Exact Test Of Population Differentiation Research Articles

Genetic diversity and population structure of humpback whales (Megaptera novaeangliae) from Ecuador based on mitochondrial DNA analyses

Information on the genetic characterisation of humpback whales (Megaptera novaeangliae) wintering off Ecuador (Breeding Stock G) is presented. Mitochondrial DNA was extracted and sequenced from 230 skin samples collected between 2002 and 2008 to establish the genetic diversity of this population. From 182 usable samples, 41 different haplotypes were found, eight of which were new and unique. Haplotype diversity (h ± SD) was estimated to be 0.922 ± 0.012 and the nucleotide diversity (π ± SD) 0.019 ± 0.009. A comparison with other areas within the Southeast Pacific (Colombia and Magellan Strait) and the Antarctic Peninsula suggested panmixia within Breeding Stock G, even though significant differentiation was found with Magellan Strait (p < 0.0001 in both FST and ΦST). An additional analysis with the exact test of population differentiation showed significant differences in haplotype frequencies between breeding areas in Ecuador and southern Colombia (p < 0.01), suggesting some level of stratification at breeding grounds as supported by photo-identification studies. The Ecuadorian dataset included haplotypes reported in all three Southern Hemisphere ocean basins indicating recent gene flow within the Southern Hemisphere. The population showed a male-biased sex ratio in adult animals of 2.16:1. Further research and a larger number of samples from breeding areas in the north (Panama and Costa Rica) are required to appropriately assess the extent of structure in this population.

Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA.

This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region. Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed. Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FST comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout. These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia.

Genetic polymorphism and forensic application of 23 autosomal STR loci in the Han population of Panjin City, Liaoning Province, Northeastern China

Background Short tandem repeats (STRs) are consecutive repetition of a repeat motif and widely used in forensic medicine and human genetics because of their high polymorphism. Subjects and methods In the current study, 23 autosomal STR loci were genotyped from 1263 unrelated healthy individuals living in Panjin City, Liaoning Province, Northeastern China using the VeriFilerTM Express PCR Amplification Kit. The population comparison was performed between the Panjin Han population and the other relevant groups to further explore the structure of Panjin Han and its relationship with the other groups. Results The results found 316 alleles across the 23 STRs and the corresponding allelic frequencies ranged from 0.5198 to 0.0004. Except for D3S1358, TPOX, TH01, and D3S1358, all STR loci were highly polymorphic (PIC > 0.7), with the Penta E locus having the highest degree of polymorphism (0.9147). For population comparison, the exact test of population differentiation found that no significant difference was observed between the Panjin Han and the other Han populations, except for Guangdong Han and Jiangxi Han. Conclusion The Panjin Han population showed significant differences with the other ethnic groups in China (Bouyei, Dong, Hui, Miao, Tibetan, and Uygur) and the foreign ethnic groups.

Population genetic data for 21 autosomal STR loci in the Azerbaijani population using the Globalfiler™ kit.

The Republic of Azerbaijan is located in the southern Caucasus mountains, a region which is linguistically and ethnically diverse. We report allele frequency data for 21 autosomal loci from the Globalfiler™ kit in the Azerbaijani population using 467 individuals from Baku. Exact tests for Hardy Weinberg Equilibrium and Linkage Equilibrium were conducted, and all forensic parameters were estimated. High levels of Expected Heterozygosity HE were seen, with a minimum of 0.637 for TPOX and a maximum of 0.949 for SE33. Polymorphism Information Content (PIC) values for all STR loci were high, ranging from 0.587 for TPOX to 0.947 for SE33. Matching probability (MP) estimates ranged from 0.006 for SE33 to 0.178 for TPOX. Power of Discrimination (PD) values for most of the tested loci (17/21) were ≥ 0.9. The Combined Matching Probability (CMP) and the Combined Power of Discrimination (CPD) for all 21 loci were 7.84 × 10-27 and 1.0 respectively. Exact tests for population differentiation using all available Globalfiler™ datasets from across Europe and Asia reveal a general trend of higher differentiation with increasing geographical separation, but there is a need for additional population data from neighboring regions of Azerbaijan.

