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We present a geometry-based interpretation of the f -statistics framework, commonly used in population genetics to estimate phylogenetic relationships from genomic data. The focus is on the determination of the mixing coefficients in population admixture events subject to post-admixture drift. The interpretation takes advantage of the high dimension of the dataset and analyzes the problem as a dimensional reduction issue. We show that it is possible to think of the f -statistics technique as an implicit transformation of the genomic data from a phase space into a subspace where the mapped data structure is more similar to the ancestral admixture configuration. The 2-way mixing coefficient is, as a matter of fact, carried out implicitly in this subspace. In addition, we propose the admixture test to be evaluated in the subspace because the comparison with the conventional one provides an important assessment of the admixture model. The overarching geometric framework provides slightly more general formulas than the f -formalism by using a different rationale as a starting point. Explicitly addressed are 2- and 3-way admixtures. The mixture proportions are provided by suitable linear fits, in 2 or 3 dimensions, that can be easily visualized. The difficulties encountered with introgression and gene flow are also addressed. The developments and findings are illustrated with numerical simulations and real-world cases. [ABSTRACT FROM AUTHOR]

Both trio and population designs are popular study designs for identifying risk genetic variants in genome-wide association studies (GWASs). The trio design, as a family-based design, is robust to confounding due to population structure, whereas the population design is often more powerful due to larger sample sizes. Here, we propose KnockoffHybrid, a knockoff-based statistical method for hybrid analysis of both the trio and population designs. KnockoffHybrid provides a unified framework that brings together the advantages of both designs and produces powerful hybrid analysis while controlling the false discovery rate (FDR) in the presence of linkage disequilibrium and population structure. Furthermore, KnockoffHybrid has the flexibility to leverage different types of summary statistics for hybrid analyses, including expression quantitative trait loci (eQTL) and GWAS summary statistics. We demonstrate in simulations that KnockoffHybrid offers power gains over non-hybrid methods for the trio and population designs with the same number of cases while controlling the FDR with complex correlation among variants and population structure among subjects. In hybrid analyses of three trio cohorts for autism spectrum disorders (ASDs) from the Autism Speaks MSSNG, Autism Sequencing Consortium, and Autism Genome Project with GWAS summary statistics from the iPSYCH project and eQTL summary statistics from the MetaBrain project, KnockoffHybrid outperforms conventional methods by replicating several known risk genes for ASDs and identifying additional associations with variants in other genes, including the PRAME family genes involved in axon guidance and which may act as common targets for human speech/language evolution and related disorders. We introduce KnockoffHybrid, a statistical method to identify risk genetic variants for the population and trio designs built upon a recently developed knockoff framework. KnockoffHybrid controls the false discovery rate, protects against confounding due to population structure, and is more powerful than conventional methods that control the family-wise error rate. [ABSTRACT FROM AUTHOR]

The genome of an individual from an admixed population consists of segments originated from different ancestral populations. Most existing ancestry inference approaches focus on calling these segments for the extant individual. In this paper, we present a general ancestry inference approach for inferring recent ancestors from an extant genome. Given the genome of an individual from a recently admixed population, our method can estimate the proportions of the genomes of the recent ancestors of this individual that originated from some ancestral populations. The key step of our method is the inference of ancestors (called founders) right after the formation of an admixed population. The inferred founders can then be used to infer the ancestry of recent ancestors of an extant individual. Our method is implemented in a computer program called PedMix2. To the best of our knowledge, there is no existing method that can practically infer ancestors beyond grandparents from an extant individual’s genome. Results on both simulated and real data show that PedMix2 performs well in ancestry inference. [ABSTRACT FROM AUTHOR]

Chinese Tajiks are an Indo‐Iranian‐speaking population in Xinjiang, northwest China. Although the complex demographic history has been characterized, the ancestral sources and genetic admixture of Indo‐Iranian‐speaking groups in this region remain poorly understood. We here provide the genome‐wide genotyping data for over 700 000 single‐nucleotide polymorphisms (SNPs) and mtDNA multiplex sequencing data in 64 Chinese male Tajik individuals from two dialect groups, Wakhi and Selekur. We applied principal component analysis (PCA), ADMIXTURE, f‐statistics, treemix, qpWave/qpAdm, Admixture‐induced Linkage Disequilibrium for Evolutionary Relationships (ALDER), and Fst analyses to infer a fine‐scale population genetic structure and admixture history. Our results reveal that Chinese Tajiks showed the closest affinity and similar genetic admixture pattern with ancient Xinjiang populations, especially Xinjiang samples in the historical era. Chinese Tajiks also have gene flow from European and Neolithic Iran farmers‐related populations. We observed a genetic substructure in the two Tajik dialect groups. The Selekur‐speaking group who lived in the county had more gene flow from East Asians than Wakhi‐speaking people who inhabited the village. These results document the population movements contributed to the influx of diverse ancestries in the Xinjiang region. [ABSTRACT FROM AUTHOR]

Background: Obesity is a complex trait caused by a combination of genetic, environmental and lifestyle factors that contributes to the risks of numerous serious diseases. Predictive measures of body mass index (BMI) hold significant promise, with implications for the prevention and early intervention of obesity, promoting overall improvement in health. Main body: An effective BMI polygenic risk score (PRS) model can assist with the prediction and early detection of obesity at the individual level, aligning with the objectives of precision medicine in the management of obesity. However, potential health disparities may emerge among under-represented populations with a high prevalence of obesity, primarily due to the lack of genomic data available for these populations. The development of a trans-ethnic (TE) PRS for BMI necessitates collective action from the research community, and requires genomic data from diverse populations. Conclusion: The current BMI-PRS model exhibits moderate performance, which could be improved in several key areas: integrating genomic information through TE GWAS studies, including admixed populations, considering gene--environment interactions, implementing advanced machine learning techniques, and incorporating genomic-informed risk assessment (GIRA) with the inclusion of family history, environmental and lifestyle factors for the risk prediction. [ABSTRACT FROM AUTHOR]

Abstract Background Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between the diploid’s alleles. However, PSMC does not infer the admixture event. Results Here, we proposed eSMC, an extended PSMC model for admixture inference from a single source. We evaluated our model’s performance on both in silico data and real data. We simulated population admixture events at an admixture time range from 5 kya to 100 kya (5 years/generation) with population admix ratio at 1:1, 2:1, 3:1, and 4:1, respectively. The root means the square error is $$\pm 7.61$$ ± 7.61 kya for all experiments. Then we implemented our method to infer the historical admixture events in human, donkey and goat populations. The estimated admixture time for both Han and Tibetan individuals range from 60 kya to 80 kya (25 years/generation), while the estimated admixture time for the domesticated donkeys and the goats ranged from 40 kya to 60 kya (8 years/generation) and 40 kya to 100 kya (6 years/generation), respectively. The estimated admixture times were concordance to the time that domestication occurred in human history. Conclusion Our eSMC effectively infers the time of the most recent admixture event in history from a single individual’s genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC .

Ethiopia is the center of origin of sorghum (Sorghum bicolor L.). Understanding of the genetic diversity of the species is fundamental to design appropriate conservation and management strategies. The present study addressed the genetic diversity of sorghum accessions collected from major growing regions of Ethiopia. Eighty sorghum accessions representing five populations namely Amhara, Dire Dawa, Oromia, Southern Nations, Nationalities and Peoples (SNNP) and Tigray were analyzed with 11 simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) was conducted to evaluate genetic variation within and among populations. The unweighted neighbour-joining-based cluster analysis, principal components of analysis (PCoA) and structure analysis were done to elucidate clustering of populations. The polymorphic information contents (PIC) ranges from 0.50 to 0.86. A high within-populations genetic diversity was confirmed with gene diversity values ranging from 0.51 to 0.77. AMOVA revealed 93.26% of the total genetic variation within populations and 6.74% among populations. Cluster analyses did not show clear grouping of accessions according to their geographical origins, confirming gene flow (Nm = 6.65) among populations. In conclusion, the SSR markers used were polymorphic and highly informative Oromia and Amhara populations displayed genetic diversity greater than mean value of 0.67 suggesting possible target populations for breeding and conservation.

Background: While polygenic risk scores hold significant promise in estimating an individual's risk of developing a complex trait such as obesity, their application in the clinic has, to date, been limited by a lack of data from non‐European populations. As a collaboration model of the International Hundred K+ Cohorts Consortium (IHCC), we endeavored to develop a globally applicable trans‐ethnic PRS for body mass index (BMI) through this relatively new international effort. Methods: The polygenic risk score (PRS) model was developed, trained and tested at the Center for Applied Genomics (CAG) of The Children's Hospital of Philadelphia (CHOP) based on a BMI meta‐analysis from the GIANT consortium. The validated PRS models were subsequently disseminated to the participating sites. Scores were generated by each site locally on their cohorts and summary statistics returned to CAG for final analysis. Results: We show that in the absence of a well powered trans‐ethnic GWAS from which to derive marker SNPs and effect estimates for PRS, trans‐ethnic scores can be generated from European ancestry GWAS using Bayesian approaches such as LDpred, by adjusting the summary statistics using trans‐ethnic linkage disequilibrium reference panels. The ported trans‐ethnic scores outperform population specific‐PRS across all non‐European ancestry populations investigated including East Asians and three‐way admixed Brazilian cohort. Conclusions: Here we show that for a truly polygenic trait such as BMI adjusting the summary statistics of a well powered European ancestry study using trans‐ethnic LD reference results in a score that is predictive across a range of ancestries including East Asians and three‐way admixed Brazilians. [ABSTRACT FROM AUTHOR]

Cryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human‐ and ruminant‐derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and most are probably recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long‐term evolutionary consequences of these events. Our results suggest that increased globalization and close human‐animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host–parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race. [ABSTRACT FROM AUTHOR]

Population admixture results in the combinations of genetic components derived from distinct ancestral populations, which may impact diversity at the genetic, transcriptomic, and phenotypic levels, as well as postadmixture adaptive evolution. Here, we systematically investigated the genomic and transcriptomic diversity in Kazaks, Uyghurs, and Huis—three admixed populations of various Eurasian ancestries living in Xinjiang, China. All three populations showed elevated genetic diversity and closer genetic distance compared with the reference populations across the Eurasian continent. However, we also observed differentiated genomic diversity and inferred different demographic histories among the three populations. Varying ancestry proportions observed in both the global and local aspects corresponded to the population-differentiated genomic diversity, with the most representative signals observed in the genes EDAR , SULT1C4 , and SLC24A5. The varying local ancestry partly resulted from the postadmixture local adaptation, with the most significant signals observed in immunity- and metabolism-related pathways. Admixture-shaped genomic diversity further influenced the transcriptomic diversity in the admixed populations; in particular, population-specific regulatory effects were associated with immunity- and metabolism-involved genes such as MTHFR , FCER1G , SDHC , and BDH2. Furthermore, differentially expressed genes between the populations were identified, many of which could be explained by the population-specific regulatory properties, including genes related to health concerns (e.g. AHI1 between Kazak and Uyghurs [ P < 6.92 × 10−5] and CTRC between Huis and Uyghurs [ P < 2.32 × 10−4]). Our results demonstrate genetic admixture as a driving force in shaping the genomic and transcriptomic diversity of human populations. [ABSTRACT FROM AUTHOR]

Background: Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between the diploid's alleles. However, PSMC does not infer the admixture event. Results: Here, we proposed eSMC, an extended PSMC model for admixture inference from a single source. We evaluated our model's performance on both in silico data and real data. We simulated population admixture events at an admixture time range from 5 kya to 100 kya (5 years/generation) with population admix ratio at 1:1, 2:1, 3:1, and 4:1, respectively. The root means the square error is ± 7.61 kya for all experiments. Then we implemented our method to infer the historical admixture events in human, donkey and goat populations. The estimated admixture time for both Han and Tibetan individuals range from 60 kya to 80 kya (25 years/generation), while the estimated admixture time for the domesticated donkeys and the goats ranged from 40 kya to 60 kya (8 years/generation) and 40 kya to 100 kya (6 years/generation), respectively. The estimated admixture times were concordance to the time that domestication occurred in human history. Conclusion: Our eSMC effectively infers the time of the most recent admixture event in history from a single individual's genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC. [ABSTRACT FROM AUTHOR]

The Mongolian population exceeds six million and is the largest population among the Mongolic speakers in China. However, the genetic structure and admixture history of the Mongolians are still unclear due to the limited number of samples and lower coverage of single-nucleotide polymorphism (SNP). In this study, we genotyped genome-wide data of over 700,000 SNPs in 38 Mongolian individuals from Fuxin in Liaoning Province to explore the genetic structure and population history based on typical and advanced population genetic analysis methods [principal component analysis (PCA), admixture, FST, f3-statistics, f4-statistics, qpAdm/qpWave, qpGraph, ALDER, and TreeMix]. We found that Fuxin Mongolians had a close genetic relationship with Han people, northern Mongolians, other Mongolic speakers, and Tungusic speakers in East Asia. Also, we found that Neolithic millet farmers in the Yellow River Basin and West Liao River Basin and Neolithic hunter--gatherers in the Mongolian Plateau and Amur River Basin were the dominant ancestral sources, and there were additional gene flows related to Eurasian Steppe pastoralists and Neolithic Iranian farmers in the gene pool of Fuxin Mongolians. These results shed light on dynamic demographic history, complex population admixture, and multiple sources of genetic diversity in Fuxin Mongolians. [ABSTRACT FROM AUTHOR]

Abstract Background Computer simulations have been widely applied in population genetics and evolutionary studies. A great deal of effort has been made over the past two decades in developing simulation tools. However, there are not many simulation tools suitable for studying population admixture. Results We here developed a forward-time simulator, AdmixSim 2, an individual-based tool that can flexibly and efficiently simulate population genomics data under complex evolutionary scenarios. Unlike its previous version, AdmixSim 2 is based on the extended Wright-Fisher model, and it implements many common evolutionary parameters to involve gene flow, natural selection, recombination, and mutation, which allow users to freely design and simulate any complex scenario involving population admixture. AdmixSim 2 can be used to simulate data of dioecious or monoecious populations, autosomes, or sex chromosomes. To our best knowledge, there are no similar tools available for the purpose of simulation of complex population admixture. Using empirical or previously simulated genomic data as input, AdmixSim 2 provides phased haplotype data for the convenience of further admixture-related analyses such as local ancestry inference, association studies, and other applications. We here evaluate the performance of AdmixSim 2 based on simulated data and validated functions via comparative analysis of simulated data and empirical data of African American, Mexican, and Uyghur populations. Conclusions AdmixSim 2 is a flexible simulation tool expected to facilitate the study of complex population admixture in various situations.

Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g. LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g. NKAIN3), or different loci in an identical gene (e.g. TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g. DDB1/DAK) or genetic convergence driven by admixture (e.g. MTHFD1 and RAD18), new mutations (e.g. STK11), or notably purifying selection (e.g. MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples. [ABSTRACT FROM AUTHOR]

Background Chuanqing is an unrecognised ethnic group in Guizhou, southwest China. The genetic history of the Chuanqing people is hotly debated due to a lack of available genetic data. Aim To infer the genetic structure and population history of the Chuanqing people and genetic relationships of the Chuanqing with other East Asians. Subjects and methods We collected samples from 14 Chuanqing individuals from Guizhou and genotyped about 690,000 genome-wide single nucleotide polymorphisms (SNPs). We used Principal Component Analysis (PCA), ADMIXTURE analysis, and f statistics to infer the population genetic structure and admixture. Results Chuanqing people show a distinct genetic profile from indigenous Tai-Kadai and Tibeto-Burman speaking populations in southwest China, but they are genetically similar to southern Han Chinese, Miao, She and Tujia populations. The Han Chinese characteristic Y chromosomal lineages reach high frequencies in the Chuanqing. Conclusions The genetic formation of the Chuanqing people has been greatly influenced by Han Chinese related populations.

Ethiopia is the center of origin of sorghum (Sorghum bicolor L.). Understanding of the genetic diversity of the species is fundamental to design appropriate conservation and management strategies. The present study addressed the genetic diversity of sorghum accessions collected from major growing regions of Ethiopia. Eighty sorghum accessions representing five populations namely Amhara, Dire Dawa, Oromia, Southern Nations, Nationalities and Peoples (SNNP) and Tigray were analyzed with 11 simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) was conducted to evaluate genetic variation within and among populations. The unweighted neighbour-joining-based cluster analysis, principal components of analysis (PCoA) and structure analysis were done to elucidate clustering of populations. The polymorphic information contents (PIC) ranges from 0.50 to 0.86. A high within-populations genetic diversity was confirmed with gene diversity values ranging from 0.51 to 0.77. AMOVA revealed 93.26% of the total genetic variation within populations and 6.74% among populations. Cluster analyses did not show clear grouping of accessions according to their geographical origins, confirming gene flow (Nm = 6.65) among populations. In conclusion, the SSR markers used were polymorphic and highly informative Oromia and Amhara populations displayed genetic diversity greater than mean value of 0.67 suggesting possible target populations for breeding and conservation. [ABSTRACT FROM AUTHOR]

Background: Computer simulations have been widely applied in population genetics and evolutionary studies. A great deal of effort has been made over the past two decades in developing simulation tools. However, there are not many simulation tools suitable for studying population admixture. Results: We here developed a forward-time simulator, AdmixSim 2, an individual-based tool that can flexibly and efficiently simulate population genomics data under complex evolutionary scenarios. Unlike its previous version, AdmixSim 2 is based on the extended Wright-Fisher model, and it implements many common evolutionary parameters to involve gene flow, natural selection, recombination, and mutation, which allow users to freely design and simulate any complex scenario involving population admixture. AdmixSim 2 can be used to simulate data of dioecious or monoecious populations, autosomes, or sex chromosomes. To our best knowledge, there are no similar tools available for the purpose of simulation of complex population admixture. Using empirical or previously simulated genomic data as input, AdmixSim 2 provides phased haplotype data for the convenience of further admixture-related analyses such as local ancestry inference, association studies, and other applications. We here evaluate the performance of AdmixSim 2 based on simulated data and validated functions via comparative analysis of simulated data and empirical data of African American, Mexican, and Uyghur populations. Conclusions: AdmixSim 2 is a flexible simulation tool expected to facilitate the study of complex population admixture in various situations. [ABSTRACT FROM AUTHOR]

Background & objectives: Aedes aegypti is the most prominent vector for dengue virus worldwide. Accurate identification of the species and understanding its colonization pattern are essential prerequisites in vector control. Thus, the present study was aimed to genetically characterize Ae. aegypti mosquitoes collected from different regions of Sri Lanka based on mitochondrial COI gene. Methods: Thirty-three Ae. aegypti larval samples were collected from 19 districts. A 735bp region of the mitochondrial COI gene was amplified and analyzed for genetic diversity indices. Phylogenetic trees were constructed using Sri Lankan samples and also including mosquito samples reported from other parts of the world. Results: High genetic diversity was observed within the samples analysed (gene diversity: 0.949; average number of nucleotide differences: 6.371). There were 20 haplotypes presented within the 19 localities investigated. The phylogenetic tree derived two main clades. However, no distinguishable clustering pattern was observed in the phylogenetic tree except for the districts in the northern corner indicating extensive admixing among different populations. When samples from other countries were included in the phylogenetic tree, Anuradhapura, and Mannar samples were clustered together with samples from India, Venezuela, USA, Portugal and Cambodia while Rathnapura was clustered with Bolivia and France. Interpretation & conclusion: Our results suggest that Sri Lanka has undergone multiple invasions of Ae. aegypti from various parts of the world over an extensive period. Further, the mosquito control campaigns had not caused a significant effect on the Ae. aegypti populations which is existing in mutation-drift equilibrium.

Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from the ancestral nonadmixed populations is previously identified. In spite of its frequent use, some studies have indicated that ancestry estimates may not always be reliable. We simulated population data under different conditions with regard to the genetic differentiation between ancestral populations, number of loci considered, number of alleles per marker and hybridization rate, and analysed data with STRUCTURE. When reference samples were not included, the comparison of the known degree of admixture for each simulated individual and the value estimated with STRUCTURE revealed a strong underestimation of the level of introgression, classifying many admixed individuals as nonadmixed. This derives from an inaccurate estimation of the ancestral allele frequencies. When samples from the nonadmixed ancestral population were included as reference in the analyses, the bias in the estimations was reduced. The most accurate estimates were obtained when potentially admixed samples were few in relation to reference samples. Thus, whenever possible, a very large proportion of nonadmixed reference samples should be included in admixture assessments and different approaches should be combined. The misestimate of the amount of introgression can impair our understanding of the evolutionary history of species and misguide conservation efforts. [ABSTRACT FROM AUTHOR]

A detailed derivation of the f-statistics formalism is made from a geometrical framework. It is shown that the f-statistics appear when a genetic distance matrix is constrained to describe a four population phylogenetic tree. The choice of genetic metric is crucial and plays an outstanding role as regards the tree-like-ness criterion. The case of lack of treeness is interpreted in the formalism as the presence of population admixture. In this respect, four formulas are given to estimate the admixture proportions. One of them is the so-called f 4 -ratio estimate and we show that a second one is related to a known result developed in terms of the fixation index F ST . An illustrative numerical simulation of admixture proportion estimates is included. Relationships of the formalism with coalescence times and pairwise sequence differences are also provided. [ABSTRACT FROM AUTHOR]

The origin and diversification of Muslim Hui people in China via demic or simple cultural diffusion is a long-going debate. We here generated genome-wide data at nearly 700,000 single nucleotide polymorphisms (SNPs) from 45 Hui and 14 Han Chinese individuals collected from Guizhou province in southwest China. We applied principal component analysis (PCA), ADMIXTURE, f-statistics, qpWave, and qpAdm analysis to infer the population genetic structure and admixture history. Our results revealed the Guizhou Hui people have a limited amount of West Eurasian related ancestry at a proportion of 6%, but show massive genetic assimilation with indigenous southern Han Chinese and Tibetan or Tungusic/Mongolic related northern East Asians. We also detected a high frequency of North Asia or Central Asia related paternal Y-chromosome but not maternal mtDNA lineages in Guizhou Hui. Our observation supports the cultural diffusion has played a vital role in the formation of Hui people and the migration of Hui people to southwest China was probably a sex-biased male-driven process.

Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily Bos Taurus, and the cattle in southern China are primarily Bos indicus. Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When K = 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the FST approach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds.

Background: Population admixture is a common phenomenon in humans, animals, and plants, and it plays a very important role in shaping individual genetic architecture and population genetic diversity. Inference of population admixture, however, is very challenging and typically relies on in silico simulation. We are aware of the lack of a computerized tool for such a purpose. A simulator capable of generating data under various complex admixture scenarios would facilitate the study of recombination, linkage disequilibrium, ancestry tracing, and admixture dynamics in admixed populations. We described such a simulator here.Results: We developed a forward-time simulator (AdmixSim) under the standard Wright Fisher model. It can simulate the following admixed populations: (1) multiple ancestral populations; (2) multiple waves of admixture events; (3) fluctuating population size; and (4) admixtures of fluctuating proportions. Analysis of the simulated data by AdmixSim showed that our simulator can quickly and accurately generate data resembling real-world values. We included in AdmixSim all possible parameters that would allow users to modify and simulate any kind of admixture scenario easily, so it is very flexible. AdmixSim records recombination break points and traces of each chromosomal segment from different ancestral populations, with which users can easily perform further analysis and comparative studies with empirical data.Conclusions:AdmixSim facilitates the study of population admixture by providing a simulation framework with the flexible implementation of various admixture models and parameters.

Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chosen based on their central location within the subpopulation on a principal component analysis (PCA) and the degree to which they were admixed. Novel genomic variations among the different subgroups of the UAE population are reported here. Specifically, the WGS analysis identified 4,161,067–4,798,806 variants in the four individual samples, where approximately 80% were single nucleotide polymorphisms (SNPs) and 20% were insertions or deletions (indels). An average of 2.75% was found to be novel variants according to dbSNP (build 151). This is the first report of structural variants (SV) from WGS data from UAE nationals. There were 15,677–20,339 called SVs, of which around 13.5% were novel. The four samples shared 1,399,178 variants, each with distinct variants as follows: 1,085,524 (for the individual denoted as UAE S011), 1,228,559 (UAE S012), 791,072 (UAE S013), and 906,818 (UAE S014). These results show a previously unappreciated population diversity in the region. The synergy of WGS and genotype array data was demonstrated through variant annotation of the former using 2.3 million allele frequencies for the local population derived from the latter technology platform. This novel approach of combining breadth and depth of array and WGS technologies has guided the choice of population genetic representatives and provides complementary, regionalized allele frequency annotation to new genomes comprising millions of loci.

With high consanguinity rates on the Arabian Peninsula, it would not have been unexpected if the population of the United Arab Emirates (UAE) was shown to be relatively homogenous. However, this study of 1000 UAE nationals provided a contrasting perspective, one of a relatively heterogeneous population. Located at the apex of Europe, Asia, and Africa, the observed diversity could be explained by a plethora of migration patterns since the first Out-of-Africa movement. A strategy to explore the extent of genetic variation of the population of the UAE is presented. The first step involved a comprehensive population stratification study that was instructive for subsequent whole genome sequencing (WGS) of suitable representatives (which is described elsewhere). When these UAE data were compared to previous smaller studies from the region, the findings were consistent with a population that is a diverse and admixed group of people. However, rather than sharp and distinctive clusters, cluster analysis reveals low levels of stratification throughout the population. UAE emirates exhibit high within-Emirate-distance/among-Emirate distance ratios. Supervised admixture analysis showed a continuous gradient of ancestral populations, suggesting that admixture on the south eastern tip of the Arabian Peninsula occurred gradually. When visualized using a unique technique that combined admixture ratios and principal component analysis (PCA), unappreciated diversity was revealed while mitigating projection bias of conventional PCA. We observe low population stratification in the UAE in terms of homozygosity versus separation cluster coefficients. This holds for the UAE in a global context as well as for isolated cluster analysis of the Emirati birthplaces. However, the subtle clustering observed in the Emirates reflects geographic proximity and historic migration events. The analytical strategy used here highlights the complementary nature of data from genotype array and WGS for anthropological studies. Specifically, genotype array data were instructive to select representative subjects for WGS. Furthermore, from the 2.3 million allele frequencies obtained from genotype arrays, we identified 46,481 loci with allele frequencies that were significantly different with respect to other world populations. This comparison of allele frequencies facilitates variant prioritization in common diseases. In addition, these loci bear great potential as biomarkers in anthropological and forensic studies.

Abstract Background Introduced biological control agents have opportunities of population admixture through multiple introductions in the field. However, the importance of population admixture for their establishment success often remains unclear. Previous studies based on genetic markers have suggested a history of population admixture in the predatory ladybird Cryptolaemus montrouzieri Mulsant in China. Results We tested whether population admixture may lead to fitness changes under laboratory conditions. We first found no mating barrier or strong bias between two parental populations, despite their differences in genetics and phenotypes. Then, our experimental evidence supported the hypothesis that admixed populations have a higher potential of establishment success, due to their superior reproductive ability, and hunger and cold tolerance inherited from one of the parental populations. Conclusions We suggest that population admixture can be a breeding method to improve the performance of biological control agents, particularly when used in a classical biological control approach, but that consequences for potential invasiveness need to be considered.

