; yet, turning this intuition into a proper research program has met with serious methodological difficulties, especially affecting language comparisons. This article takes advantage of two new tools of comparative linguis- tics: a refined list of Indo-European cognate words, and a novel method of language comparison estimating linguistic diversity from a universal inventory of grammatical poly- morphisms, and hence enabling comparison even across different families. We corroborated the method and used it to compare patterns of linguistic and genomic variation in Europe. Materials and Methods: Two sets of linguistic dis- tances, lexical and syntactic, were inferred from these data and compared with measures of geographic and genomic distance through a series of matrix correlation tests. Lin- guistic and genomic trees were also estimated and com- pared. A method (Treemix) was used to infer migration episodes after the main population splits. Results: We observed significant correlations between genomic and lin- guistic diversity, the latter inferred from data on both Indo-European and non-Indo-European languages. Con- trary to previous observations, on the European scale, lan- guage proved a better predictor of genomic differences than geography. Inferred episodes of genetic admixture fol- lowing the main population splits found convincing corre- lates also in the linguistic realm. Discussion: These results pave the ground for previously unfeasible cross- disciplinary analyses at the worldwide scale, encompassing populations of distant language families. Am J Phys Anthropol 000:000-000, 2015. V C 2015 Wiley Periodicals, Inc.

Vai, Stefania et al., In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration., This work was supported by the Italian Ministry for Universities and Research (MIUR), PRIN 2012 funds to DC, AA, AT and GB, FIRB funds “Futuro in Ricerca” 2008 (RBFR08U07M) and 2012 (RBFR126B8I) to AA, AO and ER; Compagnia di San Paolo, Turin to DC; the Anneliese Maier Research Award of the Alexander von Humboldt Foundation and the German Federal Ministry for Education and Research to PG; FEDER and Spanish Government grant BFU2012-34157 to CLF; European Research Council (ERC Advanced Grant No. 295733 “LanGeLin”) to GB.

Objective: Estimating the effective population size (Ne) is crucial to understanding how populations evolved, expanded or shrunk. One possible approach is to compare DNA diversity, so as to obtain an average Ne over many past generations; however as the population sizes change over time, another possibility is to describe this change. Linkage Disequilibrium (LD) patterns contain information about these changes, and, whenever a large number of densely linked markers are available, can be used to monitor fluctuating population size through time. Here, we present a new R package, NeON that has been designed to explore population’s LD patterns to reconstruct two key parameters of human evolution: the effective population size and the divergence time between populations. Methods: NeON starts with binary or pairwise-LD PLINK files, and allows (a) to assign a genetic map position using HapMap (NCBI release 36 or 37) (b) to calculate the effective population size over time exploiting the relationship between Ne and the average squared correlation coefficient of LD (r2LD) within predefined recombination distance categories, and (c) to calculate the confidence interval about Ne based on the observed variation of the estimator across chromosomes; the outputs of the functions are both numerical and graphical. This package also offers the possibility to estimate the divergence time between populations given the Ne values calculated from the within-population LD data and a matrix of between-populations FST. These routines can be adapted to any species whenever genetic map positions are available. Results and Conclusion: The functions contained in the R package NeON provide reliable estimates of effective population sizes of human chromosomes from LD patterns of genome-wide SNPs data, as it is shown here for the populations contained in the CEPH panel. The NeON package enables to accommodate variable numbers of individuals, populations and genetic markers, allowing analyzing those using standard personal computers.

Lari, Martina et al., In 1993, a fossil hominin skeleton was discovered in the karst caves of Lamalunga, near Altamura, in southern Italy. Despite the fact that this specimen represents one of the most extraordinary hominin specimens ever found in Europe, for the last two decades our knowledge of it has been based purely on the documented on-site observations. Recently, the retrieval from the cave of a fragment of bone (part of the right scapula) allowed the first dating of the individual, the quantitative analysis of a diagnostic morphological feature, and a preliminary paleogenetic characterization of this hominin skeleton from Altamura. Overall, the results concur in indicating that it belongs to the hypodigm of Homo neanderthalensis, with some phenetic peculiarities that appear consistent with a chronology ranging from 172 ± 15 ka to 130.1 ± 1.9 ka. Thus, the skeleton from Altamura represents the most ancient Neanderthal from which endogenous DNA has ever been extracted., This study was supported in part by the Italian Ministry of Universities (MIUR), projects PRIN 2008 (2008TE2B8S_002) and PRIN 2010-2011 (2010EL8TXP_003), attributed to GB and DC. The paleoanthropological and morphometric parts of this research were supported by resources from the Sapienza University of Rome (GM). CLF is supported by a BFU2012-34157 grant from the MINECO of Spain. ER is funded by RBFR126B8I_003 e RBFR08U07M_003 grants from Italian MIUR.

