Genetic Admixture Analysis Research Articles

Myofiber-specific lipidomics unveil differential contributions to insulin sensitivity in individuals of African and European ancestry

AimsIndividuals of African ancestry (AA) present with lower insulin sensitivity compared to their European counterparts (EA). Studies show ethnic differences in skeletal muscle fiber type (lower type I fibers in AA), muscle fat oxidation capacity (lower in AA), whilst no differences in total skeletal muscle lipids. However, skeletal muscle lipid subtypes have not been examined in this context. We hypothesize that lower insulin sensitivity in AA is due to a greater proportion of type II (non-oxidative) muscle fibers, and that this would result in an ancestry-specific association between muscle lipid subtypes and peripheral insulin sensitivity. To test this hypothesis, we examined the association between insulin sensitivity and muscle lipids in AA and EA adults, and in an animal model of insulin resistance with muscle-specific fiber types. MethodsIn this cross-sectional study, muscle biopsies were obtained from individuals with a BMI ranging from normal to overweight with AA (N = 24) and EA (N = 19). Ancestry was assigned via genetic admixture analysis; peripheral insulin sensitivity via hyperinsulinaemic–euglycemic clamp; and myofiber content via myosin heavy chain immunohistochemistry. Further, muscle types with high (soleus) and low (vastus lateralis) type I fiber content were obtained from high-fat diet-induced insulin resistant F1 mice and littermate controls. Insulin sensitivity in mice was assessed via intraperitoneal glucose tolerance test. Mass spectrometry (MS)-based lipidomics was used to measure skeletal muscle lipid. ResultsCompared to EA, AA had lower peripheral insulin sensitivity and lower oxidative type 1 myofiber content, with no differences in total skeletal muscle lipid content. Muscles with lower type I fiber content (AA and vastus from mice) showed lower levels of lipids associated with fat oxidation capacity, i.e., cardiolipins, triacylglycerols with low saturation degree and phospholipids, compared to muscles with a higher type 1 fiber content (EA and soleus from mice). Further, we found that muscle diacylglycerol content was inversely associated with insulin sensitivity in EA, who have more type I fiber, whereas no association was found in AA. Similarly, we found that insulin sensitivity in mice was associated with diacylglycerol content in the soleus (high in type I fiber), not in vastus (low in type I fiber).Conclusions; Our data suggest that the lipid contribution to altered insulin sensitivity differs by ethnicity due to myofiber composition, and that this needs to be considered to increase our understanding of underlying mechanisms of altered insulin sensitivity in different ethnic populations.

Indigenous cattle of Sri Lanka: Genetic and phylogeographic relationship with Zebu of Indus Valley and South Indian origin.

The present study reports the population structure, genetic admixture and phylogeography of cattle breeds of Sri Lanka viz. Batu Harak, Thawalam and White cattle. Moderately high level of genetic diversity was observed in all the three Sri Lankan zebu cattle breeds. Estimates of inbreeding for Thawalam and White cattle breeds were relatively high with 6.1% and 7.2% respectively. Genetic differentiation of Sri Lankan Zebu (Batu Harak and White cattle) was lowest with Red Sindhi among Indus Valley Zebu while it was lowest with Hallikar among the South Indian cattle. Global F statistics showed 6.5% differences among all the investigated Zebu cattle breeds and 1.9% differences among Sri Lankan Zebu breeds. The Sri Lankan Zebu cattle breeds showed strong genetic relationships with Hallikar cattle, an ancient breed considered to be ancestor for most of the Mysore type draught cattle breeds of South India. Genetic admixture analysis revealed high levels of breed purity in Lanka White cattle with >97% Zebu ancestry. However, significant taurine admixture was observed in Batu Harak and Thawalam cattle. Two major Zebu haplogroups, I1 and I2 were observed in Sri Lankan Zebu with the former predominating the later in all the three breeds. A total of 112 haplotypes were observed in the studied breeds, of which 50 haplotypes were found in Sri Lankan Zebu cattle. Mismatch analysis revealed unimodal distribution in all the three breeds indicating population expansion. The sum of squared deviations (SSD) and raggedness index were non-significant in both the lineages of all the three breeds except for I1 lineage of Thawalam cattle (P<0.01) and I2 lineage of Batu Harak cattle (P<0.05). The results of neutrality tests revealed negative Tajima's D values for both the lineages of Batu Harak (P>0.05) and White cattle (P>0.05) indicating an excess of low frequency polymorphisms and demographic expansion. Genetic dilution of native Zebu cattle germplasm observed in the study is a cause for concern. Hence, it is imperative that national breeding organizations consider establishing conservation units for the three native cattle breeds to maintain breed purity and initiate genetic improvement programs.

