Haplotype Diversity In Populations Research Articles

Phylogeographic Substructuring in the Southernmost Refugium of the European Common Frog Rana temporaria.

Rana temporaria is one of the most widespread Palearctic brown frogs. We aimed to clarify distribution pattern of two main genetic clades in the understudied Balkan peninsula by using 16SrRNA and MT-CYTB sequences, already widely applied in analyses of populations from other parts of Europe, while focusing on the broad area along the Morava river (central Balkans) as a known gap in the species distribution. Additionally, we were interested in revealing the extent of haplotype diversity within the main genetic clades in the Balkans, particularly around the supposed suture zone. The results revealed a suture zone between the Western and Eastern Clades in the central part of the Balkan Peninsula. This indicated the existence of a historical barrier between the Balkan Mountain Belt and geographically close mountains surrounding the Vlasina Plateau (Rhodope/Serbian-Macedonian Massif). The overall observed haplotype diversity in populations of R. temporaria from the Balkan Peninsula seems high. Harboring both main genetic clades of R. temporaria qualifies the Balkan Peninsula as another important center of species' genetic diversity, as well as rich in unique haplotypes. This points out the necessity of applying conservation measures focused on the common European frog populations and habitats in this part of the species' distribution area.

Marine bivalves voucher DNA barcoding from Eastern Mediterranean, with evidence for Ostrea stentina invasion

Abstract Bivalve molluscs are a diverse group of animals with particular economic and ecological importance. Their morphological characteristics frequently confuse their identification leading to mislabelling of edible species. Genetic diversity is critical to the resilience of marine bivalve populations in the face of environmental stressors such as ocean acidification and warming. In this study, we characterized the phylogeny and defined the first DNA barcodes of six marine bivalves [Ostrea edulis (Linnaeus, 1758) Arca noae (Linnaeus, 1758), Pinctada radiata (Leach, 1814), Venus verrucosa (Linnaeus, 1758), Calllista chione (Linnaeus, 1758) and Ruditapes decussatus (Linnaeus, 1758)] sampled from different coastal areas of Aegean and Ionian Seas using the molecular markers cytochrome c oxidase subunit I (COI) and 18S ribosomal RNA (18S rRNA). Further, COI gene was employed to investigate the population genetic diversity since 18S rRNA exhibited no conspecific differences. The sequence of 18S rRNA successfully discriminated the bivalves at family or superfamily level but occasionally proved insufficient for species identification. Contrariwise, COI was highly informative and could reliably distinguish all species. Population haplotype diversity was moderate to high and was always accompanied by generally low nucleotide diversity, indicating genetically closely related haplotypes. The invasive Pinctada radiata was found to be panmictic even among distant sampling areas, while Ostrea edulis was the only species that exhibited moderate levels of population subdivision. Finally, here we report for the first time the presence of Ostrea stentina in Thermaikos Gulf sampled among Ostrea edulis specimens, demonstrating a new invasive bivalve species in Eastern Mediterranean.

Immunogenetics of HLA-B: SNP, allele, and haplotype diversity in populations from different continents and ancestry backgrounds.

HLA-B is among the most variable gene in the human genome. This gene encodes a key molecule for antigen presentation to CD8+ T lymphocytes and NK cell modulation. Despite the myriad of studies evaluating its coding region (with an emphasis on exons 2 and 3), few studies evaluated introns and regulatory sequences in real population samples. Thus, HLA-B variability is probably underestimated. We applied a bioinformatics pipeline tailored for HLA genes on 5347 samples from 80 different populations, which includes more than 1000 admixed Brazilians, to evaluate the HLA-B variability (SNPs, indels, MNPs, alleles, and haplotypes) in exons, introns, and regulatory regions. We observed 610 variable sites throughout HLA-B; the most frequent variants are shared worldwide. However, the haplotype distribution is geographically structured. We detected 920 full-length haplotypes (exons, introns, and untranslated regions) encoding 239 different protein sequences. HLA-B gene diversity is higher in admixed populations and Europeans while lower in African ancestry individuals. Each HLA-B allele group is associated with specific promoter sequences. This HLA-B variation resource may improve HLA imputation accuracy and disease-association studies and provide evolutionary insights regarding HLA-B genetic diversity in human populations.

Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences

This study was performed by using D-loop region sequences to investigate genetic diversity and population structure across eight representative groups of M. nipponense from south to north China. Eight populations comprising a total of 144 individuals were from Songhua River (SHJ), Yellow River (HH), Yangtze River (YZ), Pearl River (ZJ), Weishan Lake (WSH), Taihu Lake (TH), Bosten Lake (BH) and Wanquan River (WQH). The 1130-bp D-loop region exhibited a higher content of A + T (79.04%) than C + G (20.95%). In addition, 239 variable sites and 73 haplotypes were detected. The population haplotype diversity (h) were ranked as follows: WQH (0.9810) > YZ (0.9571) > WSH (0.9429) > ZJ (0.8901) > SHJ (0.8791) > HH (0.8693) > TH (0.8667) > BH (0.3684); the nucleotide diversity (π) were ranked as: WQH (0.0607) > YZ (0.0299) > SHJ(0.0236) > WSH(0.0221) > TH(0.0132) > ZJ(0.0131) > HH(0.0118) > BH(0.0011). The pairwise FST values reached highly significant level (P < 0.01). The gene flow (Nm) results revealed abundant gene exchange between WSH and TH (11.057), HH (7.226) and ZJ (6.255). The maximum likelihood (ML) phylogenetic tree showed that 73 haplotypes were divided into two main branches. Only the haplotypes of the BH population clustered together, indicating the low genetic diversity of this population, whereas a high diversity was observed in other populations. Network results were consistent with phylogenetic tree results. The analysis of mismatch distribution showed that all eight populations presented multimodal distribution. Fu’s Fs test and Tajima’s D tests were applied to determine the population expansion. All eight populations showed non-significant negative values, which suggests that the M. nipponense population in China did not experience population expansion.

A method for the allocation of sequencing resources in genotyped livestock populations

BackgroundThis paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population.MethodsWe present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level. We tested the performance of the two algorithms in simulated pedigrees. For each pedigree, we evaluated the proportion of population haplotypes that are carried by the focal individuals and compared our results to a variant of the widely-used key ancestors approach and to two haplotype-based approaches. We calculated the expected phasing accuracy of the haplotypes of a focal individual at the sequence level given the proportion of the fixed sequencing budget allocated to its family.ResultsAlphaSeqOpt maximises the ability to capture and phase the most frequent haplotypes in a population in three ways. First, it selects focal individuals that collectively represent a larger portion of the population haplotype diversity than existing methods. Second, it selects focal individuals from across the pedigree whose haplotypes can be easily phased using family-based phasing and imputation algorithms, thus maximises the ability to impute sequence into the rest of the population. Third, it allocates more of the fixed sequencing budget to focal individuals whose haplotypes are more frequent in the population than to focal individuals whose haplotypes are less frequent. Unlike existing methods, we additionally present an algorithm to allocate part of the sequencing budget to the families (i.e. immediate ancestors) of focal individuals to ensure that their haplotypes can be phased at the sequence level, which is essential for enabling and maximising subsequent sequence imputation.ConclusionsWe present a new method for the allocation of a fixed sequencing budget to focal individuals and their families such that the final sequenced haplotypes, when phased at the sequence level, represent the maximum possible portion of the haplotype diversity in the population that can be sequenced and phased at that budget.

Genetic diversity of mitochondrial control region (D-Loop) polymorphisms in Coilia ectenes taihuensis inhabiting Taihu Lake, China.