The origin and diversification of Muslim Hui people in China via demic or simple cultural diffusion is a long-going debate. We here generated genome-wide data at nearly 700,000 single nucleotide polymorphisms (SNPs) from 45 Hui and 14 Han Chinese individuals collected from Guizhou province in southwest China. We applied principal component analysis (PCA), ADMIXTURE, f -statistics, qpWave , and qpAdm analysis to infer the population genetic structure and admixture history. Our results revealed the Guizhou Hui people have a limited amount of West Eurasian related ancestry at a proportion of 6%, but show massive genetic assimilation with indigenous southern Han Chinese and Tibetan or Tungusic/Mongolic related northern East Asians. We also detected a high frequency of North Asia or Central Asia related paternal Y-chromosome but not maternal mtDNA lineages in Guizhou Hui. Our observation supports the cultural diffusion has played a vital role in the formation of Hui people and the migration of Hui people to southwest China was probably a sex-biased male-driven process. [ABSTRACT FROM AUTHOR]

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Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily Bos Taurus , and the cattle in southern China are primarily Bos indicus. Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When K = 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the F ST approach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds. [ABSTRACT FROM AUTHOR]

Background: Population admixture is a common phenomenon in humans, animals, and plants, and it plays a very important role in shaping individual genetic architecture and population genetic diversity. Inference of population admixture, however, is very challenging and typically relies on in silico simulation. We are aware of the lack of a computerized tool for such a purpose. A simulator capable of generating data under various complex admixture scenarios would facilitate the study of recombination, linkage disequilibrium, ancestry tracing, and admixture dynamics in admixed populations. We described such a simulator here. Results: We developed a forward-time simulator (AdmixSim) under the standard Wright Fisher model. It can simulate the following admixed populations: (1) multiple ancestral populations; (2) multiple waves of admixture events; (3) fluctuating population size; and (4) admixtures of fluctuating proportions. Analysis of the simulated data by AdmixSim showed that our simulator can quickly and accurately generate data resembling real-world values. We included in AdmixSim all possible parameters that would allow users to modify and simulate any kind of admixture scenario easily, so it is very flexible. AdmixSim records recombination break points and traces of each chromosomal segment from different ancestral populations, with which users can easily perform further analysis and comparative studies with empirical data. Conclusions: AdmixSim facilitates the study of population admixture by providing a simulation framework with the flexible implementation of various admixture models and parameters. [ABSTRACT FROM AUTHOR]

Chuanqing is an unrecognised ethnic group in Guizhou, southwest China. The genetic history of the Chuanqing people is hotly debated due to a lack of available genetic data. To infer the genetic structure and population history of the Chuanqing people and genetic relationships of the Chuanqing with other East Asians. We collected samples from 14 Chuanqing individuals from Guizhou and genotyped about 690,000 genome-wide single nucleotide polymorphisms (SNPs). We used Principal Component Analysis (PCA), ADMIXTURE analysis, and f statistics to infer the population genetic structure and admixture. Chuanqing people show a distinct genetic profile from indigenous Tai-Kadai and Tibeto-Burman speaking populations in southwest China, but they are genetically similar to southern Han Chinese, Miao, She and Tujia populations. The Han Chinese characteristic Y chromosomal lineages reach high frequencies in the Chuanqing. The genetic formation of the Chuanqing people has been greatly influenced by Han Chinese related populations. [ABSTRACT FROM AUTHOR]

Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chosen based on their central location within the subpopulation on a principal component analysis (PCA) and the degree to which they were admixed. Novel genomic variations among the different subgroups of the UAE population are reported here. Specifically, the WGS analysis identified 4,161,067–4,798,806 variants in the four individual samples, where approximately 80% were single nucleotide polymorphisms (SNPs) and 20% were insertions or deletions (indels). An average of 2.75% was found to be novel variants according to dbSNP (build 151). This is the first report of structural variants (SV) from WGS data from UAE nationals. There were 15,677–20,339 called SVs, of which around 13.5% were novel. The four samples shared 1,399,178 variants, each with distinct variants as follows: 1,085,524 (for the individual denoted as UAE S011), 1,228,559 (UAE S012), 791,072 (UAE S013), and 906,818 (UAE S014). These results show a previously unappreciated population diversity in the region. The synergy of WGS and genotype array data was demonstrated through variant annotation of the former using 2.3 million allele frequencies for the local population derived from the latter technology platform. This novel approach of combining breadth and depth of array and WGS technologies has guided the choice of population genetic representatives and provides complementary, regionalized allele frequency annotation to new genomes comprising millions of loci. [ABSTRACT FROM AUTHOR]

We used microsatellite loci to understand the current population genetics of Japanese harbor seals, and found that they were subdivided into two distinct populations, one in Erimo and the other in eastern Hokkaido, despite being only 150 km apart and having no obvious geographical boundaries between them. Strong population subdivision between the two areas may be due to the small number of haul‐out sites and population size, and that a single habitat type is used for haul‐out sites in Japan. Also, at Erimo, there are numerous rocky reefs at a single haul‐out site that stretch up to 1.3 km offshore from land, while 10 haul‐out sites in eastern Hokkaido, separated by a maximum of 30 km, are interspersed along 75 km of the coast. The direction in which the rocky reefs stretch away from land or in which the haul‐out sites are facing may be limiting the movement of Japanese harbor seals and causing strong population subdivision between Erimo and eastern Hokkaido. No recent genetic bottlenecks were detected, although the seals in Erimo and eastern Hokkaido were reported to have experienced declines in population size over the past few decades. [ABSTRACT FROM AUTHOR]

With high consanguinity rates on the Arabian Peninsula, it would not have been unexpected if the population of the United Arab Emirates (UAE) was shown to be relatively homogenous. However, this study of 1000 UAE nationals provided a contrasting perspective, one of a relatively heterogeneous population. Located at the apex of Europe, Asia, and Africa, the observed diversity could be explained by a plethora of migration patterns since the first Out-of-Africa movement. A strategy to explore the extent of genetic variation of the population of the UAE is presented. The first step involved a comprehensive population stratification study that was instructive for subsequent whole genome sequencing (WGS) of suitable representatives (which is described elsewhere). When these UAE data were compared to previous smaller studies from the region, the findings were consistent with a population that is a diverse and admixed group of people. However, rather than sharp and distinctive clusters, cluster analysis reveals low levels of stratification throughout the population. UAE emirates exhibit high within-Emirate-distance/among-Emirate distance ratios. Supervised admixture analysis showed a continuous gradient of ancestral populations, suggesting that admixture on the south eastern tip of the Arabian Peninsula occurred gradually. When visualized using a unique technique that combined admixture ratios and principal component analysis (PCA), unappreciated diversity was revealed while mitigating projection bias of conventional PCA. We observe low population stratification in the UAE in terms of homozygosity versus separation cluster coefficients. This holds for the UAE in a global context as well as for isolated cluster analysis of the Emirati birthplaces. However, the subtle clustering observed in the Emirates reflects geographic proximity and historic migration events. The analytical strategy used here highlights the complementary nature of data from genotype array and WGS for anthropological studies. Specifically, genotype array data were instructive to select representative subjects for WGS. Furthermore, from the 2.3 million allele frequencies obtained from genotype arrays, we identified 46,481 loci with allele frequencies that were significantly different with respect to other world populations. This comparison of allele frequencies facilitates variant prioritization in common diseases. In addition, these loci bear great potential as biomarkers in anthropological and forensic studies. [ABSTRACT FROM AUTHOR]