The Kra-Dai linguistic family includes Thai and Lao as well as a great number of languages spoken by ethnic minorities in Southeast Asia. In Thailand, a dozen of other Kra-Dai languages are spoken in addition to Thai, the national language. The genetic structure of the Kra-Dai-speaking populations in Thailand has been studied extensively using uniparentally inherited markers. To extend this line of genetic investigation, this study used 15 autosomal microsatellites of 500 individuals from 11 populations, belonging to nine Kra-Dai ethnicities, namely, the Kaleung, Phu Thai, Saek, Nyo, Lao Isan, Yuan, Black Tai, Phuan and Lue. These ethnolinguistic groups are dispersed in three different geographic regions of Thailand, that is, Northern, Northeastern and Central. The results show a very low average of pairwised F(st) (0.0099), as well as no population substructure based on STRUCTURE analysis, indicating genetic homogeneity within the Kra-Dai-speaking group, possibly owing to shared linguistic ancestry. The Mantel test, an analysis of molecular variance, and the approximate Bayesian computation procedure employed to evaluate potential factors for driving genetic diversity revealed that language is the predominant factor affecting genetic variations, whereas geography is not. The result of distance-based clustering analyses and spatial analysis of molecular variance revealed genetic distinctions of some populations, reflecting the effects of genetic drift and gene flow on allele frequency within populations, in concordance with the result of R-matrix regression. The genetic and linguistic affiliations of the contemporary Kra-Dai-speaking groups are consistent with each other despite certain deviation due to various evolutionary factors that may have occurred during their migrations and resettlements.

The aim of this study is to analyse different models describing demographic scenarios of Atlantic Bluefin Tuna in the Mediterranean Sea using an ABC approach to model the complex dynamics of this pelagic fish. Indeed, in spite of recent progress due to genetic surveys and intensive electronic tagging experiments, its spatial dynamics are still partially unknown. These complex dynamics are difficult to explore with classical population genetics tools (likelihood-based or Bayesian methods) because of the lack of flexibility required to describe these scenarios. Moreover in a recent study (Riccioni et al. 2010 ) we could not ascertain thoroughly the presence of signals of bottleneck in the Mediterranean sea as the results are not fully coherent and each subpopulation shows its own demographic history. In reason of these difficulties we propose to determine if these results describe the real ecological and demographic history of ABFT using ABC to test different scenarios taking into account the colonization of the Mediterranean sea (~ 12000 ya, Alvarado Bremer et al. 2005). Indeed Pleistocene glaciations may have limited inter-oceanic gene flow and reproduction of Atlantic bluefin tuna. Oceanographic studies suggest that temperatures in the Mediterranean during the LGM most likely prevented bluefin tuna reproduction (sea surface temperature lower than 24°C). Therefore we can hypothesize a more recent re-colonization of the Mediterranean sea by ABFT during the Holocene. The small scale structuring detected in the Mediterranean sea suggest a possible split into several partially independent subpopulations in this basin . This kind of complex scenario can be compared to alternative ones with ABC enabling the identification of the model that better reproduces the current genetic diversity.

Background Archaeology reports millenary cultural contacts between Peruvian Coast-Andes and the Amazon Yunga, a rainforest transitional region between Andes and Lower Amazonia. To clarify the relationships between cultural and biological evolution of these populations, in particular between Amazon Yungas and Andeans, we used DNA-sequence data, a model-based Bayesian approach and several statistical validations to infer a set of demographic parameters. Results We found that the genetic diversity of the Shimaa (an Amazon Yunga population) is a subset of that of Quechuas from Central-Andes. Using the Isolation-with-Migration population genetics model, we inferred that the Shimaa ancestors were a small subgroup that split less than 5300 years ago (after the development of complex societies) from an ancestral Andean population. After the split, the most plausible scenario compatible with our results is that the ancestors of Shimaas moved toward the Peruvian Amazon Yunga and incorporated the culture and language of some of their neighbors, but not a substantial amount of their genes. We validated our results using Approximate Bayesian Computations, posterior predictive tests and the analysis of pseudo-observed datasets. Conclusions We presented a case study in which model-based Bayesian approaches, combined with necessary statistical validations, shed light into the prehistoric demographic relationship between Andeans and a population from the Amazon Yunga. Our results offer a testable model for the peopling of this large transitional environmental region between the Andes and the Lower Amazonia. However, studies on larger samples and involving more populations of these regions are necessary to confirm if the predominant Andean biological origin of the Shimaas is the rule, and not the exception. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0174-3) contains supplementary material, which is available to authorized users.

