Patterns Of Admixture Research Articles

Genetic Diversity of Cameroon Cattle and a Putative Genomic Map for Resistance to Bovine Tuberculosis.

Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurization of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding European taurine cattle, such as Holsteins for increased resistance to bTB is feasible. The utility of such an approach is still unknown for African cattle populations. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture of cattle in Cameroon. We conducted a cross-sectional study of 2,346 slaughter cattle in Cameroon. Retropharyngeal lymph node samples were collected and cultured on Lowenstein Jensen media and the BACTEC MGIT 960 system, and M. bovis was identified using the Hain® Genotype kits. A total of 153 cattle were positive for M. bovis and were archived along with a random selection of negative samples. In this study, we genotyped archived samples from 212 cattle. Their genomic diversity was characterized using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous research on this study population have shown that Fulani cattle are more susceptible to bTB than mixed breeds. However, here we show that these apparent phenotypic differences in breeds are not reflected by clear genomic differences. At the genetic level, both the Fulani and mixed cattle show similar patterns of admixture with evidence of both taurine and indicine ancestry. There was little European taurine introgression within the studied population. Hierarchical clustering showed clusters of cattle that differed in their susceptibility to bTB. Our findings allude to bTB resistance being polygenic in nature. This study highlights the potential for genetic control of bTB in Africa and the need for further research into the genetics of bTB resistance within African cattle populations.

Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People.

The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.

High connectivity and migration potentiate the invasion of Limnoperna fortunei (Mollusca: Mytilidae) in South America

Even after almost 30 years of Limnoperna fortunei introduction into South America, it is still unclear how the source and propagules are connected. Here, we present genetic evidence of population connectivity and gene flow of L. fortunei propagules from Asia into South America, proposing the main invasion routes into South America. To achieve that we expanded the sampling effort to cover all occurrence points of L. fortunei in South America. We sequenced the mtDNA COI gene and genotyped eight microsatellite loci (ML), and we evaluated the genetic source of the recently introduced population in Sobradinho hydroelectric power plant reservoir in Northeast Brazil. Our results revealed that China is the main genetic source of propagules for the Sobradinho population. We also found COI haplotypes and ML genotypes unique to South American populations, demonstrating a bridgehead effect likely caused by local mutation, adaptation, and admixture patterns that are maintained by high levels of gene flow among them. However, two genetic barriers were also detected. We concluded that L. fortunei is a well-established invader and is still rapidly expanding in Brazil, and the Amazon hydrographic basin is under an alarming threat of invasion.

Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction

Worldwide, many mangrove species are experiencing significant population declines, including Rhizophora apiculata, which is one of the most widespread and economically important species in tropical Asia. In Malaysia, there has been an alarming decline in R. apiculata populations driven primarily by anthropogenic activities. However, the lack of genetic and demographic information on this species has hampered local efforts to conserve it. To address these gaps, we generated novel genetic information for R. apiculata, based on 1,120 samples collected from 39 natural populations in Peninsular Malaysia. We investigated its genetic diversity and genetic structure with 19 transcriptome and three nuclear microsatellite markers. Our analyses revealed a low genetic diversity (mean He: 0.352) with significant genetic differentiation (FST: 0.315) among populations of R. apiculata. Approximately two-third of the populations showed significant excess of homozygotes, indicating persistent inbreeding which might be due to the decrease in population size or fragmentation. From the cluster analyses, the populations investigated were divided into two distinct clusters, comprising the west and east coasts of Peninsular Malaysia. The western cluster was further divided into two sub-clusters with one of the sub-clusters showing strong admixture pattern that harbours high levels of genetic diversity, thus deserving high priority for conservation.

High-depth African genomes inform human migration and health.

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.

Landscape Genomics of a Widely Distributed Snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia.

Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius.

A reassessment of the diversity of green toads (Bufotes) in the circum-Aegean region.