Extended blood group profiles for Malays, Chinese, and Indians in Peninsular Malaysia

BackgroundBlood group antigens are immunogenic polymorphic molecules presented on the surface of RBCs. This study aimed to determine extended blood group profiles (ABO, Rhesus, Kell, Kidd, Duffy, MNS, Cartwright, Dombrock, Colton, Lutheran, and Vel) in Malays, Chinese, and Indians in Peninsular Malaysia.ResultsHere, ABO Type O, DCCee, MNs, and Fy (a+b−) were the most frequent major blood group phenotypes in all three ethnic groups. Other minor blood group systems distributed differently across these ethnic groups, except for the Kell, Lutheran, Cartwright, and Vel blood group systems, where only K−k+, Lu (8+14), Yt (a+b−), and Vel (+) phenotypes were observed. Exact tests of population differentiation generally showed no significant differences between Malays included in the present study vs. other ethnically similar datasets from previous surveys. However, many significant differences were recorded in comparison between blood group datasets from ethnically unrelated populations (Malays vs. Chinese vs. Indians) especially for Rhesus, Kidd, and Duffy blood group systems. A Principal component analysis (PCA) plot showed that population groups from the Peninsular Malaysia map closely together as compared with population groups from other geographical regions.ConclusionsOverall, our present study has successfully provided an extended blood group profiles for Malays, Chinese, and Indians in Peninsular Malaysia. These new blood group datasets can be used as guidelines for donor recruitment and as reference standards for studying diseases associated with blood group systems.

A paleogenetic perspective of the Sabana de Bogotá (Northern South America) population history over the Holocene (9000–550 cal BP)

On the basis of distinct lines of evidence, detailed reconstructions of the Holocene population history of the Sabana de Bogotá (SB) region, Northern South America, have been performed. Currently, there exist two competing models that support temporal continuity or, alternatively, divergence. Despite recent bioarchaeological and isotopic research that lends support to the population discontinuity model, several discrepancies remain, calling for other kinds of evidences to be explored for a more detailed picture of Holocene biocultural evolution. In this study, 15 new complete mitochondrial genomes obtained from 30 individuals recovered from several archaeological sites spanning from the late Pleistocene (11,950–11,262 cal BP) until the initial late Holocene (2941–2752 cal BP) along with published data (n = 20) from the region dating ~9000–540 cal BP were used to investigate diachronic genetic change. Genetic diversity and distance indices were calculated, and demographic models tested in an approximate Bayesian computation (ABC) framework to evaluate whether patterns of genetic affinities of the SB prehispanic populations support genetic continuity or discontinuity. The results show that mitochondrial genomes of the complete dataset fall within the Native American haplogroups A2, B2, C1b, D1 and D4h3a. Haplotype and nucleotide diversity declined over time with further evidence of genetic drift and remarkable reduction of genetic diversity during the final late Holocene. Inter-population distances and the exact test of population differentiation, as well as demographic simulations show no population differentiation and population continuity over time. Consequently, based on the analyzed data, we cannot reject the genetic continuity in the SB region as a plausible population history scenario. However, the restriction of the analyses to the Hyper Variable Region 1 of the mitochondrial genome, and the very low sample size both constitute significant limitations to infer evolutionary history.

An analysis of subspecific variation of the honeybee, Apis mellifera L., in parts of West and Central Africa using microsatellite polymorphism

The variation of two (humid and semiarid) populations of the honeybee, Apis mellifera L., from western Africa, was analysed, using microsatellite polymorphism of nuclear DNA. One worker was sampled from each of 133 colonies collected from 38 localities in Nigeria, Niger, Cameroon and Chad and analysed for 15 loci. A total of 292 different alleles were recorded for the 15 microsatellite loci. All loci were polymorphic and the number of different alleles per locus ranged between 10, in locus At163, and 31, in locus A029, while allelic frequencies ranged from 0.007 to 0.569. The mean number of different alleles per locus was 19.5 ± S.E 1.1. The unbiased expected heterozygosity was 0.861 ± S.E. 0.017 for the combined populations and 0.859 ± S.E. 0.023 and 0.864 ± S.E. 0.026 for the humid and semiarid populations, respectively. The overall FST value, which is a good estimate of genetic differentiation of populations, was very low: 0.007 ± S.E. 0.001 (0.001 - 0.014) and AMOVA revealed that the two populations were not significantly different from each other (p > 0.05). Similarly, Raymond and Rousset’s exact test of population differentiation revealed that the two populations were not significantly differentiated at p = 0.05. Furthermore a Bayesian assignment test did not produce clear grouping of the populations. In a nutshell, according to microsatellite analysis, the honeybees of the area of study belonged to a genetically undifferentiated population.