The genetics of autism spectrum disorder in an East African familial cohort

Autism spectrum disorder (ASD) is a group of complex neurodevelopmental conditions affecting communication and social interaction in 2.3% of children. Studies that demonstrated its complex genetic architecture have been mainly performed in populations of European ancestry. We investigate the genetics of ASD in an East African cohort (129 individuals) from a population with higher prevalence (5%). Whole-genome sequencing identified 2.13 million private variants in the cohort and potentially pathogenic variants in known ASD genes (including CACNA1C, CHD7, FMR1, and TCF7L2). Admixture analysis demonstrated that the cohort comprises two ancestral populations, African and Eurasian. Admixture mapping discovered 10 regions that confer ASD risk on the African haplotypes, containing several known ASD genes. The increased ASD prevalence in this population suggests decreased heterogeneity in the underlying genetic etiology, enabling risk allele identification. Our approach emphasizes the power of African genetic variation and admixture analysis to inform the architecture of complex disorders.

Diverged subpopulations in tropical Urochloa (Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution.

Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. Here we aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction. We explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and they tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-sequencing to generate 1.1 million single nucleotide polymorphism loci. We employed genetic admixture, principal component and phylogenetic analyses to define subpopulations. We observed three highly differentiated subpopulations in U. brizantha, which were unrelated to ploidy: one intermixed with U. decumbens, and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola, unrelated to ploidy; one subpopulation had fewer accessions but included the only characterized sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima. Polyploid U. decumbens are more closely related to polyploid U. brizantha than to diploid U. decumbens, which supports the divergence of both polyploid groups from a common tetraploid ancestor and provides evidence for the hybridization barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can probably be utilized in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha, U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual-apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas.

Genetic Characterization and Population Connectedness of North American and European Dairy Goats.

Genomic prediction of breeding values is routinely performed in several livestock breeding programs around the world, but the size of the training populations and the genetic structure of populations evaluated have, in many instances, limited the increase in the accuracy of genomic estimated breeding values. Combining phenotypic, pedigree, and genomic data from genetically related populations can be a feasible strategy to overcome this limitation. However, the success of across-population genetic evaluations depends on the pedigree connectedness and genetic relationship among individuals from different populations. In this context, this study aimed to evaluate the genetic connectedness and population structure of Alpine and Saanen dairy goats from four countries involved in the European project SMARTER (SMAll RuminanTs Breeding for Efficiency and Resilience), including Canada, France, Italy, and Switzerland. These analyses are paramount for assessing the potential feasibility of an across-country genomic evaluation in dairy goats. Approximately, 9,855 genotyped individuals (with 51% French genotyped animals) and 6,435,189 animals included in the pedigree files were available across all four populations. The pedigree analyses indicated that the exchange of breeding animals was mainly unilateral with flows from France to the other three countries. Italy has also imported breeding animals from Switzerland. Principal component analyses (PCAs), genetic admixture analysis, and consistency of the gametic phase revealed that French and Italian populations are more genetically related than the other dairy goat population pairs. Canadian dairy goats showed the largest within-breed heterogeneity and genetic differences with the European populations. The genetic diversity and population connectedness between the studied populations indicated that an international genomic evaluation may be more feasible, especially for French and Italian goats. Further studies will investigate the accuracy of genomic breeding values when combining the datasets from these four populations.

Genetic admixture and population structure analysis of Indian water buffaloes (Bubalus bubalis) using STR markers.