The dynamic biogeography of glacial refugia may cause complex patterns of genetic admixture between parapatric taxa, which in turn can mislead their systematics, diversity, and distributions. We investigated this issue for green toads (Bufotes) inhabiting the circum-Aegean region, a biodiversity hotspot of the Eastern Mediterranean. A previous phylogeographic study based on mitochondrial and microsatellite loci identified the hybrid zone between the European (viridis) and Anatolian (sitibundus) lineages of B. viridis all over the Balkan Peninsula, but subsequent range-wide genomic analyses (>1000 SNPs) located this transition in Turkey, a thousand kilometers eastwards. In order to clarify the diversity and taxonomy of the circum-Aegean populations, we reconciled these conflicting findings by integrating previous data with pure sitibundus individuals. Our results confirmed that the viridis/sitibundus hybrid zone extends in Western Anatolia, but that southeastern European populations feature cytonuclear discordances and a high and structured microsatellite diversity. This remarkable situation may stem from a massive geographic displacement of the hybrid zone during the last glacial fluctuations, an underappreciated yet seemingly common feature among the herpetofauna of the region. Our study thus contributes to the rising view that mitochondrial DNA can be a poor predictor of current phylogeographic structure, hence the need for genomic data, especially for narrowly distributed taxa. Finally, the analyses unambiguously support the distinction of a micro-endemic clade of green toads unique to some Cyclades islands, for which we provide a formal taxonomic description.

Host plants and Wolbachia shape the population genetics of sympatric herbivore populations.

Changing climate and land‐use practices have the potential to bring previously isolated populations of pest insects into new sympatry. This heightens the need to better understand how differing patterns of host–plant association, and unique endosymbionts, serve to promote genetic isolation or integration. We addressed these factors in populations of potato psyllid, Bactericera cockerelli (Šulc), a generalist herbivore that vectors a bacterial pathogen (Candidatus Liberibacter solanacearum, causal pathogen of zebra chip disease) of potato (Solanum tuberosum L.). Genome‐wide SNP data revealed two major genetic clusters—psyllids collected from potato crops were genetically similar to psyllids found on a common weed, Lycium spp., but dissimilar from those found on another common non‐crop host, Solanum dulcamara L. Most psyllids found on Lycium spp. and potato represented a single mitochondrial cytochrome oxidase I (COI) haplotype that has been suggested to not be native to the region, and whose arrival may have been concurrent with zebra chip disease first emerging. The putatively introduced COI haplotype usually co‐occurred with endosymbiotic Wolbachia, while the putatively resident COI haplotype generally did not. Genetic intermediates between the two genetic populations of insects were rare, consistent with recent sympatry or reproductive isolation, although admixture patterns of apparent hybrids were consistent with introgression of genes from introduced into resident populations. Our results suggest that both host–plant associations and endosymbionts are shaping the population genetic structure of sympatric psyllid populations associated with different non‐crop hosts. It is of future interest to explicitly examine vectorial capacity of the two populations and their potential hybrids, as population structure and hybridization might alter regional vector capacity and disease outbreaks.

Y Haplogroup Diversity of the Dominican Republic: Reconstructing the Effect of the European Colonization and the Trans-Atlantic Slave Trades.

The Dominican Republic is one of the two countries on the Hispaniola island, which is part of the Antilles. Hispaniola was affected by the European colonization and massive deportation of African slaves since the XVI century and these events heavily shaped the genetic composition of the present-day population. To shed light about the effect of the European rules, we analyzed 92 single nucleotide polymorphisms on the Y chromosome in 182 Dominican individuals from three different locations. The Dominican Y haplogroup composition was characterized by an excess of northern African/European lineages (59%), followed by the African clades (38%), whereas the Native-American lineages were rare (3%). The comparison with the mitochondrial DNA variability, dominated by African clades, revealed a sex-biased admixture pattern, in line with the colonial society dominated by European men. When other Caribbean and non-Caribbean former colonies were also considered, we noted a difference between territories under a Spanish rule (like the Dominican Republic) and British/French rule, with the former characterized by an excess of European Y lineages reflecting the more permissive Iberian legislation about mixed people and slavery. Finally, we analyzed the distribution in Africa of the Dominican lineages with a putative African origin, mainly focusing on central and western Africa, which were the main sources of African slaves. We found that most (83%) of the African lineages observed in Santo Domingo have a central African ancestry, suggesting that most of the slaves were deported from regions.

Genetic characteristics of Korean Jeju Black cattle with high density single nucleotide polymorphisms.

ObjectiveConservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula.MethodsJeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei’s genetic distance and Weir and Cockerham’s FST.ResultsOur results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was −0.076 for Jeju Black, while −0.018 to −0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo.ConclusionThis study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.

Secondary contact and genomic admixture between rhesus and long-tailed macaques in the Indochina Peninsula.

