Last hunter-gatherers and first farmers of Europe

Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds

During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.

Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros

We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).

Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution

BACKGROUND

Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations' survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations.

RESULTS

Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations.

CONCLUSIONS

We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations - like that ascribed to a viral epidemic - exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans' peopling history. We thus propose a model where chimpanzees' MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.

The Pastoral Origin of Semiotically Functional Tonal Organization of Music

This paper presents a new line of inquiry into when and how music as a semiotic system was born. Eleven principal expressive aspects of music each contains specific structural patterns whose configuration signifies a certain affective state. This distinguishes the tonal organization of music from the phonetic and prosodic organization of natural languages and animal communication. The question of music’s origin can therefore be answered by establishing the point in human history at which all eleven expressive aspects might have been abstracted from the instinct-driven primate calls and used to express human psycho-emotional states. Etic analysis of acoustic parameters is the prime means of cross-examination of the typical patterns of expression of the basic emotions in human music versus animal vocal communication. A new method of such analysis is proposed here. Formation of such expressive aspects as meter, tempo, melodic intervals, and articulation can be explained by the influence of bipedal locomotion, breathing cycle, and heartbeat, long before Homo sapiens. However, two aspects, rhythm and melodic contour, most crucial for music as we know it, lack proxies in the Paleolithic lifestyle. The available ethnographic and developmental data leads one to believe that rhythmic and directional patterns of melody became involved in conveying emotion-related information in the process of frequent switching from one call-type to another within the limited repertory of calls. Such calls are usually adopted for the ongoing caretaking of human youngsters and domestic animals. The efficacy of rhythm and pitch contour in affective communication must have been spontaneously discovered in new important cultural activities. The most likely scenario for music to have become fully semiotically functional and to have spread wide enough to avoid extinctions is the formation of cross-specific communication between humans and domesticated animals during the Neolithic demographic explosion and the subsequent cultural revolution. Changes in distance during such communication must have promoted the integration between different expressive aspects and generated the basic musical grammar. The model of such communication can be found in the surviving tradition of Scandinavian pastoral music - kulning. This article discusses the most likely ways in which such music evolved.

Early evidence of sheep lambing de-seasoning in the Western Mediterranean in the sixth millennium BCE

Today, sheep farmers in the Western Mediterranean de-season their ewes to achieve autumnal births. This strategy contrasts sharply with spring lambing further north, and provides benefits in terms of out-of-season availability of animal products. These competences are closely linked to specific sheep physiology and favorable Western Mediterranean climatic conditions. It is not known exactly how far back in the past the ability to de-season Mediterranean sheep breeds extends. This study shows that this practice existed seven millennia ago in Southern France, at an early stage of the major agricultural expansion of the Neolithic into the Western Mediterranean. To achieve this reproductive management regime, three prerequisites were required: (i) the ability of sheep to give birth in autumn, constituting early evidence for the genetic selection of specimens with prolonged reproductive fertility; (ii) intentional management of female and male interactions within the herd, which would have required good knowledge of the timing of the fertility cycle in ewes, and; (iii) adequate pasture resources to support lactation in the autumn, possibly favored by autumnal rains, substantiating previous paleoclimatological data for the existence of a Mediterranean-type precipitation regime at that time. Moreover, we also show that winter foddering of sheep occurred, using forest resources, and that this maintained good body weights for spring mating. These findings add pivotal information about shepherding practices and the socio-economic abilities of Early Neolithic communities, which allowed for the extension of their areas of influence from the Eastern Mediterranean area to the West during the Early Neolithic agricultural expansion in Europe.

Bone spoons for prehistoric babies: Detection of human teeth marks on the Neolithic artefacts from the site Grad-Starčevo (Serbia)

Around 8000 years ago, throughout the Neolithic world a new type of artefact appeared, small spoons masterly made from cattle bone, usually interpreted as tools, due to their intensive traces of use. Contrary to those interpretations, the small dimensions of spoons and presence of intensive traces of use led us to the assumption that they were used for feeding babies. In order to test that assumption we compared 2230 marks on three spoons from the Neolithic site of Grad-Starčevo in Serbia (5800-5450 cal BC) with 3151 primary teeth marks produced experimentally. This study has shown that some of the marks on spoons were made by primary teeth, which indicate their usage in feeding babies. The production of a new type of artefact to feed babies is probably related to the appearance of a new type of weaning food, and the abundance of spoons indicates that new baby gruels became an important innovation in prehistoric baby-care.

Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds

Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; n = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; n = 16, 11, 5, 5, 2, 13), and their ancestral species (Capra aegagrus; n = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for Salmonella infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes (Salmonella infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of Capra hircus.

New world goat populations are a genetically diverse reservoir for future use

Western hemisphere goats have European, African and Central Asian origins, and some local or rare breeds are reported to be adapted to their environments and economically important. By-in-large these genetic resources have not been quantified. Using 50 K SNP genotypes of 244 animals from 12 goat populations in United States, Costa Rica, Brazil and Argentina, we evaluated the genetic diversity, population structure and selective sweeps documenting goat migration to the "New World". Our findings suggest the concept of breed, particularly among "locally adapted" breeds, is not a meaningful way to characterize goat populations. The USA Spanish goats were found to be an important genetic reservoir, sharing genomic composition with the wild ancestor and with specialized breeds (e.g. Angora, Lamancha and Saanen). Results suggest goats in the Americas have substantial genetic diversity to use in selection and promote environmental adaptation or product driven specialization. These findings highlight the importance of maintaining goat conservation programs and suggest an awaiting reservoir of genetic diversity for breeding and research while simultaneously discarding concerns about breed designations.

Pioneer farming in southeast Europe during the early sixth millennium BC: Climate-related adaptations in the exploitation of plants and animals

The Old World farming system arose in the semi-arid Mediterranean environments of southwest Asia. Pioneer farmers settling the interior of the Balkans by the early sixth millennium BC were among the first to introduce southwest Asian-style cultivation and herding into areas with increasingly continental temperate conditions. Previous research has shown that the bioarchaeological assemblages from early farming sites in southeast Europe vary in their proportions of plant and animal taxa, but the relationship between taxonomic variation and climate has remained poorly understood. To uncover associations between multiple species and environmental factors simultaneously, we explored a dataset including altitude, five bioclimatic and 30 bioarchaeological variables (plant and animal taxa) for 57 of the earliest farming sites in southeast Europe using Canonical Correspondence Analysis (CCA). An extension of correspondence analysis, CCA is widely used in applied ecology to answer similar questions of species-environment relationships, but has not been previously applied in prehistoric archaeology to explore taxonomic and climatic variables in conjunction. The analyses reveal that the changes in plant and animal exploitation which occurred with the northward dispersal of farmers, crops and livestock correlate with south-north climate gradients, and emphasize the importance of adaptations in the animal domain for the initial establishment of farming beyond the Mediterranean areas.

Animal Board Invited Review: Sheep birth distribution in past herds: a review for prehistoric Europe (6th to 3rd millennia BC)

In temperate latitudes sheep have a seasonal reproductive behaviour, which imposes strong constraints on husbandry in terms of work organization and availability of animal products. During the last 50 years, researchers have focused on understanding the mechanisms driving small ruminants' reproduction cycles and finding ways to control them. This characteristic is inherited from their wild ancestor. However, the history of its evolution over the 10 millennia that separates present day European sheep from their Near Eastern ancestors' remains to be written. This perspective echoes archaeologists' current attempts at reconstructing ancient pastoral societies' socio-economical organization. Information related to birth seasonality may be retrieved directly from archaeological sheep teeth. The methodology consists of reconstructing the seasonal cycle record in sheep molars, through sequential analysis of the stable oxygen isotope composition (δ 18O) of enamel. Because the timing of tooth development is fixed within a species, inter-individual variability in this parameter reflects birth seasonality. A review of the data obtained from 10 European archaeological sites dated from the 6th to the 3rd millennia BC is provided. The results demonstrate a restricted breeding season for sheep: births occurred over a period of 3 to 4 months, from late winter to early summer at latitudes 43°N to 48°N, while a later onset was observed at a higher latitude (59°N). All conclusions concurred with currently held expectations based on present day sheep physiology, which, aside from the historical significance, contributes to the reinforcing of the methodological basis of the approach. Further study in this area will permit regional variability attributable to technical choices, within global schemes, to be fully reported.

