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Background: Understanding the genetic substructure of a population is essential for proper forensic genetic analysis. The Lebanese population has a high rate of endogamous and consanguineous marriages and is segregated based on religious belongings. However, no genetic population studies have been performed up to date to estimate the degree of genetic substructure and inbreeding coefficients. Methods: The present study analyzed a compendium of 23 autosomal STRs typed in 1400 individuals belonging to the seven major Lebanese religious subcommunities. Inbreeding coefficients such as F statistics were estimated. Results: Results showed a Fst (theta) value of 0.002, indicating a low genetic subdivision within the Lebanese population. Conclusion: This study aimed at assessing the genetic substructure of the Lebanese population by analyzing 1400 Lebanese citizens' samples using 23 STR markers. F statistics were computed to evaluate the degree of genetic substructure. Results showed a Fst value of 0.002, indicating a low genetic subdivision within the Lebanese population. [ABSTRACT FROM AUTHOR]

We analysed the forensic characteristics and substructure of the Handan Han population based on 36 Y-STR (short tandem repeat) and Y-SNP (single nucleotide polymorphism) markers. The two most dominant haplogroups in Handan Han, O2a2b1a1a1-F8 (17.95%) and O2a2b1a2a1a (21.51%), and their abundant downstream branches, reflected the strong expansion of the precursor of the Hans in Handan. The present results enrich the forensic database and explore the genetic relationships between Handan Han and other neighbouring and/or linguistically close populations, which suggests that the current concise overview of the Han intricate substructure remains oversimplified.

Abstract Background Understanding the genetic substructure of a population is essential for proper forensic genetic analysis. The Lebanese population has a high rate of endogamous and consanguineous marriages and is segregated based on religious belongings. However, no genetic population studies have been performed up to date to estimate the degree of genetic substructure and inbreeding coefficients. Methods The present study analyzed a compendium of 23 autosomal STRs typed in 1400 individuals belonging to the seven major Lebanese religious subcommunities. Inbreeding coefficients such as F statistics were estimated. Results Results showed a Fst (theta) value of 0.002, indicating a low genetic subdivision within the Lebanese population. Conclusion This study aimed at assessing the genetic substructure of the Lebanese population by analyzing 1400 Lebanese citizens' samples using 23 STR markers. F statistics were computed to evaluate the degree of genetic substructure. Results showed a Fst value of 0.002, indicating a low genetic subdivision within the Lebanese population.

We analysed the forensic characteristics and substructure of the Handan Han population based on 36 Y-STR (short tandem repeat) and Y-SNP (single nucleotide polymorphism) markers. The two most dominant haplogroups in Handan Han, O2a2b1a1a1-F8 (17.95%) and O2a2b1a2a1a (21.51%), and their abundant downstream branches, reflected the strong expansion of the precursor of the Hans in Handan. The present results enrich the forensic database and explore the genetic relationships between Handan Han and other neighbouring and/or linguistically close populations, which suggests that the current concise overview of the Han intricate substructure remains oversimplified. [ABSTRACT FROM AUTHOR]

Sui people, which belong to the Tai-Kadai-speaking family, remain poorly characterized due to a lack of genome-wide data. To infer the fine-scale population genetic structure and putative genetic sources of the Sui people, we genotyped 498,655 genome-wide single-nucleotide polymorphisms (SNPs) using SNP arrays in 68 Sui individuals from seven indigenous populations in Guizhou province and Guangxi Zhuang Autonomous Region in Southwest China and co-analyzed with available East Asians via a series of population genetic methods including principal component analysis (PCA), ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave, and qpAdm. Our results revealed that Guangxi and Guizhou Sui people showed a strong genetic affinity with populations from southern China and Southeast Asia, especially Tai-Kadai- and Hmong-Mien-speaking populations as well as ancient Iron Age Taiwan Hanben, Gongguan individuals supporting the hypothesis that Sui people came from southern China originally. The indigenous Tai-Kadai-related ancestry (represented by Li), Northern East Asian-related ancestry, and Hmong-Mien-related lineage contributed to the formation processes of the Sui people. We identified the genetic substructure within Sui groups: Guizhou Sui people were relatively homogeneous and possessed similar genetic profiles with neighboring Tai-Kadai-related populations, such as Maonan. While Sui people in Yizhou and Huanjiang of Guangxi might receive unique, additional gene flow from Hmong-Mien-speaking populations and Northern East Asians, respectively, after the divergence within other Sui populations. Sui people could be modeled as the admixture of ancient Yellow River Basin farmer-related ancestry (36.2–54.7%) and ancient coastal Southeast Asian-related ancestry (45.3–63.8%). We also identified the potential positive selection signals related to the disease susceptibility in Sui people via integrated haplotype score (iHS) and number of segregating sites by length (nSL) scores. These genomic findings provided new insights into the demographic history of Tai-Kadai-speaking Sui people and their interaction with neighboring populations in Southern China.