Understanding the process and consequences of hybridization is one of the major challenges in evolutionary biology. A growing body of literature has reported evidence of ancient hybridization events or natural hybrid zones in primates, including humans; however, we still have relatively limited knowledge about the pattern and history of admixture because there have been little studies that simultaneously achieved genome-scale analysis and a geographically wide sampling of wild populations. Our study applied double-digest restriction site-associated DNA sequencing to samples from the six localities in and around the provisional hybrid zone of rhesus and long-tailed macaques and evaluated population structure, phylogenetic relationships, demographic history, and geographic clines of morphology and allele frequencies. A latitudinal gradient of genetic components was observed, highlighting the transition from rhesus (north) to long-tailed macaque distribution (south) as well as the presence of one northern population of long-tailed macaques exhibiting unique genetic structure. Interspecific gene flow was estimated to have recently occurred after an isolation period, and the migration rate from rhesus to long-tailed macaques was slightly greater than in the opposite direction. Although some rhesus macaque-biased alleles have widely introgressed into long-tailed macaque populations, the inflection points of allele frequencies have been observed as concentrated around the traditionally recognized interspecific boundary where morphology discontinuously changed; this pattern was more pronounced in the X chromosome than in autosomes. Thus, due to geographic separation before secondary contact, reproductive isolation could have evolved, contributing to the maintenance of an interspecific boundary and species-specific morphological characteristics.

Genetic Consequences of the Transatlantic Slave Trade in the Americas

According to historical records of transatlantic slavery, traders forcibly deported an estimated 12.5 million people from ports along the Atlantic coastline of Africa between the 16th and 19th centuries, with global impacts reaching to the present day, more than a century and a half after slavery’s abolition. Such records have fueled a broad understanding of the forced migration from Africa to the Americas yet remain underexplored in concert with genetic data. Here, we analyzed genotype array data from 50,281 research participants, which—combined with historical shipping documents—illustrate that the current genetic landscape of the Americas is largely concordant with expectations derived from documentation of slave voyages. For instance, genetic connections between people in slave trading regions of Africa and disembarkation regions of the Americas generally mirror the proportion of individuals forcibly moved between those regions. While some discordances can be explained by additional records of deportations within the Americas, other discordances yield insights into variable survival rates and timing of arrival of enslaved people from specific regions of Africa. Furthermore, the greater contribution of African women to the gene pool compared to African men varies across the Americas, consistent with literature documenting regional differences in slavery practices. This investigation of the transatlantic slave trade, which is broad in scope in terms of both datasets and analyses, establishes genetic links between individuals in the Americas and populations across Atlantic Africa, yielding a more comprehensive understanding of the African roots of peoples of the Americas.

Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees.

Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species' present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt Calotriton asper (Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex-biased dispersal. This work highlights the importance of integrating past evolutionary processes and present-day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies already exist for this species but contain pervasive assembly errors and are highly fragmented, which limits their values. Our purpose here was to improve the assembly of the D. suzukii genome and to annotate it in a way that facilitates comparisons with D. melanogaster. For this, we generated PacBio long-read sequencing data and assembled a novel, high-quality D. suzukii genome assembly. It is one of the largest Drosophila genomes, notably because of the expansion of its repeatome. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome. As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our assembly and annotation constitute a high-quality genomic resource that can be used for both high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii.

Complex migration history is revealed by genetic diversity of tomato samples collected in Italy during the eighteenth and nineteenth centuries

Native to South America, the tomato is now grown almost worldwide. During its domestication and improvement, important selection signatures were fixed in certain agronomic and adaption traits. Such traits include fruit morphology, which became a major target for selection over the centuries. However, little is known about precisely when some mutations arose and how they spread through the germplasm. For instance, elongated fruit variants, originating both via mutations in SUN and OVATE genes, may have arisen prior to domestication or during tomato cultivation in Europe. To gain insights into the tomato admixture and selection pattern, the genome of two tomato herbarium specimens conserved in the Herbarium Porticense (PORUN) was sequenced. Comparison of the DNA of herbarium samples collected in Italy between 1750 and 1890 with that of living tomato accessions yielded insights into the history of tomato loci selection. Interestingly, the genotype of the more recent sample (LEO90), classified in 1890 as the oblungum variety, shows several private variants in loci implicated in fruit shape determination, also present also in wild tomato samples. In addition, LEO90, sampled in the nineteenth century, is genetically more distant from cultivated varieties than the SET17 genotype, collected in the eighteenth century, suggesting that elongated tomato varieties may originate from a cross between a landrace and a wild ancestor. Findings from our study have major implications for the understanding of tomato migration patterns and for the conservation of allelic diversity and loci recovery.

Reticulate evolution as a management challenge: Patterns of admixture with phylogenetic distance in endemic fishes of western North America.