Despite broad consensus on Africa as the main place of origin for anatomically modern humans, their dispersal pattern out of the continent continues to be intensely debated. In extant human populations, the observation of decreasing genetic and phenotypic diversity at increasing distances from sub-Saharan Africa has been interpreted as evidence for a single dispersal, accompanied by a series of founder effects. In such a scenario, modern human genetic and phenotypic variation was primarily generated through successive population bottlenecks and drift during a rapid worldwide expansion out of Africa in the Late Pleistocene. However, recent genetic studies, as well as accumulating archaeological and paleoanthropological evidence, challenge this parsimonious model. They suggest instead a “southern route” dispersal into Asia as early as the late Middle Pleistocene, followed by a separate dispersal into northern Eurasia. Here we test these competing out-of-Africa scenarios by modeling hypothetical geographical migration routes and assessing their correlation with neutral population differentiation, as measured by genetic polymorphisms and cranial shape variables of modern human populations from Africa and Asia. We show that both lines of evidence support a multiple-dispersals model in which Australo-Melanesian populations are relatively isolated descendants of an early dispersal, whereas other Asian populations are descended from, or highly admixed with, members of a subsequent migration event.

The Etruscan culture is documented in Etruria, Central Italy, from the 8(th) to the 1(st) century BC. For more than 2,000 years there has been disagreement on the Etruscans' biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans' and modern populations in the same genealogy. We extracted and typed the hypervariable region of mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals from the Mediterranean basin. Comparing ancient (30 Etruscans, 27 Medieval individuals) and modern DNA sequences (370 Tuscans), with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the current inhabitants of Casentino and Volterra, but not to the general contemporary population of the former Etruscan homeland. By further considering two Anatolian samples (35 and 123 individuals) we could estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, and not as an immediate consequence of immigration from the Eastern Mediterranean shores.

There is general agreement among scientists about a recent (less than 200,000 yrs ago) African origin of anatomically modern humans, whereas there is still uncertainty about whether, and to what extent, they admixed with archaic populations, which thus may have contributed to the modern populations' gene pools. Data on cranial morphology have been interpreted as suggesting that, before the main expansion from Africa through the Near East, anatomically modern humans may also have taken a Southern route from the Horn of Africa through the Arabian peninsula to India, Melanesia and Australia, about 100,000 yrs ago. This view was recently supported by archaeological findings demonstrating human presence in Eastern Arabia >90,000 yrs ago. In this study we analyzed genetic variation at 111,197 nuclear SNPs in nine populations (Kurumba, Chenchu, Kamsali, Madiga, Mala, Irula, Dalit, Chinese, Japanese), chosen because their genealogical relationships are expected to differ under the alternative models of expansion (single vs. multiple dispersals). We calculated correlations between genomic distances, and geographic distances estimated under the alternative assumptions of a single dispersal, or multiple dispersals, and found a significantly stronger association for the multiple dispersal model. If confirmed, this result would cast doubts on the possibility that some non-African populations (i.e., those whose ancestors expanded through the Southern route) may have had any contacts with Neandertals.

Tuscany was home to the Etruscan culture, in the first millennium ad and is one of the few areas of Europe for which the genealogical relationships between past and present inhabitants have been thoroughly investigated at the genetic level. Analyses of deoxyribonucleic acid show that the contemporary Tuscans have affinities with people from the Near East but share very few mitochondrial haplotypes with the local Iron-age population, that is, the Etruscans. These results do not imply that the Etruscans got extinct, but certainly that they cannot be regarded as ancestral to most modern people of Tuscany. By contrast, there is evidence of genealogical continuity between Medieval and current times, which suggests that the main demographic change(s) occurred in previous centuries. Key Concepts: Comparison of DNAs in ancient and modern individuals provides evidence about their genealogical relationships. Modern methods to infer genealogical relationships from DNA data are based on extensive computer simulations. The available evidence demonstrates that current populations are not necessarily descended from pre-historic ancestors who dwelt in the same places, although there are a few cases of genealogical continuity across the past 2500 years. Genetic variation in modern and ancient Tuscany shows that the Etruscans cannot be regarded as the direct ancestors of the bulk of the contemporary population. It also suggests that one or more immigration processes, probably occurring in the first millennium ad, have reshaped the population structure. Keywords: population genetics; demography; ancient DNA; mitochondrial DNA; Etruscans

Populations of anatomically archaic (Neandertal) and early modern (Cro-Magnoid) humans are jointly documented in the European fossil record, in the period between 40 000 and 25 000 years BP, but the large differences between their cultures, morphologies and DNAs suggest that the two groups were not close relatives. However, it is still unclear whether any genealogical continuity between them can be ruled out. Here, we simulated a broad range of demographic scenarios by means of a serial coalescence algorithm in which Neandertals, Cro-Magnoids and modern Europeans were either part of the same mitochondrial genealogy or of two separate genealogies. Mutation rates, population sizes, population structure and demographic growth rates varied across simulations. All models in which anatomically modern (that is, Cro-Magnoid and current) Europeans belong to a distinct genealogy performed better than any model in which the three groups were assigned to the same mitochondrial genealogy. The maximum admissible level of gene flow between Neandertals and the ancestors of current Europeans is 0.001% per generation, one order of magnitude lower than estimated in previous studies not considering genetic data on Cro-Magnoid people.