India has a vast riverine and swamp buffalo diversity adapted to various agro-ecological conditions. In the present study, genetic diversity data for 10 different buffalo populations of India, using 20 highly polymorphic microsatellite markers has been generated for the genetic diversity analysis. The buffalo populations of Eastern Odisha state, were the primary focus. The minimal spanning network based on Bruvo's distance, PCA (Principal Component Analysis) based on the Fst (Fixation Index) values, and genetic admixture analysis using both the STRUCTURE and 'snapclust' were performed. The analysis could identify the Manda population as distinct from other Odisha buffalo breeds as well as adjoining Chhattisgarhi buffalo breeds. The total observed number of alleles ranged between 143 (Manda) and 301 (Paralakhemundi) with an average of 204 alleles per breed. The Sambhalpuri buffalo population also clustered into two separate subpopulations, half of the unique sub-population located geographically south-wards, displayed no admixture with any of the adjacent buffalo populations. The Manda buffalo population has shown sufficient allelic richness and heterozygosity under random mating being practiced in the field conditions. The study has led to the identification of the Manda as a distinct buffalo population, and the germplasm has been registered as a new Indian buffalo breed. Whereas, the Sambhalpuri population requires elaborate analysis to confirm the existence of two distinct sub-populations.

Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations.

Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human‐mediated hybridization between a domesticated species and its wild relative. We analysed whole‐genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and admixture showed that wolves and dogs were well‐separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had <1% mixed ancestry, levels comparable to the degree of mixed ancestry in many dogs, and likely not resulting from recent wolf–dog hybridization. We also show that the founders of the Scandinavian wolf population were genetically inseparable from Finnish and Russian Karelian wolves, pointing at the geographical origin of contemporary Scandinavian wolves. Moreover, we found Scandinavian‐born animals among wolves sampled in Finland, demonstrating bidirectional gene flow between the Scandinavian Peninsula and eastern countries. The low incidence of admixture between wolves and dogs in Fennoscandia may be explained by the fact that feral dogs are rare in this part of Europe and that careful monitoring and management act to remove hybrids before they backcross into wolf populations.

Genetic Admixture Analysis in the Population of Tacuarembó-Uruguay Using Alu Insertions

Genetic Admixture Analysis in the Population of Tacuarembó-Uruguay Using Alu Insertions

Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes.&#x0D; Keywords: genetic variability, molecular characterization, population differentiation

A global overview of cassava genetic diversity.

Although numerous studies of diversity have been conducted in cassava, there is no comprehensive assessment of global genetic diversity. Here we draw on previous studies and breeders’ knowledge to select diversity sets from the International Institute of Tropical Agriculture (IITA) and the International Center for Tropical Agriculture (CIAT) genebanks and breeders’ germplasm, as well as elite germplasm and landraces from eastern, southern and central (ESC) Africa to make a global assessment of diversity in cassava, using a SNP based GoldenGate (Illumina Inc.) assay. A synthesis of results from genetic distance and ADMIXTURE analysis essentially revealed four populations (i) South American germplasm characterised by relatively higher genetic diversity with hypothetical ancestral founder genotypes from Brazil, (ii) a smaller group of African introduction germplasm which is more distantly related to all other germplasm, (iii) West Africa germplasm dominated by IITA breeding lines, containing sources of cassava mosaic disease resistance, and IITA genebank accessions from West Africa, both characterised by slightly lower diversity, and (iv) a less cohesive group of African germplasm, termed ‘Other’, with moderate levels of diversity and a majority of germplasm from ESC Africa. This study highlights opportunities for heterosis breeding, purging of duplicates in genebanks and the need for conservation of ESC Africa landraces.

Bloodmeal, Host Selection, and Genetic Admixture Analyses of Culex pipiens Complex (Diptera: Culicidae) Mosquitoes in Chicago, IL.