Genetic Differentiation and Origin of Naturalized Rainbow Trout Populations From Southern Chile, Revealed by the mtDNA Control Region Marker.

Numerous self-sustaining naturalized or introduced populations of rainbow trout (Oncorhynchus mykiss) are widely distributed throughout the freshwaters of southern Chile. In this study, analysis of the mitochondrial DNA control region (CR) marker was conducted to investigate the level of genetic divergence among populations and their phylogenetic relationships with respect to native lineages. This information provided a framework to interpret the genetic structure and origin that was shaped during historical trout introduction efforts. To this end, we analyzed eleven naturalized populations of lakes and rivers from five basins. The CR marker revealed five haplotypes. The overall haplotype (H) and nucleotide (Π) diversities were 0.684 ± 0.030 and 0.00460 ± 0.00012, respectively. Global F ST was 0.169, with several pairwise F ST estimates showing significant differences (P < 0.05). The exact test of population differentiation corroborated this result (P < 0.001). Significant geographic structure was found (P < 0.05), with variations explained primarily by differences within populations (61.65%) and among group basins (20.82%). Maximum likelihood phylogenetic analysis resolved two distinct clades with medium bootstrap support when naturalized populations were aligned in conjunction with reference native lineages. The haplotype network revealed a close association between naturalized populations and four main haplotypes representative of three native ecotypes or lineages from western North America (rainbow trout, steelhead trout and redband trout). These results indicate a genetic population structuring for naturalized rainbow trout from southern Chile and an origin probably represented by multiple lineages sources. Thus, mitochondrial DNA data strongly suggest that stocking of rainbow trout from different origins may have occurred during or after the initial introduction efforts.

Phylogeography of higher Diptera in glacial and postglacial grasslands in western North America

BackgroundPleistocene glaciations have had an important impact on the species distribution and community composition of the North American biota. Species survived these glacial cycles south of the ice sheets and/or in other refugia, such as Beringia. In this study, we assessed, using mitochondrial DNA from three Diptera species, whether flies currently found in Beringian grasslands (1) survived glaciation as disjunct populations in Beringia and in the southern refugium; (2) dispersed northward postglacially from the southern refugium; or (3) arose by a combination of the two. Samples were collected in grasslands in western Canada: Prairies in Alberta and Manitoba; the Peace River region (Alberta); and the southern Yukon Territory. We sequenced two gene regions (658 bp of cytochrome c oxidase subunit I, 510 bp of cytochrome b) from three species of higher Diptera: one with a continuous distribution across grassland regions, and two with disjunct populations between the regions. We used a Bayesian approach to determine population groupings without a priori assumptions and performed analysis of molecular variance (AMOVA) and exact tests of population differentiation (ETPD) to examine their validity. Molecular dating was used to establish divergence times.ResultsTwo geographically structured populations were found for all species: a southern Prairie and Peace River population, and a Yukon population. Although AMOVA did not show significant differentiation between populations, ETPD did. Divergence time between Yukon and southern populations predated the Holocene for two species; the species with an ambiguous divergence time had high haplotype diversity, which could suggest survival in a Beringian refugium.ConclusionsPopulations of Diptera in Yukon grasslands could have persisted in steppe habitats in Beringia through Pleistocene glaciations. Current populations in the region appear to be a mix of Beringian relict populations and, to a lesser extent, postglacial dispersal northward from southern prairie grasslands.