Abstract Background The distribution of mitochondrial DNA (mtDNA) lineages in Brazil is heterogeneous due to different regional colonization dynamics. Northeastern Brazil, although being an important region in terms of human imigration and ethnic admixture, has little information regarding its population mtDNA composition. Here, we determine which mitochondrial lineages contributed to the formation of the Northeastern Brazilian population. Our sample consisted of 767 individuals distributed as follows i) 550 individuals from eight Northeastern states (Piauí, Ceará, Rio Grande do Norte, Paraíba, Pernambuco, Alagoas, Sergipe, and Bahia) which were sequenced for mtDNA hypervariable segments I, II, and III; ii) 217 individuals from Alagoas and Pernambuco (previously published data). Data analysis was performed through sequence alignment and Haplogrep 2.0 haplogroup assignment tools. Furthermore, maternal ancestry distribution was contextualized and, when possible, related to historical events to better understand the biological interactions and population dynamics that occurred in this region since the beginning of colonization. Results Unexpectedly, Amerindian mitochondrial ancestry was the highest in the Northeastern region overall, followed by African, European and non-Amerindian Asian, unlike previous results for this region. Alagoas and Pernambuco states, however, showed a larger African mtDNA frequency. The Northeastern region showed an intraregional heterogeneous distribution regarding ancestral groups, in which states/mesoregions located to the north had a prevalent Amerindian ancestral frequency and those to the south had predominance of African ancestry. Moreover, results showed great diversity of European haplogroups and the presence of non-Amerindian Asian haplogroups. Conclusions Our findings are in disagreement with previous investigations that suggest African mitochondrial ancestry is the most prevalent in the Brazilian Northeast. The predominance of Amerindian lineages exemplifies the importance of indigenous women in the formation of the population, despite intense African slave entry and conflicts with European settlers. The variable distribution of ancestral groups observed in the Northeast is in accordance with historical records showing the similarities with colonization dynamics occurred in the Amazon region and the Brazilian Southeast. Moreover, the variety of European haplogroups suggests multiple origins of founding groups, specially those found in Western European populations.

Background: Spodoptera frugiperda is a destructive pest that often imposes difficult management due to its high polyphagy and rapid insecticide resistance evolution. Knowledge of species diversification, population structure, and host preference can aid efforts to manage pest populations. Here, we investigated the patterns of hybridization, genetic structure, and gene flow in S. frugiperda populations, discussing how we can apply this knowledge to insect resistance management programs in South America. Results: The corn‐strain CS‐h2 of S. frugiperda was the most frequent haplotype in all sampled populations. Spodoptera frugiperda populations are experiencing demographic expansion, and the ecoregions partially explain the genetic structure and not strains. We did not find a correlation between gene flow and susceptibility levels to flubendiamide and lufenuron insecticides, but populations with high LC50 sent a great number of migrants to all other locations, maintaining resistance alleles in the geographic range. Conclusion: High levels of population admixture, including between corn‐ and rice‐strains, were found in sampled populations. We showed that S. frugiperda immigrants will not necessarily cause an increase in LC50 upon arrival in a new location but will assure the constant presence of resistance alleles in the area. Increases in LC50 largely depend on the local pesticide management adopted in the areas. Our results indicate that pesticide resistance management must be adopted on a local or small regional scale. © 2019 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

• Large-scale ancestry-informative marker panel assembled for Ion Torrent-based massively parallel sequencing. • The first time single-site binary and multiple-allele SNPs plus microhaplotypes have been combined in a forensic test. • Extensive reference and test population samples compiled for STRUCTURE genetic cluster analysis in several hundred worldwide populations. • STRUCTURE data shows optimum differentiation of seven population groups; distinguishing Middle East and South Asian individuals efficiently. Current forensic ancestry-informative panels are limited in their ability to differentiate populations in the Asia-Pacific region. MAPlex (Multiplex for the Asia-Pacific), a massively parallel sequencing (MPS) assay, was developed to improve differentiation of East Asian, South Asian and Near Oceanian populations found in the extensive cross-continental Asian region that shows complex patterns of admixture at its margins. This study reports the development of MAPlex; the selection of SNPs in combination with microhaplotype markers; assay design considerations for reducing the lengths of microhaplotypes while preserving their ancestry-informativeness; adoption of new population-informative multiple-allele SNPs; compilation of South Asian-informative SNPs suitable for forensic AIMs panels; and the compilation of extensive reference and test population genotypes from online whole-genome-sequence data for MAPlex markers. STRUCTURE genetic clustering software was used to gauge the ability of MAPlex to differentiate a broad set of populations from South and East Asia, the West Pacific regions of Near Oceania, as well as the other globally distributed population groups. Preliminary assessment of MAPlex indicates enhanced South Asian differentiation with increased divergence between West Eurasian, South Asian and East Asian populations, compared to previous forensic SNP panels of comparable scale. In addition, MAPlex shows efficient differentiation of Middle Eastern individuals from Europeans. MAPlex is the first forensic AIM assay to combine binary and multiple-allele SNPs with microhaplotypes, adding the potential to detect and analyze mixed source forensic DNA. [ABSTRACT FROM AUTHOR]

Objectives: The Hui people are the adherents of Muslim faith and distributing throughout China. There are two contrasting hypotheses about the origin and diversification of the Hui people, namely, the demic diffusion involving the mass movement of people or simple cultural diffusion. Materials and methods: We collected 621 unrelated male individuals from 23 Hui populations all over China. We comprehensively genotyped more than 100 informative Y‐chromosomal single nucleotide polymorphisms and 17 Y‐chromosomal short tandem repeats (STRs) on those samples. Results: Co‐analyzed with published worldwide populations, our results suggest the origin of Hui people has involved massive assimilation of indigenous East Asians with about 70% in total of the paternal ancestry could be traced back to East Asia and the left 30% to various regions in West Eurasia. Discussion: The genetic structure of the extant Hui populations was primarily shaped by the indigenous East Asian populations as they contribute the majority part of the paternal lineages of Hui people. The West Eurasian admixture was probably a sex‐biased male‐driven process since we have not found such a high proportion of West Eurasian gene flow on autosomal STRs and maternal mtDNA. [ABSTRACT FROM AUTHOR]