The area in and around Chicago, IL, is a hotspot of West Nile virus activity. The discovery of a Culex pipiens form molestus Forskӓl population in Chicago in 2009 added to speculation that offspring from hybridization between Cx. pipiens f. pipiens L. and f. molestus could show a preference for feeding on humans. We collected blood-fed female mosquitoes (N = 1,023) from eight residential sites and one public park site in Chicago in July and August 2012. Bloodmeal analysis using the COI (cytochrome c oxidase subunit I) gene was performed to ascertain host choice. Almost all (99%) bloodmeals came from birds, with American Robins (Turdus migratorius L.) and House Sparrows (Passer domesticus L.) making up the largest percentage (74% combined). A forage ratio analysis comparing bird species fed upon and available bird species based on point count surveys indicated Northern Cardinals (Cardinalis cardinalis) and American Robins (Turdus migratorius) appeared to be over-utilized, whereas several species were under-utilized. Two human bloodmeals came from Culex pipiens complex mosquitoes. Admixture and population genetic analyses were conducted with 15 microsatellite loci on head and thorax DNA from the collected blood-fed mosquitoes. A modest amount of hybridization was detected between Cx. pipiens f. pipiens and f. molestus, as well as between f. pipiens and Cx. quinquefasciatus Say. Several pure Cx. quinquefasciatus individuals were noted at the two Trumbull Park sites. Our data suggest that Cx. pipiens complex mosquitoes in the Chicago area are not highly introgressed with f. molestus and appear to utilize avian hosts.

Genomic diversity and population structure of Mexican and Spanish bovine Lidia breed.

The Lidia bovine breed is distinguished for its low genetic exchangeability given its selection on aggressive behavior, its management uniqueness and its subdivided structure. In this study, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture of 468 animals from Mexican and Spanish Lidia breed populations and 64 samples belonging to 10 Spanish native and American-creole breeds using 37148 single nucleotide polymorphisms. We found similar average inbreeding values in the Lidia breed, with different distributions within groups; variability of inbreeding values among Spanish lineages was significant and no differences were found among the Mexican sub-populations. Together, the high FIS of the lineages and the behavior of the runs of homozygosity are consequences of the lineage's small effective population sizes, contributing to their inbreeding increase. Population admixture analysis discarded any influence on the genetic structure of the Lidia populations from the Spanish native and American-creole breeds. In addition, both Lidia populations depicted different genetic origins, with the exception of some Mexican individuals whose origins traced back to recent Spanish importations.

A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín.

At least 20% of Colombians identify as having African ancestry, yielding the second largest population of Afro-descendants in Latin America. To date, there have been relatively few studies focused on the genetic ancestry of Afro-Latino populations. We report a comparative analysis of the genetic ancestry of Chocó, a state located on Colombia’s Pacific coast with a population that is >80% Afro-Colombian. We compared genome-wide patterns of genetic ancestry and admixture for Chocó to six other admixed American populations, with an emphasis on a Mestizo population from the nearby Colombian city of Medellín. One hundred sample donors from Chocó were genotyped across 610,545 genomic sites and compared with 94 publicly available whole genome sequences from Medellín. At the continental level, Chocó shows mostly African genetic ancestry (76%) with a nearly even split between European (13%) and Native American (11%) fractions, whereas Medellín has primarily European ancestry (75%), followed by Native American (18%) and African (7%). Sample donors from Chocó self-identify as having more African ancestry, and conversely less European and Native American ancestry, than can be genetically inferred, as opposed to what we previously found for Medellín, where individuals tend to overestimate levels of European ancestry. We developed a novel approach for subcontinental ancestry assignment, which allowed us to characterize subcontinental source populations for each of the three distinct continental ancestry fractions separately. Despite the clear differences between Chocó and Medellín at the level of continental ancestry, the two populations show overall patterns of subcontinental ancestry that are highly similar. Their African subcontinental ancestries are only slightly different, with Chocó showing more exclusive shared ancestry with the modern Yoruba (Nigerian) population, and Medellín having relatively more shared ancestry with West African populations in Sierra Leone and Gambia. Both populations show very similar Spanish ancestry within Europe and virtually identical patterns of Native American ancestry, with main contributions from the Embera and Waunana tribes. When the three subcontinental ancestry components are considered jointly, the populations of Chocó and Medellín are shown to be most closely related, to the exclusion of the other admixed American populations that we analyzed. We consider the implications of the existence of shared subcontinental ancestries for Colombian populations that appear, at first glance, to be clearly distinct with respect to competing notions of national identity that emphasize ethnic mixing (mestizaje) vs. group-specific identities (multiculturalism).