Population Structure of the Red Macroalga Botryocladia occidentalis (Børgesen) Kylin (Rhodymeniaceae, Rhodymeniales) in the Gulf of Mexico Before the Deepwater Horizon Oil Spill

Studies on the population structure of common widespread macroalgae in the Gulf of Mexico (GoMx) are scarce, and this knowledge gap limits our understanding on how disturbances affect the genetic diversity of macroalgae in this basin. The latter is due to the lack of a baseline that can be compared with allele frequency surveys conducted after a major disturbance such as the 2010 Deepwater Horizon oil spill (DWH), which leaked 780,000 m3 of crude oil in the vicinity of highly diverse macroalgal communities. Fortunately, quantitative assessments of the population structure pre-DWH can be accomplished for several macroalgae with dried specimens collected from research cruises conducted before 2010 in the offshore GoMx. Based on three markers (cytochrome c oxidase subunit I, COX II-III intergenic spacer, and the RuBisCO large subunit), this study reconstructed the allele frequencies pre-DWH for a GoMx-widespread macroalga, Botryocladia occidentalis, and revealed the existence of distinct populations in each of three distant regions of the GoMx: Florida Middle Grounds (FL), Campeche Banks (CB), and offshore Louisiana (LA). Population structure was assessed with exact tests of population differentiation and Analyses of Molecular Variance. FL harbored the most differentiated and genetically diverse population due to the presence and abundance of unique haplotypes. Interestingly, FL haplotypes were not closely phylogenetically related to each other and included the most divergent lineages of the entire GoMx; this phylogeographic pattern suggests a strong influence of migrants from the Caribbean on the FL population. Additionally, likelihood ratio tests with a small sample collected post-DWH indicated that the LA population underwent strong changes, showing statistically significant differences before (LA) vs. after (L2) the disaster. Whereas the LA population had affinity to CB, L2 showed a FL haplotype that, before the disaster, had never been reported in LA or CB. Such changes may not be permanent but rather a temporary response to disturbance; also, they may not necessarily be caused by the spilled oil but by other factors associated with the DWH.

What is cultivated oyster mushroom? Phylogenetic and physiological study of Pleurotus ostreatus and related taxa

The wild and cultivated isolates of Pleurotus ostreatus were the subject of a phylogenetic analysis, AMOVA of DNA sequences, exact test of population differentiation, estimation of evolutionary divergence, and cardinal temperature measurement. Two significantly genetically separated groups (OA and OB) with limited mutual gene flow were revealed. While OA is identical with P. ostreatus sensu stricto and includes mainly wild isolates, OB is a more genetically variable group of cultivated isolates of unclear geographical origin. The delimitation of the two groups is confirmed by three genetic markers (ITS, TEF1 and RPB2). Limited gene flow between those two groups was detected, but this is comparable to the putative gene flow between OA, OB on the one hand and P. eryngii and P. pulmonarius on the other. This gene flow between OA and OB may be caused by artificial breeding activities, but the number of such hybridisation events is limited. The genetic differences are also confirmed by the different growth rates of the two groups. The centre of distribution of P. ostreatus s. s. is in Eurasia, while the origin of the OB group is unknown. The availability of a validly published taxonomic name for OB is discussed.

Distinguishing recent dispersal from historical genetic connectivity in the coastal California gnatcatcher

Habitat loss and fragmentation are primary threats to biodiversity worldwide. We studied the impacts of habitat loss and fragmentation on genetic connectivity and diversity among local aggregations of the California gnatcatcher (Polioptila californica californica) across its U.S. range. With a dataset of 268 individuals genotyped at 19 microsatellite loci, we analyzed genetic structure across the range using clustering analyses, exact tests for population differentiation, and a pedigree analysis to examine the spatial distribution of first-order relatives throughout the study area. In addition, we developed a habitat suitability model and related percent suitable habitat to genetic diversity indices within aggregations at two spatial scales. We detected a single genetic cluster across the range, with weak genetic structure among recently geographically isolated aggregations in the northern part of the range. The pedigree analysis detected closely related individuals across disparate aggregations and across large geographic distances in the majority of the sampled range, demonstrating that recent long-distance dispersal has occurred within this species. Genetic diversity was independent of suitable habitat at a local 5-km scale, but increased in a non-linear fashion with habitat availability at a broader, 30-km scale. Diversity declined steeply when suitable habitat within 30-km fell below 10%. Together, our results suggest that California gnatcatchers retain genetic connectivity across the majority of the current distribution of coastal sage scrub fragments, with the exception of some outlying aggregations. Connectivity may help support long-term persistence under current conservation and management strategies. However, emerging structure among more remote aggregations and associations between available habitat and genetic diversity also suggest that continued loss of habitat could threaten diversity and connectivity in the future.