Sui people, which belong to the Tai-Kadai-speaking family, remain poorly characterized due to a lack of genome-wide data. To infer the fine-scale population genetic structure and putative genetic sources of the Sui people, we genotyped 498,655 genome-wide single-nucleotide polymorphisms (SNPs) using SNP arrays in 68 Sui individuals from seven indigenous populations in Guizhou province and Guangxi Zhuang Autonomous Region in Southwest China and co-analyzed with available East Asians via a series of population genetic methods including principal component analysis (PCA), ADMIXTURE, pairwise Fst genetic distance, f -statistics, qpWave , and qpAdm. Our results revealed that Guangxi and Guizhou Sui people showed a strong genetic affinity with populations from southern China and Southeast Asia, especially Tai-Kadai- and Hmong-Mien-speaking populations as well as ancient Iron Age Taiwan Hanben, Gongguan individuals supporting the hypothesis that Sui people came from southern China originally. The indigenous Tai-Kadai-related ancestry (represented by Li), Northern East Asian-related ancestry, and Hmong-Mien-related lineage contributed to the formation processes of the Sui people. We identified the genetic substructure within Sui groups: Guizhou Sui people were relatively homogeneous and possessed similar genetic profiles with neighboring Tai-Kadai-related populations, such as Maonan. While Sui people in Yizhou and Huanjiang of Guangxi might receive unique, additional gene flow from Hmong-Mien-speaking populations and Northern East Asians, respectively, after the divergence within other Sui populations. Sui people could be modeled as the admixture of ancient Yellow River Basin farmer-related ancestry (36.2–54.7%) and ancient coastal Southeast Asian-related ancestry (45.3–63.8%). We also identified the potential positive selection signals related to the disease susceptibility in Sui people via integrated haplotype score (iHS) and number of segregating sites by length (nSL) scores. These genomic findings provided new insights into the demographic history of Tai-Kadai-speaking Sui people and their interaction with neighboring populations in Southern China. [ABSTRACT FROM AUTHOR]

We studied HLA class I (HLA-A , -B) and class II (HLA-DRB1 , -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ'≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A / -B / -DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources. [ABSTRACT FROM AUTHOR]

The mexican backyard turkey, is a native breed in danger of extinction, at present the habit of conserving the native genetic resources of each population has been lost, trying to cross animals with commercial lines for the production of turkey meat, damaging and losing the genetic stock of native turkeys in México. The objective of this work is to carry out the genetic characterization of the mexican transfer turkey using microsatellites and to study the possible genetic structure of this population. A panel of 38 microsatellites is analyzed in 51 samples of transfer turkey, taken from different areas of the city of Veracruz, México. The main parameters of genetic diversity have been evaluated: expected and observed heterozygosity, number of alleles, F statistics and Correspondence Factor Analysis using the GENETIX software. Genetic distances between individuals (DSA) with which a dendrogram has been constructed using the POPULATIONS program are calculated. The tree is displayed with the TREEVIEW program. The genetic structure is studied with the STRUCTURE program. All microsatellites used polymorphic results, with a minimum of 2 alleles found on the MNT 264 microsatellite and a maximum of 14 alleles on the MNT274 and RHT024 markers, with an average number of alleles of 6.79. The average values of HE and HO are 0.619 and 0.620 respectively. The following F statistics show the following values in the total sample: FIS 0.128 (P <0.05), FIT 0.152 (P <0.05) and FST 0.027, (P <0.05). The characterized backyard turkey population does not have genetic substructures. [ABSTRACT FROM AUTHOR]