Coilia ectenes is a commercially important fishery species in China. C. ectenes taihuensis is an endemic and dominant species found in Taihu Lake of China. When compared with C. ectenes, C. ectenes taihuensis lacks anadromous behavior, and can independently grow and reproduce in Taihu Lake. In this study, the mitochondrial DNA control region (D-loop) sequences were employed to investigate the genetic diversity and population structure of C. ectenes taihuensis. Sixty-eight individuals collected from 4 localities in Taihu Lake were examined. Results indicated that in the 887-bp D-loop region, seventy-seven (8.68%) sites were variant, contributing to 53 distinct haplotypes. Although the population haplotype diversity (Hd = 0.971 to 1.000) was generally high, the nucleotide diversity (π = 0.616 to 0.731%) was relatively low among the 4 populations. Additionally, the genetic distances ranged from 0.62 to 0.74% within the populations and from 0.67 to 0.74% between the populations. The neighbor-joining tree indicated that a distinct distribution of phylogenetic structure existed among haplotypes. Analysis of molecular variance and FST statistics suggested that a divergence existed among populations in 4 localities, indicating that gene communication might have occurred among those populations. Furthermore, neutral tests and analysis of mismatch distribution reflected that C. ectenes taihuensis might have undergone a population expansion during the evolution process. Our study showed the population genetic diversity and structure of C. ectenes taihuensis. Results from this study might be helpful in the development and protection of fishery resource within the localities in Taihu Lake in future.

Comparing genetic diversity of Sitophilus zeamais (Motchulsky) popula-tions sampled in several agro-ecological areas between Central African Republic and Senegal

Maize is attacked by many post-harvest pests including Sitophilus spp and Prostephanus spp, which causes remarkable loss during storage. Approxi-mately 30 to 40 % loss in the absence of treatment has been reported world-wide. This study compare genetically Central African and Senegalese popula-tions of Sitophilus zeamais from various agroecological zones using 3 mark-ers namely cytochrome b, cytochrome oxidase and nuclear 28S gene. S. zeamais samples were analyzed on both of two other sites 34 for the 28S gene; 68 for cytochrome b and 36 for the cytochrome oxydase. Results ana-lyzed by AMOVA have shown high genetic variation outside population of each country (6.17 % with Cyt b; 21.45 % with 49.83 % and COI in the case of 28S) and low within subpopulations (-10.06 % for Cyt b, 9.36 % for the COI and -15.23 % for 28S). Majority haplotype is shared between the two popula-tions for 28S and cytochrome b genes and there is a very high haplotype di-versity in populations of Senegal considering the Cytochrome b gene (0.781 + / - 0.00364) while with COI and 28S, high values of diversity are observed in Central African sequences, respectively 1.000 + / - 0.00274 and 0.867 + / - 0.011. Genetic differentiation obtained according to the geographical origin is significant between the two populations; however, it is not at the level of subpopulations. Developed by the three approaches (parsimony, likelihood and Bayesian) phylogenetic trees are resolved and show a speciation of the two populations according to the geographical origin.

Comparative analysis of genetic diversity ofDosidicus gigasfrom eastern Pacific Ocean based on molecular markers of mitochondrial DNA

The worldwide climate and marine environmental changes have significant impacts on the distributions and fishery resources abundance fluctuations of Dosidicus gigas in the East Pacific Ocean. It is important to investigate genetic variance and population genetic structure of D. gigas in order to exploit and manage this squid scientifically. In this study,the genetic diversity and the genetic differentiation betw een tw o geographical populations of D. gigas w ere analyzed based on tw o mitochondrial DNA molecular markers. The results show ed that the number of haplotype,haplotype diversities,nucleotide diversities and average nucleotide differences w ere 7,( 0. 397 ± 0. 079),( 0. 001 09 ± 0. 000 96) and 0. 600 respectively in all Cytb sequences of tw o geographical populations,and haplotype diversity in population off the coast of Peru w as only( 0. 282 ± 0. 101) w hich w as significantly low er than that of equatorial w aters. On the other hand,the number of haplotype,haplotype diversities,nucleotide diversities and average nucleotide differences in all COⅠ sequences w ere 17,( 0. 787 ± 0. 051),( 0. 002 90 ± 0. 001 38) and 1. 802 respectively. The pairw ise fixation index F st and median netw ork revealed lack of genetic structure betw een populations of equatorial w aters and off the coast of Peru( Cytb: F st= 0. 055 23,P 0. 05; CO Ⅰ: F st= 0. 005 91,P 0. 05),and this might be caused by equational oceanographic current. The minimum spanning netw ork tree,mismatch distribution analysis and neutrality tests suggested that D. gigas experienced a recent population expansion,possibly 138 900 to 167 900 years ago.