Morphological and molecular evaluation of the Far East fruit genetic resources of Lonicera caerulea L.—vegetation, ethnobotany, use and conservation

Blue honeysuckle, Lonicera caerulea L. s.l. has a high nutritional and medicinal value of the fruits and a very high organoleptic evaluation may enable to fill gaps in the health food market. A joint project was undertaken in the north-eastern part of its distribution in Kamchatka and Sakhalin. The localities were characterised ecologically, phytosociological releves were noted and threat factors were assessed as a prerequisite for in situ conservation. Ninety-one samples were collected for herbarium, propagation in vitro and molecular characterisation. An additional 20 available Russian fruit cultivars were evaluated for comparison with ecotypes. The sites of blue honeysuckle differ ecologically and geobotanically between Kamchatka and Sakhalin. Phenotyping on sites and in cultivation revealed a great diversity in morphologic characters. It is possible to distinguish between genotypes from Sakhalin and Kamchatka by a combination of characters and thus our data support the taxonomic concept on the subspecific level. It is possible to classify the found genotypes of Lonicera caerulea into two geographical subspecies: L. caerulea subsp. kamtschatica (Pojark.) Plekhanova, and another subspecies, L. caerulea L. subsp. ochotensis Smekal., Holubec et Svobodova, subsp. nova, with distribution in Sakhalin and the adjacent Kuril Islands. Cluster analysis and Principal Coordinate analysis based on AFLP data indicate remarkable differences between L. caerulea populations from Kamchatka and Sakhalin. It was supported also by AMOVA analysis and by the exact test of population differentiation (p < 0.01). The top 12 genotypes were selected based on fruit characters, 10 from Kamchatka and 2 from Sakhalin for further use in breeding.

Genetic differentiation of Rubus chamaemorus populations in the Czech Republic and Norway after the last glacial period.

The population structure of cloudberry (Rubus chamaemorus L.), collected from Krkonose Mountains (the Czech Republic), continental Norway and Spitsbergen, was examined using microsatellite analyses (SSR). Among 184 individuals, 162 different genotypes were identified. The overall unbiased gene diversity was high (h^=0.463). A high level of genetic differentiation among populations (FST = 0.45; p < .01) indicated restricted gene flow between populations. Using a Bayesian approach, six clusters were found which represented the genetic structure of the studied cloudberry populations. The value of correlation index between genetic and geographical distances (r = .44) indicates that gene flow, even over a long distance, could exist. An exact test of population differentiation showed that Rubus chamaemorus populations from regions (Krkonose Mountains, continental Norway and Spitsbergen) are differentiated although some individuals within populations share common alleles even among regions. These results were confirmed by AMOVA, where the highest level of diversity was found within populations (70.8%). There was no difference between 87 pairs of populations (18.7%) mostly within cloudberry populations from continental Norway and from Spitsbergen. Based on obtained results, it is possible to conclude that Czech and Norwegian cloudberry populations are undergoing differentiation, which preserves unique allele compositions most likely from original populations during the last glaciation period. This knowledge will be important for the creation and continuation of in situ and ex situ conservation of cloudberry populations within these areas.

Genetic characterisation of 19 autosomal STR loci in a population sample from the Southeastern Anatolia Region of Turkey

Background: Southeastern Anatolia is the smallest, yet the most densely populated region among the seven major geographic constituents of Turkey. Situated in the Upper Mesopotamia, Southeastern Anatolia was also the northernmost extension of the Fertile Crescent, which is often considered as the earliest cradle of civilisation.Aim: To investigate the autosomal STR polymorphisms associated with a truly representative population sample pool from Southeastern Anatolia.Subjects and methods: Samples from a total of 257 volunteers were analysed by 19-loci autosomal STRs using the commercially available COrDIS Plus Kit. Allele frequencies, statistical parameters of forensic interest and Nei’s DA distances with respect to the nearby and distant populations were calculated, besides performing exact tests of population differentiation with the same populations.Results: A combined matching probability of 1.49978 × 10−23 and a combined power of exclusion of 0.999999961 were obtained for the novel Southeastern Anatolian autosomal STR dataset. Furthermore, the Southeastern Anatolia population was found to have close genetic affinities with the other regional populations from Turkey, along with those from an apparent genetic continuum extending from the Near East to Southeastern Europe.Conclusions: The novel Southeastern Anatolian dataset is expected to be useful in regional forensic genetics investigations and molecular anthropology applications.