• A total of 650 Hui males from nine geographical regions in China were genotyped with 157 Y-SNP and 27 Y-STR markers. • High haplogroup diversity and haplotype diversity were found in Hui populations. • The high-resolution panel with Y-SNPs and Y-STRs indicated that Hui populations can be divided into three groups. • Hui populations had close relationships with East Asian populations, especially the Chinese Han population. The Hui group is the second largest ethnic minority and one of the most widespread ethnic groups in China. However, the genetic architecture of the Hui population remains largely unexplored, particularly with respect to the male-specific region of the Y chromosome. Here, we studied nine Hui populations (Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, Henan, Shandong, Sichuan, Yunnan) using 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 27 short tandem repeats (Y-STRs) to unravel their genetic substructure and forensic characteristics. A total of 650 unrelated male samples from the Hui populations were genotyped by SNaPshot®, a single base extension (SBE) assay. Finally, 95 terminal haplogroups and high haplotype diversity (0.9999) were observed in Hui populations. Frequency heat map matrices, genetic distance (F ST) and network analysis within Hui populations indicated that these nine Hui populations can be divided into three groups: Hui populations from the northwest (NWH), Hui populations from Sichuan and Shandong (SSH), and Hui populations from Yunnan (YNH). Our results suggested that we should use different databases for different Hui samples in forensic cases. Comparison with other populations that used different population genetic analysis revealed that the Hui populations had close relationships with East Asian populations, especially Chinese Han population. Overall, the high-resolution panel with Y-SNPs and Y-STRs gives new and complete insight into Hui populations, which can be used to interpret the genetic substructure of Hui populations and affect the utility of forensic databases. [ABSTRACT FROM AUTHOR]

The landscape genetics framework is typically applied to broad regions that occupy only small portions of a species' range. Rarely is the entire range of a taxon the subject of study. We examined the landscape genetic structure of the endangered Point Arena mountain beaver ( Aplodontia rufa nigra), whose isolated geographic range is found in a restricted (85 km) but heterogenous region in California. Based on its diminutive range we may predict widespread gene flow and a relatively weak role for landscape variation in defining genetic structure. We used skin, bone, tissue and noninvasively collected hair samples to describe genetic substructure and model gene flow. We examined spatial partitioning of multilocus DNA genotypes and mitochondrial DNA haplotypes. We identified 3 groups from microsatellite data, all of which had low estimates of effective population size consistent with significant tests for historical bottlenecks. We used least-cost-path analysis with the microsatellites to examine how vegetation type affects gene flow in a landscape genetics framework. Gene flow was best predicted by a model with 'Forest' as the most permeable, followed by 'Riparian'. Agricultural lands demonstrated the highest resistance. MtDNA data revealed only two haplotypes: one was represented in all 57 individuals that occurred north of the east-west flowing Garcia River. South of the river, however, both haplotypes occurred, often at the same site suggesting that the river may have affected historical patterns of genetic divergence. [ABSTRACT FROM AUTHOR]