Genetic variability and historic stability of the California spiny lobster Panulirus interruptus in the Gulf of California

The California spiny lobster Panulirus interruptus ranges from California into the Gulf of California in Mexico. In Mexico, the lobster supports an economically important fishery. Lobsters in the Gulf of California may belong to a small and genetically distinct population. We determined the genetic diversity and population structure of P. interruptus, using mitochondrial DNA sequences of the control region and the 16SrRNA gene. Samples were collected in the Gulf of California, the west central and southwest coast of the Baja California Peninsula, and the United States. We found a slightly higher genetic diversity in the Gulf of California populations than in the Pacific, but no significant genetic differentiation was shown by an analysis of molecular variance. Using a spatial clustering model and Bayesian methods, the weak population structure was consistent with the absence of a phylogeographic pattern and genetic admixture analysis. However, mismatch distribution analysis suggests that lobster from the gulf represents a more stable and older population than the Pacific, which fitted a model of sudden population expansion. The clinal trend in several genetic parameters between the Gulf of California and the Pacific suggests a historical separation that has not yet resulted in a significant genetic differentiation by genetic drift, mainly because of the large size of the population. Implementation of independent fisheries management practices between these regions could be justified; however, biological and ecological information should be used to support genetic data.

Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system.

The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population.

Evidence for genetic erosion of a California native tree, Platanus racemosa, via recent, ongoing introgressive hybridization with an introduced ornamental species

When non-native, genetically diverse species are introduced, hybridization with native congeners may erode the genetic composition of local species, perhaps even resulting in extinction. While such events may lead to adverse consequences at the community and ecosystem level, few studies exist on ecologically important tree species. In the genus Platanus, introgressive hybridization is widespread, and one common ornamental species, introduced to California during the late 19th century, is itself a hybrid. Our microsatellite analysis of more than 400 Platanus trees from north-central California reveals a complex pattern of invasion and hybridization in an age-structured population. By using size as a proxy for age, we have demonstrated that the Platanus population of north-central California has recently gained genetic diversity and effective population size. Principal coordinate analysis (PCoA) and genetic admixture analysis (STRUCTURE) both reveal a strong differentiation of genotypes into two main genetic clusters, with a large number of admixed genotypes. One of the genetic clusters identified is heavily biased towards younger trees, including samples from locations with relatively recently planted ornamental trees likely to be P. × hispanica (formerly known as P. × acerifolia). We conclude that the two genetic clusters correspond to the native P. racemosa and the introduced invasive hybrid species P. × hispanica. Additional hybridization between the invasive ornamental and the native species has occurred in California, and recent hybrid trees are more likely to be younger than trees without admixture. Our findings suggest that the observed increase in genetic diversity among California Platanus is due to rampant ongoing introgression, which may be threatening the continued genetic distinctiveness of the native species. This is cause for concern from a conservation standpoint, due to a direct loss of genetic distinctiveness, and a potential reduction in habitat value of associated species.

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures.