Patterns of population structure and dispersal in the long-lived “redwood” of the coral reef, the giant barrel sponge (Xestospongia muta)

Sponges are one of the dominant fauna on Florida and Caribbean coral reefs, with species diversity often exceeding that of scleractinian corals. Despite the key role of sponges as structural components, habitat providers, and nutrient recyclers in reef ecosystems, their dispersal dynamics are little understood. We used ten microsatellite markers to study the population structure and dispersal patterns of a prominent reef species, the giant barrel sponge (Xestospongia muta), the long-lived “redwood” of the reef, throughout Florida and the Caribbean. F-statistics, exact tests of population differentiation, and Bayesian multi-locus genotype analyses revealed high levels of overall genetic partitioning (F ST = 0.12, P = 0.001) and grouped 363 individuals collected from the Bahamas, Honduras, US Virgin Islands, Key Largo (Florida), and the remainder of the Florida reef tract into at minimum five genetic clusters (K = 5). Exact tests, however, revealed further differentiation, grouping sponges sampled from five locations across the Florida reef tract (~250 km) into three populations, suggesting a total of six genetic populations across the eight locations sampled. Assignment tests showed dispersal over ecological timescales to be limited to relatively short distances, as the only migration detected among populations was within the Florida reef tract. Consequently, populations of this major coral reef benthic constituent appear largely self-recruiting. A combination of levels of genetic differentiation, genetic distance, and assignment tests support the important role of the Caribbean and Florida currents in shaping patterns of contemporary and historical gene flow in this widespread coral reef species.

The Frequency of the LCT*-13910C>T Polymorphism Associated with Lactase Persistence Diverges among Euro-Descendant Groups from Brazil

Objective: The aim of this study was to investigate the frequency of the LCT*-13910C>T polymorphism associated with a high expression of lactase in the small intestine during adulthood, and to infer the lactase persistence and adult-type hypolactasia phenotypes among Euro-Brazilians and Mennonites from South Brazil. Materials and Meth ods: A sequence-specific PCR method to genotype the LCT*-13910C>T polymorphism in 292 Euro-Brazilians and 151 Mennonites (a group with European ancestry and a long history of endogamy) was developed. Using an exact test of population differentiation, the genotype and allele frequency between these and other Brazilian populations were compared. Results: The frequency of -13910*T was significantly higher among the Mennonites when compared to the Euro-Brazilian cohort (0.63 vs. 0.33, p < 0.000001). Accordingly, Mennonites had a higher prevalence of the lactase persistence genotype (88.1 vs. 55.5%, p < 0.000001). The distribution of -13910*T differed between Mennonites and all other Brazilian groups (p < 0.0001). The Euro-Brazilians from Curitiba displayed differences when compared to all other Brazilian groups (p < 0.0001), even to Euro-Brazilians from a different geographic region (p = 0.0003), but were similar to those from Porto Alegre (p = 0.2). Conclusion: Differences in the -13910*T-associated lactase persistence distribution among Euro-Brazilian groups reflect the ancestry and admixture of each particular group and should be considered for adult-type hypolactasia screening.

Genetic variation and population structure of spottybelly greenling (Hexagrammos agrammus) in Korean coasts analyzed by DNA markers emphasizing on microsatellites

Two nuclear microsatellite DNA loci along with partial sequences of mitochondrial DNA tRNA PRO -D-loop region were analyzed to assess the genetic diversity and population genetic structure of spottybelly greenling ( Hexagrammos agrammus ). A total of 85 individuals were investigated from two different locations at the East and the South coasts of Korea which are Imwonjin (IM) and Tongyeong (TN), respectively. In the analysis of genetic diversity, nucleotide diversities were low showing 0.01 whereas haplotype diversities were as high as 0.92 and 0.97 in IM and TN populations, respectively indicating population bottleneck after rapid growth of these populations. No significant genealogical branches or clusters were recognized on the neighbor-joining phylogenetic tree. Pairwise population statistics FST and the exact test of population differentiation from the analysis of microsatellite DNA loci demonstrated no significant genetic difference between two populations investigated in the Korean coasts. In addition, significant deviations from Hardy-Weinberg equilibrium and heterozygote deficiencies were found from the microsatellite DNA loci. The results of the study will help to make a plan for fisheries management of the species.