Phylogeography of Buddleja crispa (Buddlejaceae) and its correlation with drainage system evolution in southwestern China

Southwestern China is an area of active tectonism and erosion, yielding a dynamic, deeply eroded landscape that is hypothesized to have influenced the genetic structure of the resident populations of plants and animals. However, few studies have been conducted to examine the influence of changing river channels, particularly in the Yarlung Tsangpo area, on genetic distributions in plants. We here examine the population structure of Buddleja crispa, a dominant element of the dry, warm/hot river-valley communities, seeking to delimit the current population genetic structure and its relation to past changes in the courses of the major rivers in this area. • Two chloroplast DNA fragments were used to estimate the genetic variation and phylogeographic structure of the populations, and to infer nested clades, of the species. • We detected low intrapopulational haplotype diversity and higher overall population haplotype diversity (h(S) = 0.085, h(T) = 0.781). Molecular variance was mainly observed between groups (81.42%). Robust population genetic structure were detected by AMOVA (F(ST) = 0.967), coinciding with three nested clades (identified by NCPA) and five phylo-groups linked with paleo-drainage systems (identified by SAMOVA). No support for extensive spatial or demographical expansion was obtained. • A general pattern of genetic isolation by vicariance was inferred, and detected disjunct patterns strongly indicate that currently discontinuous drainage systems were historically linked. Most importantly, population subdivisions and genetic variation perfectly reflect the putative Paleo-Red-River drainage pattern, and Yarlung Tsangpo populations are closely related to Central Yunnan Plateau populations, indicating that they were previously connected by ancient river courses. Divergence times between these river systems estimated by molecular dating (in the Pleistocene) agree with previous findings.

西藏牦牛mtDNA D-loop区的遗传多样性及其遗传分化

To investigate the genetic diversity,clustering relationships and genetic differentiation of Tibetan yak(Bos grunniens) populations,we analyzed the complete sequence of the mitochondrial DNA control region(D-loop) of 114 individuals from 11 yak populations.To clarify the origin,phylogeny and taxonomic position of B.grunniens,we retrieved a further 48 D-loop sequences from five diverse populations of B.runniens,resulting in 162 sequences from 16 populations in total.Results showed some nucleotide bias in the 890—896bp bp Tibetan yak mtDNA D-loop sequence,with nucleotide frequencies of 28.5%,25.3%,32.4% and 13.8% for T,C,A and G respectively.A total of 90 haplotypes were identified,with 130 polymorphic sites(14.33% of total analyzed sites).Of these,45 sites represented single nucleotide polymorphisms;while a further 85 sites were parsimony-informative.The population haplotype diversity ranged from 0.93—1.00 with an average of 0.98±0.008,indicating a high level of genetic diversity within Tibetan yak populations.The majority of polymorphisms were A/G and T/C transitions or A/T transversions.Polymorphisms were more frequent in the Sangri yak and Baqing yak populations,and occurred less frequently in the Kangbu yak and Jiali yak populations.The 90 haplotypes were divided into two clusters by constructing a network relationship chart.This result suggests that Tibetan yaks may be derived from two separate maternal lineages.The degree of nucleotide difference among the 11 populations ranged from 0.503%—1.416%.The Sangri and Baqing populations had the highest degree of difference,whereas the lowest difference was observed between the Kangbu and Jiali populations.Because of this data,we suggest an apparent genetic differentiation between the Sangri and Baqing populations.Tajima′s test of selective neutrality was significant(0.01P0.05) for the Leiwuqi yak,Dingqing yak,Jiangda yak,and Gongbujiangda yak populations,but not significant(P0.05) for other populations.These results suggested that the Leiwuqi,Dingqi,Jiangda,and Gongbujiangda populations may have undergone expansions.The molecular variance among groups of the 16 Bovinae populations,as well as differences observed in the significant test,indicated that Bison bison is likely the ancestor of B.grunniens,and that there may be 2 maternal lineages.There also appears to be a high level of genetic diversity within Tibetan yak populations.The clustering relationship and analysis of molecular variance also suggested that Tibetan yak could be divided into two species.These study results not only provide an important theoretical basis for assessment and selection of genetic diversity in Tibetan yak populations,but are of great significance for elucidating the origin and classification of B.grunniens,and for the conservation of genetic resources.

Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia

South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes.

Habitat fragmentation, genetic diversity, and inbreeding depression in a threatened grassland legume: is genetic rescue necessary?

Kincaid’s lupine (Lupinus oreganus), a threatened perennial legume of western Oregon grasslands, is composed of small, fragmented populations that have consistently low natural seed set, suggesting they may have accumulated high enough levels of genetic load to be candidates for genetic rescue. We used simple sequence repeat (SSR) loci, both nuclear DNA and chloroplast DNA, to screen populations throughout the species’ range for evidence of severe inbreeding and recent genetic bottlenecks due to habitat fragmentation. After genotyping about 40% of the known populations, only one of 24 populations had strong statistical evidence for a recent genetic bottleneck (H e > H eq). Both mean nSSR fixation coefficients and genetic diversity did not statistically differ between very small, small, medium, and large lupine population size classes. Within population chloroplast DNA haplotype number was high for an animal pollinated species, ≈4.2 haplotypes/population, and within population haplotype diversity was also relatively evenly distributed. Within population patterns of nSSR and cpSSR genetic diversity suggest that genetic diversity has not been lost over the last century of habitat fragmentation. With genet lifespan thought to exceed 100 years, overlap of several to many generations, and substantial reductions in seed set from inbreeding depression that shifts cohort composition towards those generated by outcrossing events, Kincaid’s lupine is likely maintain the currently high levels of within population genetic diversity. The case of Kincaid’s lupine provides an example of how the assumptions of severe inbreeding depression with small population size and habitat fragmentation can be inaccurate.

Detecting genome-wide haplotype polymorphism by combined use of Mendelian constraints and local population structure.

Data from current gene-disease association studies motivate changes to existing haplotype inference methodologies. Many datasets are now comprised of both pedigree and population data so it is desirable to incorporate both sources of information when inferring haplotypes. The availability of high-density SNP data also makes it possible to determine and use the precise locations of recombination events. Our proposed method reconstructs haplotype structure on a genome-wide level by jointly using the information from the Mendelian law of inheritance and local population structure. The method combines in one framework new techniques of recombination event detection, maximum likelihood optimization of population haplotype diversity and our previous algorithm of zero-recombinant haplotype reconstruction. Experiments on both real and simulated datasets prove the efficiency and accuracy of our approach in reconstructing the haplotype structure. Our method makes it possible to reveal the haplotypic variation on a genome-wide level.

Emergent effects of heavy metal pollution at a population level: Littorina brevicula a study case

Changes in genetic variability and allele frequency can be responses from natural populations when encountering a novel contaminated environment. The genetic diversity and population structuring of natural populations of the gastropod Littorina brevicula from heavy-metal polluted and unpolluted environments along the southeast coast of Korea were examined using two mtDNA markers, cyt b and ND6. This study applied a nested clade analysis to test the existence of structuring association of haplotype distribution with environments (polluted and unpolluted). No genetic differences within cyt b mtDNA were detected between environments. On the other hand, differences in population haplotype diversity and structuring were found within ND6 mtDNA between polluted and unpolluted environments. The ND6-mtDNA haplotype (=genetic) diversity was significant lower in polluted environments. This decreased genetic diversity along with differences in the haplotype distribution within heavy-metal polluted environments compared to those unpolluted ones stand out as emergent effects from pollution at a population level. In this study, we propose the use of different approaches, such as the NCA, that takes into account the rare haplotypes, when assessing the effects of pollution on population genetic structuring.

Population Demographics and Genetic Diversity in Remnant and Translocated Populations of Sea Otters

Abstract: The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter ( Enhydra lutris) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Mitochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size (rs = −0.741, p = 0.038) and minimum population size (rs = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, although growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.