Recent advances in sequencing technologies have enabled the production of massive amounts of data on somatic mutations from cancer genomes. These data have led to the detection of characteristic patterns of somatic mutations or “mutation signatures” at an unprecedented resolution, with the potential for new insights into the causes and mechanisms of tumorigenesis. Here we present new methods for modelling, identifying and visualizing such mutation signatures. Our methods greatly simplify mutation signature models compared with existing approaches, reducing the number of parameters by orders of magnitude even while increasing the contextual factors (e.g. the number of flanking bases) that are accounted for. This improves both sensitivity and robustness of inferred signatures. We also provide a new intuitive way to visualize the signatures, analogous to the use of sequence logos to visualize transcription factor binding sites. We illustrate our new method on somatic mutation data from urothelial carcinoma of the upper urinary tract, and a larger dataset from 30 diverse cancer types. The results illustrate several important features of our methods, including the ability of our new visualization tool to clearly highlight the key features of each signature, the improved robustness of signature inferences from small sample sizes, and more detailed inference of signature characteristics such as strand biases and sequence context effects at the base two positions 5′ to the mutated site. The overall framework of our work is based on probabilistic models that are closely connected with “mixed-membership models” which are widely used in population genetic admixture analysis, and in machine learning for document clustering. We argue that recognizing these relationships should help improve understanding of mutation signature extraction problems, and suggests ways to further improve the statistical methods. Our methods are implemented in an R package pmsignature (https://github.com/friend1ws/pmsignature) and a web application available at https://friend1ws.shinyapps.io/pmsignature_shiny/.

Genetic diversity, paraphyly and incomplete lineage sorting of mtDNA, ITS2 and microsatellite flanking region in closely related Heliopora species (Octocorallia)

Examining genetic diversity and lineage sorting of different genes in closely related species provide useful information for phylogenetic analyses and ultimately for understanding the origins of biodiversity. In this study, we examined inter- and intraspecific genetic variation in internal transcribed spacer 2 (ITS2), partial mitochondrial gene (mtMutS), and nuclear microsatellite flanking region in two closely related octocoral species (Heliopora coerulea, HC-A and HC-B). These species were recently identified in a population genetic study using microsatellite markers. The two species have different reproductive timing, which ecologically promotes lineage sorting. In this study, we examined whether species boundaries could be detected by the commonly used nuclear ITS2 and mtMutS, as well as by possibly neutral microsatellite flanking sequences. Haplotype network analysis of microsatellite flanking region revealed that a possible ancestral haplotype was still shared between the two species, indicating on-going lineage sorting. Haplotype network analysis of ITS2 and microsatellite flanking region revealed shared haplotypes between the two lineages. The two species shared fewer ITS2 sequences than microsatellite flanking region sequences. The almost fixed point mutation at the tip of helix 3 of ITS2 was not associated with the secondary structure or compensatory base changes (CBCs). The phylogenetic tree of ITS2 showed paraphyly and that of the microsatellite flanking region indicated that lineage sorting for the two species may be incomplete. Much higher intra- and inter-individual variation of ITS2 was observed in HC-B than that in HC-A, highlighting the importance of examining ITS2 from multiple individuals to estimate genetic diversity. The mitochondrial mtMutS gene sequences from 39 individuals, including both species collected from Japan and Taiwan, showed no variation because of slow rates of mitochondrial nucleotide substitution. This study suggests caution is warranted when reciprocal monophyly in a phylogenetic tree is used as the criterion for delimiting closely related octocoral species based on ITS2 or mtMtuS sequences. Detection of boundaries between closely related species requires multi-locus analysis, such as genetic admixture analysis using multiple individuals.

Genetic admixture analysis in Prestice Black-Pied pigs

Abstract. The Prestice Black-Pied pig (PC) is a genetic resource of the Czech Republic. Information about boar variability has been provided in preceding papers. The objective of this work was to compare genetic variability of boars and sows. A total of 21 microsatellite markers were used to study genetic diversity and population structure of 149 PC breeding animals. In this paper, current parameters of assessments of diversity in PC are listed. All loci were polymorphic, and a total of 167 alleles were observed across the studied loci. The range of alleles was found to be 4 to 15 with a mean of 7.95. Overall allele frequency ranged from 0.07 to 0.25. The calculated observed and expected heterozygosity values were 0.70 and 0.73, respectively. The polymorphism information content (PIC) was 0.69 and the overall within-population inbreeding estimate (FIS) was 0.04. Genetic differentiation and population subdivision were tested. The level of admixture of breeds used for improvement of the PC breed was evaluated (Landrace, Large White and Pietrain). Five percent of analysed PC breeding boars had more than 20% admixture of other monitored breeds. The obtained results are important for the future sustainability of this local breed.

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.