Genome-wide SNP data show little differentiation between the Appaloosa and other American stock horse breeds.

The Appaloosa, American Quarter Horse (QH) and American Paint Horse (Paint) breeds are commonly referred to as stock horses, as each is used, to some extent, when managing livestock. QHs and Paint horses are genetically similar, which is predicted based on phenotype, ancestry and admixture allowed between the registries and with the Thoroughbred. In the Appaloosa, admixture is also allowed with the Thoroughbred, QH and Arabian. The Appaloosa is similar in conformation to the other stock breeds but has a unique leopard-spotting coat color pattern as well as mottled skin, white sclera of the eye and striped hooves. The goal of this study was to examine the relationship of the Appaloosa to the other stock breeds and determine whether genomic regions unique to the breed could be identified. This work will inform future clinical and genetic work of inherited phenotypes. The horses studied were sampled for other purposes and, as much as possible, represented a random sample of each breed. Second-order relationships (shared grandsire/dam) within each breed were excluded based on pedigree. The Appaloosas (n = 24) included 20 in the regular registry (had Appaloosa characteristics), two non-characteristic and two non-characteristic but with a completed certified pedigree option. Six Appaloosas had a QH parent, whereas 11 others had a QH or Thoroughbred grandsire/dam. Twenty-five QHs and 18 Paint horses were included. Diversity and F-statistics were calculated from 12 013 autosomal SNPs genotyped on the Illumina SNP50 or SNP70 BeadArray; these SNPs were selected after eliminating loci with minor allele frequency 0.2) in PLINK. The Appaloosas studied had higher diversity (expected heterozygosity) than did the QH and Paint as anticipated by pedigree. This greater degree of diversity was also noted in the number of fixed loci (of 40 281 total) within each breed (QH = 728, Paint = 1347, Appaloosa = 567). FIS did not indicate inbreeding (Table S1). Across breeds, cluster analysis (STRUCTURE) was unable to support clustering beyond K = 1 (Fig. S1). Principal component (PC) analysis in SNPRELATE revealed that PCs 1 and 2 accounted for 4.15% of the total variation. PCs 1 and 3 failed to separate the breeds, whereas PC 2 showed a trend of clustering the Appaloosas apart from the intermingled Paint and QHs (Fig. 1). Pairwise FST values were low [0.001 (Paint-QH) to 0.005 (QH-Appaloosa)] (Table S1) but significantly different from zero as determined by 15 000 permutations in ARLEQUIN; however, an exact test of population differentiation, assuming the null hypothesis that all alleles are drawn from the same pool/population, was not significant. The highest single-locus FST across populations was on ECA1 at 108.9 Mb, which also was the highest pairwise value between the Appaloosa and Paint and ranked second when comparing Appaloosa to the QH (Table S1); this SNP is 574.5 kb from the 5’ end of TRPM1, the gene implicated in Appaloosa coat color. Another SNP on ECA1, 62.5 kb from TRPM1, also had a high FST in pairwise comparisons including the Appaloosa. Therefore, although the divergence between breeds is low, these results are evidence that genomic signatures of selection for major, breed-defining phenotypes in the Appaloosa can be detected.

Genetic differentiation in Indian Major Carp, Cirrhinus mrigala (Hamilton, 1822) from Indian Rivers, as revealed by direct sequencing analysis of mitochondrial Cytochrome b region

A 307 bp segment of Cytochrome b gene of mtDNA was sequenced and analyzed for 90 individuals of Cirrhinus mrigala collected across the three rivers, namely Ganges, Narmada and Brahmaputra. Analyses revealed the presence of 14 haplotypes with haplotype diversity (h) ranging from 0.304 to 0.692, and nucleotide diversity (π) 0.002–0.043. The majority of variation was found within the population (96.21%), and the FST value (0.035) as well as the value of exact test of population differentiation (0.893) were found to be insignificant (p < 0.05). Analysis of molecular variance (AMOVA) also indicated insignificant differentiation among sub-populations. Generally, low genetic differences were observed even though those populations were from different geographic locations. The present study suggests a single panmictic population of C. mrigala across the three rivers of India.