Since Russian contact in 1741, the Aleut communities of southwestern Alaska have undergone a series of demographic upheavals stemming from forced relocations, disease epidemics, population bottlenecks, and pervasive admixture with European populations. This study investigates the impact of key historical events on the genetic structure of the Aleut population through analysis of mitochondrial and Y-chromosome DNA variation in five eastern Aleut communities. Results from HVS-I sequencing and Y-chromosome typing reveal patterns of variability that exhibit east-west geographic differentiation for the major Aleut haplogroups. This finding is underscored by SAMOVA and Monmonier analyses that identify genetic discontinuities between eastern and western Aleut populations. The majority of Aleut Y-chromosomes were characterized to haplogroups of mostly Russian, Scandinavian and Western European origin (approximately 85%), which is in stark contrast to the 3.6% of Aleut mtDNA lineages identified as non-Native American, and thus indicating a large degree of asymmetrical gene flow between European men and Aleut women. Overall, this study identifies a significant relationship between geography and genetic variation in the Aleut population, with a distinct substructure along an east-west axis that reflects the combined effects of founder events in aggregate island communities, male-biased gene flow from European populations, and the original peopling of the Aleutian Archipelago. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the relevance and necessity to account for the effects of population substructure on association studies under a case-control design in central Europe, we analysed three samples drawn from different geographic areas of Germany. Two of the three samples, POPGEN (n = 720) and SHIP (n = 709), are from north and north-east Germany, respectively, and one sample, KORA (n = 730), is from southern Germany. Methods: Population genetic differentiation was measured by classical F-statistics for different marker sets, either consisting of genome-wide selected coding SNPs located in functional genes, or consisting of selectively neutral SNPs from ‘genomic deserts’. Quantitative estimates of the degree of stratification were performed comparing the genomic control approach [Devlin B, Roeder K: Biometrics 1999;55:997–1004], structured association [Pritchard JK, Stephens M, Donnelly P: Genetics 2000;155:945–959] and sophisticated methods like random forests [Breiman L: Machine Learning 2001;45:5–32]. Results: F-statistics showed that there exists a low genetic differentiation between the samples along a north-south gradient within Germany (FST(KORA/POPGEN): 1.7 · 10–4; FST(KORA/SHIP): 5.4 · 10–4; FST(POPGEN/SHIP): –1.3 · 10–5). Conclusion: Although the FST -values are very small, indicating a minor degree of population structure, and are too low to be detectable from methods without using prior information of subpopulation membership, such as STRUCTURE [Pritchard JK, Stephens M, Donnelly P: Genetics 2000;155:945–959], they may be a possible source for confounding due to population stratification. [ABSTRACT FROM AUTHOR]

Introgressive hybridizations have often been observed between native and introduced trouts of North America ( Oncorhynchus spp.) and Europe ( Salmo spp.), including some lineages that have been isolated for more than a million years. These observations have suggested that introgression is the expected result between introduced and indigenous conspecific salmonids. However, an examination of published information reveals a high variability in such anticipated gene flow. Many studies have noted the relative ease of translocating freshwater over anadromous salmonids, and this difference has been related to the more complex adaptations of anadromous populations (e.g., freshwater and marine residence, smoltification, juvenile and adult migration) that obstruct their translocation to conspecifically colonized areas. This contrast extends to introgressive capabilities where examples of introgression among freshwater populations predominate. Despite intensive introductions of non-native salmonids, indigenous anadromous populations commonly resist introgression. However, within major lineages, anadromous populations appear to be more susceptible to introgression. Measuring the extent and dynamics of such introgressions remains challenging because subgroups within major lineages lie on or below the threshold for detection by molecular genetic markers. These substructures appear to reflect the more rapid evolution of directional selection promoting, for instance, temporal or microgeographic divergence within a population unit defined by genetic markers. Consequently, management that assumes panmixia within a particular region based on even intensive molecular genetic analysis will inevitably erode and prevent reformation of this substructure to the detriment of the overall genetic variability and productivity. [ABSTRACT FROM AUTHOR]

China, as the largest national database within the YHRD (Y chromosome haplotype reference database), has repeatedly been a research hotspot in the field of genetics, archaeology and molecular anthropology. In the present study, 23 Y-STR loci were used to investigate genetic relationships among 29 Chinese populations (6029 individuals). Pairwise genetic distance (R st value) was calculated based on haplotype frequency distributions by the Analysis of Molecular Variance. Multidimensional scaling (MDS) and phylogenetic analysis were performed on the online tool and Mega 6.0, respectively. Tibetans (R st = 0.1601 ± 0.0421), Shuis (R st = 0.0934 ± 0.0327), Uyghurs (R st = 0.0791 ± 0.0459) and Zhuangs (R st = 0.0790 ± 0.0404) showed the high genetic distance with other populations and kept relatively isolated with other reference populations in the MDS plots and Neighbor-Joining tree. Additionally, genetic distinction among same ethnicities (Han and Hui) distributed in different administrative divisions was also explored and no significant differences were identified. [ABSTRACT FROM AUTHOR]