Admixture in natural populations is a long‐standing management challenge, with population genomic approaches offering means for adjudication. We now more clearly understand the permeability of species boundaries and the potential of admixture for promoting adaptive evolution. These issues particularly resonate in western North America, where tectonism and aridity have fragmented and reshuffled rivers over millennia, in turn promoting reticulation among endemic fishes, a situation compounded by anthropogenic habitat modifications and non‐native introductions. The melding of historic and contemporary admixture has both confused and stymied management. We underscore this situation with a case study that quantifies basin‐wide admixture among a group of native and introduced fishes by employing double‐digest restriction site‐associated DNA (ddRAD) sequencing. Our approach: (a) quantifies the admixed history of 343 suckers (10 species of Catostomidae) across the Colorado River Basin; (b) gauges admixture within the context of phylogenetic distance and “ecological specialization”; and (c) extrapolates potential drivers of introgression across hybrid crosses that involve endemic as well as invasive species. Our study extends across an entire freshwater basin and expands previous studies more limited in scope both geographically and taxonomically. Our results detected admixture involving all 10 species, with habitat alterations not only accelerating the breakdown of reproductive isolation, but also promoting introgression. Hybridization occurred across the genus despite phylogenetic distance, whereas introgression was only detected within subgenera, implicating phylogenetic distance and/or ecological specialization as drivers of reproductive isolation. Understanding the extent of admixture and reproductive isolation across multiple species serves to disentangle their reticulate evolutionary histories and provides a broadscale perspective for basin‐wide conservation and management.

Defense Response in Brazilian Honey Bees (Apis mellifera scutellata × spp.) Is Underpinned by Complex Patterns of Admixture.

In 1957, an invasive and highly defensive honey bee began to spread across Brazil. In the previous year, Brazilian researchers hoped to produce a subtropical-adapted honey bee by crossing local commercial honey bees (of European origin) with a South African honey bee subspecies (Apis mellifera scutellata; an A-lineage honey bee subspecies). The resulting cross-African hybrid honey bees (AHBs)-escaped from their enclosure and spread through the Americas. Today, AHB is the most common honey bee from Northern Argentina to the Southern United States. AHBs are much more likely to sting nest intruders than managed European-derived honey bee colonies. Previous studies have explored how genetic variation contributes to differences in defense response between European-derived honey bee and AHB. Although this work demonstrated very strong genetic effects on defense response, they have yet to pinpoint which genes influence variation in defense response within AHBs, specifically. We quantified defense response for 116 colonies in Brazil and performed pooled sequencing on the most phenotypically divergent samples. We identified 65 loci containing 322 genes that were significantly associated with defense response. Loci were strongly associated with metabolic function, consistent with previous functional genomic analyses of this phenotype. Additionally, defense-associated loci had nonrandom and unexpected patterns of admixture. Defense response was not simply the product of more A-lineage honey bee ancestry as previously assumed, but rather an interaction between A-lineage and European alleles. Our results suggest that a combination of A-lineage and European alleles play roles in defensive behavior in AHBs.

Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers.

Simple SummaryThis study was conducted to evaluate the genetic variability of Turkish native donkey (Equus asinus) populations, using polymorphism of 17 microsatellite markers. The results revealed a highly mixed genotype of all the examined donkeys, suggesting that two different group of breeds can be distinguished from each other on the basis of microsatellite markers.This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean HO in the Turkish donkey was estimated to be 0.677, while mean HE was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (GST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The GST values for single loci ranged from −0.004 for LEX54 to 0.162 for COR082. Nei’s gene diversity index (Ht) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (ΔK) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations.

Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers.

Starting from 12,000 years ago in the Middle East, the Neolithic lifestyle spread across Europe via separate continental and Mediterranean routes. Genomes from early European farmers have shown a clear Near Eastern/Anatolian genetic affinity with limited contribution from hunter-gatherers. However, no genomic data are available from modern-day France, where both routes converged, as evidenced by a mosaic cultural pattern. Here, we present genome-wide data from 101 individuals from 12 sites covering today's France and Germany from the Mesolithic (N = 3) to the Neolithic (N = 98) (7000-3000 BCE). Using the genetic substructure observed in European hunter-gatherers, we characterize diverse patterns of admixture in different regions, consistent with both routes of expansion. Early western European farmers show a higher proportion of distinctly western hunter-gatherer ancestry compared to central/southeastern farmers. Our data highlight the complexity of the biological interactions during the Neolithic expansion by revealing major regional variations.

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago.

Indonesia is the world’s fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.