The common wall lizard has been widely introduced across Europe and overseas. We investigated the origin of putatively introduced Podarcis muralis populations from two southern Europe localities: (i) Ljubljana (Slovenia), where uncommon phenotypes were observed near the railway tracks and (ii) the port of Vigo (Spain), where the species was recently found 150 km far from its previously known range. We compared cytochrome-b mtDNA sequences of lizards from these populations with published sequences across the native range. Our results support the allochthonous status and multiple, long-distance origins in both populations. In Ljubljana, results support two different origins, Serbia and Italy. In Vigo, at least two separate origins are inferred, from western and eastern France. Such results confirm that human-mediated transport is promoting biological invasion and lineage admixture in this species. Solid knowledge of the origin and invasion pathways, as well as population monitoring, is crucial for management strategies to be successful. [ABSTRACT FROM AUTHOR]

Abstract: Objectives: The Jing people are a recognized ethnic group in Guangxi, southwest China, who are the immigrants from Vietnam during the 16th century. They speak Vietnamese but with lots of language borrowings from Cantonese, Zhuang, and Mandarin. However, it's unclear if there is large‐scale gene flow from surrounding populations into Jing people during their language change due to the very limited genetic information of this population. Materials and Methods: We collected blood samples from 37 Jing and 3 Han Chinese individuals from Wanwei, Shanxin, and Wutou islands in Guangxi and genotyped about 600,000 genome‐wide single nucleotide polymorphisms (SNPs). We used Principal Component Analysis (PCA), ADMIXTURE analysis, f statistics, qpWave and qpAdm to infer the population genetic structure and admixture. Results: Our data revealed that the Jing people are genetically similar to the populations in southwest China and mainland Southeast Asia. But compared with Vietnamese, they show significant evidence of gene flow from surrounding East Asians. The admixture proportion is estimated to be around 35–42% in different Jing groups using southern Han Chinese as a proxy. The majority of the paternal lineages of Jing people are most likely from surrounding East Asians. Discussion: We conclude that the formation and language change of present‐day Jing people have involved genetic assimilation of surrounding East Asian populations. The language borrowing, in this case, is not only a cultural phenomenon but has involved demic diffusion. [ABSTRACT FROM AUTHOR]

We review contributions from the field of genomics that have helped to inform our understanding of the history and evolutionary ecology of tropical rainforest hunting and gathering behavior by humans, and discuss potential opportunities for future studies. This perspective encompasses i) the question of the antiquity of full-time tropical rainforest occupation, ii) the characterization of biological adaptations to the particular ecological challenges of this habitat, including small adult body size or the “pygmy” phenotype, and iii) the timing and nature of interactions between hunter-gatherer groups and the farming populations that migrated into interior tropical rainforest habitats following the origins of agriculture. [ABSTRACT FROM AUTHOR]

Background: The distribution of mitochondrial DNA (mtDNA) lineages in Brazil is heterogeneous due to different regional colonization dynamics. Northeastern Brazil, although being an important region in terms of human immigration and ethnic admixture, has little information regarding its population mtDNA composition. Here, we determine which mitochondrial lineages contributed to the formation of the Northeastern Brazilian population. Our sample consisted of 767 individuals distributed as follows i) 550 individuals from eight Northeastern states (Piauí, Ceará, Rio Grande do Norte, Paraíba, Pernambuco, Alagoas, Sergipe, and Bahia) which were sequenced for mtDNA hypervariable segments I, II, and III; ii) 217 individuals from Alagoas and Pernambuco (previously published data). Data analysis was performed through sequence alignment and Haplogrep 2.0 haplogroup assignment tools. Furthermore, maternal ancestry distribution was contextualized and, when possible, related to historical events to better understand the biological interactions and population dynamics that occurred in this region since the beginning of colonization. Results: Unexpectedly, Amerindian mitochondrial ancestry was the highest in the Northeastern region overall, followed by African, European and non-Amerindian Asian, unlike previous results for this region. Alagoas and Pernambuco states, however, showed a larger African mtDNA frequency. The Northeastern region showed an intraregional heterogeneous distribution regarding ancestral groups, in which states/mesoregions located to the north had a prevalent Amerindian ancestral frequency and those to the south had predominance of African ancestry. Moreover, results showed great diversity of European haplogroups and the presence of non-Amerindian Asian haplogroups. Conclusions: Our findings are in disagreement with previous investigations that suggest African mitochondrial ancestry is the most prevalent in the Brazilian Northeast. The predominance of Amerindian lineages exemplifies the importance of indigenous women in the formation of the population, despite intense African slave entry and conflicts with European settlers. The variable distribution of ancestral groups observed in the Northeast is in accordance with historical records showing the similarities with colonization dynamics occurred in the Amazon region and the Brazilian Southeast. Moreover, the variety of European haplogroups suggests multiple origins of founding groups, specially those found in Western European populations. [ABSTRACT FROM AUTHOR]

Indígenas, africanos y europeos conformaron, con aportes desiguales, la población uruguaya. Datos censales indican que a comienzos del siglo XIX el país tenía 36% de africanos y sus descendientes, mientras la cantidad de indígenas no estaba determinada; posteriormente, los censos no incluyen información que se refiera al origen, a excepción de los nacidos en el extranjero. En 1996-1997, la Encuesta de Hogares solicitó la autodeclaración de "raza", y en 2006, la de ancestría. La primera arroja que 5,9% de la población se consideraba "negra o negra y sus mezclas", y 0,4%, "indígena y sus mezclas", mientras que para la ancestría los valores ascendían a 9,1% y 4,5% respectivamente. Los datos genéticos muestran aportes genéticos de 6% africano y 10% indígena, mientras que la ancestría materna sube estos valores a 10% y 31% respectivamente. Se discuten los datos censales y genéticos en el marco de la identidad nacional.Indígenas, africanos e europeus conformaram, com contribuições desiguais, a população uruguaia. Dados censitários indicam que no inicio do século XIX o país tinha 36% de africanos e descendentes, enquanto a quantidade de indígenas não estava determinada. Posteriormente, os censos não incluem informação que se refira a origem, com exceção dos estrangeiros. Em 1996- 1997 a Pesquisa de Lares solicitou a auto-declaração de "raça", e em 2006, da ancestralidade. A primeira revela que 5,9 % da população se considerava "negra ou variáveis de mestiçagem com negros", e 0,4 %, indígena ou variáveis de mestiçagem com indígenas, enquanto que para a ancestralidade os valores subiam a 9,1 % e 4,5 % respectivamente. Os dados genéticos mostram aportes genéticos de 6% africano e 10% indígena, enquanto que a ancestralidade materna eleva estes valores a 10% e 31% respectivamente. Se discutem os dados censitários e genéticos no marco da identidade nacional.Native Americans, Africans and Europeans formed, to varying degrees, the Uruguayan population. At the beginning of the 19 th century, census data indicated that the country was comprised of 36% African or African descended inhabitants, while the number of Natives was not determined. After this, there is no available information on the origins of the population, with the exception of foreigners. In 1996-1997, a Household Survey asked Uruguayans to self-identify their "race", and in 2006, their ancestry. The first survey showed that 5.9% of the populations was "black or mixed-black" and 0.4% was Native or Native-descended, while the percentages of individuals who claimed African or Native ancestry increased to 9.1% and 4.5% respectively. Genetic data demonstrate that there is a contribution of 6% of African and 10% of Native American blood in the population, while maternal ancestry increases these values to 10% and 31% respectively. Census and genetic data are discussed in relation to national identity.