Amy2B copy number variation reveals starch diet adaptations in ancient European dogs

Extant dog and wolf DNA indicates that dog domestication was accompanied by the selection of a series of duplications on the Amy2B gene coding for pancreatic amylase. In this study, we used a palaeogenetic approach to investigate the timing and expansion of the Amy2B gene in the ancient dog populations of Western and Eastern Europe and Southwest Asia. Quantitative polymerase chain reaction was used to estimate the copy numbers of this gene for 13 ancient dog samples, dated to between 15 000 and 4000 years before present (cal. BP). This evidenced an increase of Amy2B copies in ancient dogs from as early as the 7th millennium cal. BP in Southeastern Europe. We found that the gene expansion was not fixed across all dogs within this early farming context, with ancient dogs bearing between 2 and 20 diploid copies of the gene. The results also suggested that selection for the increased Amy2B copy number started 7000 years cal. BP, at the latest. This expansion reflects a local adaptation that allowed dogs to thrive on a starch rich diet, especially within early farming societies, and suggests a biocultural coevolution of dog genes and human culture.

Morphological change in cranial shape following the transition to agriculture across western Eurasia

The Neolithic transition brought about fundamental social, dietary and behavioural changes in human populations, which, in turn, impacted skeletal morphology. Crania are shaped through diverse genetic, ontogenetic and environmental factors, reflecting various elements of an individual’s life. To determine the transition’s effect on cranial morphology, we investigated its potential impact on the face and vault, two elements potentially responding to different influences. Three datasets from geographically distant regions (Ukraine, Iberia, and the Levant plus Anatolia) were analysed. Craniometric measurements were used to compare the morphology of pre-transition populations with that of agricultural populations. The Neolithic transition corresponds to a statistically significant increase only in cranial breadth of the Ukrainian vaults, while facial morphology shows no consistent transformations, despite expected changes related to the modification of masticatory behaviour. The broadening of Ukrainian vaults may be attributable to dietary and/or social changes. However, the lack of change observed in the other geographical regions and the lack of consistent change in facial morphology are surprising. Although the transition from foraging to farming is a process that took place repeatedly across the globe, different characteristics of transitions seem responsible for idiosyncratic responses in cranial morphology.

Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula

The Italian peninsula has long represented a natural hub for human migrations across the Mediterranean area, being involved in several prehistoric and historical population movements. Coupled with a patchy environmental landscape entailing different ecological/cultural selective pressures, this might have produced peculiar patterns of population structure and local adaptations responsible for heterogeneous genomic background of present-day Italians. To disentangle this complex scenario, genome-wide data from 780 Italian individuals were generated and set into the context of European/Mediterranean genomic diversity by comparison with genotypes from 50 populations. To maximize possibility of pinpointing functional genomic regions that have played adaptive roles during Italian natural history, our survey included also ~250,000 exomic markers and ~20,000 coding/regulatory variants with well-established clinical relevance. This enabled fine-grained dissection of Italian population structure through the identification of clusters of genetically homogeneous provinces and of genomic regions underlying their local adaptations. Description of such patterns disclosed crucial implications for understanding differential susceptibility to some inflammatory/autoimmune disorders, coronary artery disease and type 2 diabetes of diverse Italian subpopulations, suggesting the evolutionary causes that made some of them particularly exposed to the metabolic and immune challenges imposed by dietary and lifestyle shifts that involved western societies in the last centuries.

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.

Celiac disease as a model for the evolution of multifactorial disease in humans

Celiac disease (CD) is a multifactorial chronic inflammatory condition that results in injury of the mucosal lining of the small intestine upon ingestion of wheat gluten and related proteins from barley and rye. Although the exact mechanisms leading to CD are not fully understood, the genetic basis of CD has been relatively well characterized. In this review we briefly review the history of discovery, clinical presentation, pathophysiology, and current understanding of the genetics underlying CD risk. Then, we discuss what is known about the current distribution and evolutionary history of genes underlying CD risk in light of other evolutionary models of disease. Specifically, we conclude that the set of loci underlying CD risk did not cohesively evolve as a response to a single past selection event such as the development of agriculture. Rather, deterministic and stochastic evolutionary processes have both contributed to the present distribution of variation in CD risk loci. Selection has shaped some components of this network, but this selection appears to have occurred at different points in the past. Other parts of the CD risk network have likely arisen due to stochastic processes such as genetic drift.

Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania

Current evidence suggests that pigs were first domesticated in Eastern Anatolia during the ninth millennium cal BC before dispersing into Europe with Early Neolithic farmers from the beginning of the seventh millennium. Recent ancient DNA (aDNA) research also indicates the incorporation of European wild boar into domestic stock during the Neolithization process. In order to establish the timing of the arrival of domestic pigs into Europe, and to test hypotheses regarding the role European wild boar played in the domestication process, we combined a geometric morphometric analysis (allowing us to combine tooth size and shape) of 449 Romanian ancient teeth with aDNA analysis. Our results firstly substantiate claims that the first domestic pigs in Romania possessed the same mtDNA signatures found in Neolithic pigs in west and central Anatolia. Second, we identified a significant proportion of individuals with large molars whose tooth shape matched that of archaeological (likely) domestic pigs. These large ‘domestic shape’ specimens were present from the outset of the Romanian Neolithic (6100–5500 cal BC) through to later prehistory, suggesting a long history of admixture between introduced domestic pigs and local wild boar. Finally, we confirmed a turnover in mitochondrial lineages found in domestic pigs, possibly coincident with human migration into Anatolia and the Levant that occurred in later prehistory.

Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process

The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.

Vestiges of an Ancient Border in the Contemporary Genetic Diversity of North-Eastern Europe

It has previously been demonstrated that the advance of the Neolithic Revolution from the Near East through Europe was decelerated in the northernmost confines of the continent, possibly as a result of space and resource competition with lingering Mesolithic populations. Finland was among the last domains to adopt a farming lifestyle, and is characterized by substructuring in the form of a distinct genetic border dividing the northeastern and southwestern regions of the country. To explore the origins of this divergence, the geographical patterns of mitochondrial and Y-chromosomal haplogroups of Neolithic and Mesolithic ancestry were assessed in Finnish populations. The distribution of these uniparental markers revealed a northeastern bias for hunter-gatherer haplogroups, while haplogroups associated with the farming lifestyle clustered in the southwest. In addition, a correlation could be observed between more ancient mitochondrial haplogroup age and eastern concentration. These results coupled with prior archeological evidence suggest the genetic northeast/southwest division observed in contemporary Finland represents an ancient vestigial border between Mesolithic and Neolithic populations undetectable in most other regions of Europe.

The genetic prehistory of domesticated cattle from their origin to the spread across Europe

Background

Cattle domestication started in the 9^th millennium BC in Southwest Asia. Domesticated cattle were then introduced into Europe during the Neolithic transition. However, the scarcity of palaeogenetic data from the first European domesticated cattle still inhibits the accurate reconstruction of their early demography. In this study, mitochondrial DNA from 193 ancient and 597 modern domesticated cattle (Bos taurus) from sites across Europe, Western Anatolia and Iran were analysed to provide insight into the Neolithic dispersal process and the role of the local European aurochs population during cattle domestication.

Results

Using descriptive summary statistics and serial coalescent simulations paired with approximate Bayesian computation we find: (i) decreasing genetic diversity in a southeast to northwest direction, (ii) strong correlation of genetic and geographical distances, iii) an estimated effective size of the Near Eastern female founder population of 81, iv) that the expansion of cattle from the Near East and Anatolia into Europe does not appear to constitute a significant bottleneck, and that v) there is evidence for gene-flow between the Near Eastern/Anatolian and European cattle populations in the early phases of the European Neolithic, but that it is restricted after 5,000 BCE.

Conclusions

The most plausible scenario to explain these results is a single and regionally restricted domestication process of cattle in the Near East with subsequent migration into Europe during the Neolithic transition without significant maternal interbreeding with the endogenous wild stock. Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0203-2) contains supplementary material, which is available to authorized users.

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data

Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.

Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations

HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics’ analyses) recommends avoiding outdated racial classifications and population names (e.g. ‘Caucasian’) and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. ‘pan-European’). A standard ‘HLA-NET POPULATION DATA QUESTIONNAIRE’ has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in ‘HLA-NET GUIDELINES FOR REPORTING HLA TYPINGS’. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide-binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable of dealing with ambiguous data, such as the ‘gene[rate]’ computer tools to estimate frequencies, test for Hardy–Weinberg equilibrium and selective neutrality on data containing any number and kind of ambiguities. WG4 (Ethical issues) proposes to adopt thorough general principles for any HLA population study to ensure that it conforms to (inter)national legislation or recommendations/guidelines. All HLA-NET guidelines and tools are available through its website http://hla-net.eu.