The French Paris Basin is well known as a complex cultural area of the Early/Middle Neolithic, particularly with respect to funerary practices. Gurgy “Les Noisats”, which is an important necropolis in the southern Paris basin, is a burial site (N = 128) associated with the first Neolithic groups established in that area. The understanding of the necropolis composition and organization is complicated given the substantial homogeneity of the site's spatial organization in relation to a great diversity of characterized funerary traits. The unprecedented quantity of genetic (mitochondrial DNA), osteological (sex, age), and archaeological (funerary) data obtained for the Gurgy necropolis facilitates the search for potential correlations between cultural and biological (i.e. genetic and osteological) diversity at the site level. Despite the application of the powerful geographic information system, no correlation could be detected (i) between individual maternal lineages and specific bioarchaeological profiles (ii) or between maternal lineages and spatially identified bio-archaeological clusters. Therefore, analyses were performed to test for a correlation between the maternal ancestries of the individuals (i.e., hunter-gatherer/Central European farmer and Southern European farmer ancestries) and specific funerary traits. Again, the homogeneity of the funerary treatment of all of the individuals regardless of their potential maternal ancestries is striking. Taken together, our results regarding the way in which the Gurgy necropolis functioned provide strong evidence for the acculturation of all maternal ancestries groups, at least in terms of funerary practice. In addition, the demonstration of a recurrent association of adult men and immature individuals suggests a patrilocal system, which could be consistent with the detected acculturation of women who present a hunter-gatherer ancestry. [ABSTRACT FROM AUTHOR]

There is widespread concern regarding the impacts of anthropogenic activities on connectivity among populations of plants and animals, and understanding how contemporary and historical processes shape metapopulation dynamics is crucial for setting appropriate conservation targets. We used genetic data to identify population clusters and quantify gene flow over historical and contemporary time frames in the Diamondback Terrapin ( Malaclemys terrapin). This species has a long and complicated history with humans, including commercial overharvesting and subsequent translocation events during the early twentieth century. Today, terrapins face threats from habitat loss and mortality in fisheries bycatch. To evaluate population structure and gene flow among Diamondback Terrapin populations in the Chesapeake Bay region, we sampled 617 individuals from 15 localities and screened individuals at 12 polymorphic microsatellite loci. Our goals were to demarcate metapopulation structure, quantify genetic diversity, estimate effective population sizes, and document temporal changes in gene flow. We found that terrapins in the Chesapeake Bay region harbour high levels of genetic diversity and form four populations. Effective population sizes were variable. Among most population comparisons, estimates of historical and contemporary terrapin gene flow were generally low ( m ≈ 0.01). However, we detected a substantial increase in contemporary gene flow into Chesapeake Bay from populations outside the bay, as well as between two populations within Chesapeake Bay, possibly as a consequence of translocations during the early twentieth century. Our study shows that inferences across multiple time scales are needed to evaluate population connectivity, especially as recent changes may identify threats to population persistence. [ABSTRACT FROM AUTHOR]

Deciphering the origin of invasive plant species, whether or not there have been multiple introductions, and genetic differentiations between invasive and native ranges is crucial in testing hypotheses underlying biological invasions. Here, we applied traditional population genetic analyses to unravel the phylogeographical relationships among invasive (North American) and native (North African, Mediterranean region, and Eurasian) range populations of Brassica nigra using chloroplast DNA. We sequenced chloroplast DNA intron ( trnF- trnL) for 284 individuals representing 36 native and 15 invasive range populations of B. nigra. Thirty-two haplotypes were found over the whole data set. A similarity between the invasive range and native range populations in genetic diversity combined with results from analyses of molecular variance and gene genealogies suggest that invasive B. nigra populations were introduced from multiple sources in the native range. More generally, this study adds to the growing body of data on the genetic patterns involved in biological invasions that is crucial to our understanding of the evolutionary trajectories of invasive populations. [ABSTRACT FROM AUTHOR]

The heaven tree, Ailanthus altissima (Mill.) Swingle, was intentionally introduced from China to many temperate areas globally, where it has become successfully established. Here, we investigated the patterns of genetic differentiation between introduced Japanese A. altissima populations using both plastid and nuclear microsatellite markers. Three hundred and eighty-eight trees were sampled from six planted and 12 naturalized populations. Two distinct chloroplastic haplotypes were observed, which allowed us to separate two groups of trees, H1 and H3, containing 128 and 260 trees, respectively. Nine nuclear genetic microsatellites revealed 17.7 alleles per locus on average. These data did not indicate significant isolation-by-distance. Analysis of molecular variance showed the absence of genetic differentiation between the planted and naturalized populations. In contrast, the two groups defined according to the chloroplastic haplotypes (H1 and H3) were differentiated. STRUCTURE analysis showed that, within each haplotype group, most trees were strictly assigned to one cluster, with the exception of a few (ca. 30) trees. Our results indicate that (1) geographical genetic structure was weak, with high genetic variation among populations; (2) a congruent signal was revealed by chloroplastic and nuclear markers, indicating two distinct provenances; and (3) admixture between the two lineages has occurred, but remains limited. Several other invasive plant species have already been reported to exhibit similar trends; hence, future management of A. altissima might be required in Japan. [ABSTRACT FROM AUTHOR]

Background: Uruguay exhibits one of the highest rates of breast cancer in Latin America, similar to those of developed nations, the reasons for which are not completely understood. In this study we investigated the effect that ancestral background has on breast cancer susceptibility among Uruguayan women. Methods: We carried out a case-control study of 328 (164 cases, 164 controls) women enrolled in public hospitals and private clinics across the country. We estimated ancestral proportions using a panel of nuclear and mitochondrial ancestry informative markers (AIMs) and tested their association with breast cancer risk. Results: Nuclear individual ancestry in cases was (mean ± SD) 9.8 ± 7.6% African, 13.2 ± 10.2% Native American and 77.1 ± 13.1% European, and in controls 9.1 ± 7.5% African, 14.7 ± 11.2% Native American and 76.2 ± 14.2% European. There was no evidence of a difference in nuclear or mitochondrial ancestry between cases and controls. However, European mitochondrial haplogroup H was associated with breast cancer (OR = 2.0; 95% CI 1.1, 3.5). Conclusions: We have not found evidence that overall genetic ancestry differs between breast cancer patients and controls in Uruguay but we detected an association of the disease with a European mitochondrial lineage, which warrants further investigation. [ABSTRACT FROM AUTHOR]