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FST Values (fst + value)
Kinds of FST Values Selected AbstractsGenetic signatures in an invasive parasite of Anguilla anguilla correlate with differential stock managementJOURNAL OF FISH BIOLOGY, Issue 1 2010S. Wielgoss In this article, it is shown that available genetic tools for the omnipresent parasite Anguillicoloides crassus in European eels Anguilla anguilla are sensitive to different immigration rates into local A. anguilla stocks for two separated river systems. Relying on four highly polymorphic microsatellite markers, it was inferred that under natural recruitment, nematode samples meet Hardy,Weinberg expectations for a single panmictic population, while genetic signals show signs for a strong Wahlund effect most likely due to very recent population mixing under frequent restocking of young A. anguilla. This was indicated by a low but significant FST value among within-host populations (infrapopulations) along with high inbreeding indices FIS consistent over all loci. The latter signal is shown to stem from high levels of admixture and the presence of first-generation migrants, and alternative explanations such as marker- and sex-specific biases in the nematode populations could be dismissed. Moreover, the slightly increased degree of relatedness within infrapopulations in the stocked river system cannot explain the excessive inbreeding values found and are most likely a direct consequence of recent influx of already infected fish harbouring parasites with different genetic signatures. Applying a simulation approach using known variables from the nematode's invasion history, only the artificial introduction of a Wahlund effect leads to a close match between simulated and real data, which is a strong argument for using the parasite as a biological tag for detecting and characterizing fish translocation. [source] Evidence for bias in estimates of local genetic structure due to sampling schemeANIMAL CONSERVATION, Issue 3 2006E. K. Latch Abstract Traditional population genetic analyses typically seek to characterize the genetic substructure caused by the nonrandom distribution of individuals. However, the genetic structuring of adult populations often does not remain constant over time, and may vary relative to season or life-history stages. Estimates of genetic structure may be biased if samples are collected at a single point in time, and will reflect the social organization of the species at the time the samples were collected. The complex population structures exhibited by many migratory species, where temporal shifts in social organization correspond to a large-scale shift in geographic distribution, serve as examples of the importance that time of sampling can have on estimates of genetic structure. However, it is often fine-scale genetic structure that is crucial for defining practical units for conservation and management and it is at this scale that distributional shifts of organisms relative to the timing of sampling may have a profound yet unrecognized impact on our ability to interpret genetic data. In this study, we used the wild turkey to investigate the effects of sampling regime on estimates of genetic structure at local scales. Using mitochondrial sequence data, nuclear microsatellite data and allozyme data, we found significant genetic structuring among localized winter flocks of wild turkeys. Conversely, we found no evidence for genetic structure among sampling locations during the spring, when wild turkeys exist in mixed assemblages of genetically differentiated winter flocks. If the lack of detectable genetic structure among individuals is due to an admixture of social units as in the case of wild turkeys during the spring, then the FIS value rather than the FST value may be the more informative statistic in regard to the levels of genetic structure among population subunits. [source] Genetic diversity within and among Atlantic cod (Gadus morhua) farmed in marine cages: a proof-of-concept study for the identification of escapeesANIMAL GENETICS, Issue 5 2010K. A. Glover Summary This study presents a molecular genetic characterization of Atlantic cod reared in commercial marine farms. Samples consisted of approximately 47 fish collected from nine cages located on four farms throughout Norway. In addition, 28 farmed escapees were recaptured in the sea (443 fish in total). Nine microsatellite loci and the Pan I gene were analysed, revealing a total of 181 alleles. Each sample contained 43,63% of total allelic variation. Comparing variation with published data for wild cod indicates that lower genetic variation exists within single cages than in wild populations. Significant linkage disequilibrium was observed amongst pairs of loci in all samples, suggesting a low number of contributing parental fish. Global FST was 0.049, and the highest pairwise FST value (pooled loci) was 0.085. For single loci, the Pan I gene was the most diagnostic, displaying a global FST of 0.203. Simulations amongst the samples collected on farms revealed an overall correct self-assignment percentage of 75%, demonstrating a high probability of identifying individuals to their farm of origin. Identification of the 28 escapees revealed a single cage as the most likely source of origin for half of the escapees, whilst the remaining fish were assigned to a mixture of samples, suggesting more than one source of escapees. [source] Population divergence in the amphicarpic species Amphicarpaea edgeworthii Benth. (Fabaceae): microsatellite markers and leaf morphologyBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2009ZHONG-CHENG LIANG Comparative analyses of the genetic differentiation in microsatellite markers (FST) and leaf morphology characters (QST) of Amphicarpaea edgeworthii Benth. were conducted to gain insight into the roles of random processes and natural selection in the population divergence. Simple sequence repeat analyses on 498 individuals of 19 natural populations demonstrate that a significant genetic differentiation occurs among populations (mean FST = 0.578), and A. edgeworthii is a highly self-fertilized species (mean selfing rate s = 0.989). The distribution pattern of genetic diversity in this species shows that central populations possess high genetic diversity (e.g. population WL with HE = 0.673 and population JG with HE = 0.663), whereas peripheral ones have a low HE as in population JD (0.011). The morphological divergence of leaf shape was estimated by the elliptical Fourier analysis on the data from 11 natural and four common garden populations. Leaf morphology analyses indicate the morphological divergence does not show strong correlation with the genetic differentiation (R = 0.260, P = 0.069). By comparing the 95% confidence interval of QST with that of FST, QST values for five out of 12 quantitative traits are significantly higher than the average FST value over eight microsatellite loci. The comparison of FST and QST suggests that two kinds of traits can be driven by different evolutionary forces, and the population divergence in leaf morphology is shaped by local selections. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 505,516. [source] Effects of environmental pollution on microsatellite DNA diversity in wood mouse (Apodemus sylvaticus) populationsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2005Veerle Berckmoes Abstract Ten microsatellite DNA loci were surveyed to investigate the effects of heavy metal pollution on the genetic diversity and population genetic structure of seven wood mouse (Apodemus sylvaticus) populations along a heavy metal pollution gradient away from a nonferrous smelter in the south of Antwerp (Flanders, Belgium). Analysis of soil heavy metal concentrations showed that soil Ag, As, Cd, Cu, and Pb decreased with increasing distance from the smelter. Genetic analyses revealed high levels of genetic variation in all populations, but populations from the most polluted sites in the gradient did not differ from those of less-polluted sites in terms of mean observed and expected heterozygosity level and mean allelic richness. No correlation was found between measures of genetic diversity and the degree of heavy metal pollution. However, an analysis of molecular variance and a neighbor-joining tree suggested a contamination-related pattern of genetic structuring between the most polluted and less polluted sites. Pairwise FST values indicated that populations were significantly genetically differentiated, and assignment tests and direct estimates of recent migration rates suggested restricted gene flow among populations. Additionally, genetic differentiation increased significantly with geographical distance, which is consistent with an isolation-by-distance model. We conclude that, at least for our microsatellite DNA markers, genetic diversity in the studied wood mouse populations is not affected greatly by the heavy metal pollution. [source] EFFECTS OF ENVIRONMENTAL HETEROGENEITY ON VICTIM,EXPLOITER COEVOLUTIONEVOLUTION, Issue 12 2008Sergey Gavrilets We study victim,exploiter coevolution in a spatially heterogeneous island model. In each species, fitness consequences of between-species interactions are controlled by a single haploid diallelic locus. Our emphasis is on the conditions for the maintenance of genetic variation, the dynamic patterns observed, the extent of local adaptation and genetic differentiation between different demes, and on how different parameters (such as the strength and heterogeneity in selection, migration rates, and the number of sites) affect the dynamic and static behavior of the system. We show that under spatially homogeneous selection the maintenance of genetic variation is possible through asynchronous nonlinear dynamics where the allele frequencies in a majority of demes quickly synchronize but the rest do not. Spatially heterogeneous selection can maintain genetic variation even if migration rates are maximal. This happens in an oscillatory way. Genetic variation is most likely to be maintained at high levels if the heterogeneity in selection is large. If there are some restrictions on migration, genetic variation can be maintained at a stable equilibrium. This behavior is most likely at intermediate migration rates. In this case, the system can exhibit high spatial subdivision as measured by FST values but relatively low local adaptation. [source] ADAPTIVE POPULATION DIFFERENTIATION IN PHENOLOGY ACROSS A LATITUDINAL GRADIENT IN EUROPEAN ASPEN (POPULUS TREMULA, L.): A COMPARISON OF NEUTRAL MARKERS, CANDIDATE GENES AND PHENOTYPIC TRAITSEVOLUTION, Issue 12 2007David Hall A correct timing of growth cessation and dormancy induction represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees (Rehfeldt et al. 1999; Horvath et al. 2003; Howe et al. 2003). We have studied the deciduous tree European Aspen (Populus tremula) across a latitudinal gradient and compared genetic differentiation in phenology traits with molecular markers. Trees from 12 different areas covering 10 latitudinal degrees were cloned and planted in two common gardens. Several phenology traits showed strong genetic differentiation and clinal variation across the latitudinal gradient, with QST values generally exceeding 0.5. This is in stark contrast to genetic differentiation at several classes of genetic markers (18 neutral SSRs, 7 SSRs located close to phenology candidate genes and 50 SNPs from five phenology candidate genes) that all showed FST values around 0.015. We thus find strong evidence for adaptive divergence in phenology traits across the latitudinal gradient. However, the strong population structure seen at the quantitative traits is not reflected in underlying candidate genes. This result fit theoretical expectations that suggest that genetic differentiation at candidate loci is better described by FST at neutral loci rather than by QST at the quantitative traits themselves. [source] Genetic variability in Irish populations of the invasive zebra mussel, Dreissena polymorpha: discordant estimates of population differentiation from allozymes and microsatellitesFRESHWATER BIOLOGY, Issue 7 2008ELIZABETH GOSLING Summary 1. The recent arrival and explosive spread of the zebra mussel, Dreissena polymorpha (Pallas), in Ireland provided a rare opportunity to study the population genetics of an invasive species. 2. Eight polymorphic allozyme loci (ACO-1, ACO-2, EST-D, GPI, IDH-2, MDH, OPDH and PGM) were used to investigate genetic diversity and population structure in five Irish populations, and the results were compared with those from a previous microsatellite study on the same samples. 3. The mean number of alleles per locus (2.7 ± 0.1) was similar to the mean for the same loci in European populations, suggesting that Irish founder populations were large and/or multiple colonization events took place after foundation. A deficiency of heterozygotes was observed in all populations, but was uneven across loci. 4. Pairwise comparisons, using Fisher's exact tests and FST values, revealed significant genetic differentiation among populations. The overall multilocus FST estimate was 0.118 ± 0.045, which contrasted with an estimate of 0.015 ± 0.007 from five microsatellite loci on the same samples in a previous study. 5. Assuming that microsatellites can be used as a neutral baseline, the discordant results from allozymes and microsatellites suggest that selection may be acting on some allozyme loci, specifically ACO-1, ACO-2, IDH-2 and MDH, which contributed most to the significant differentiation between samples. [source] SINE insertion polymorphism on the X chromosome differentiates Anopheles gambiae molecular formsINSECT MOLECULAR BIOLOGY, Issue 4 2005M. J. Barnes Abstract Polymorphic SINE insertions can be useful markers for assessing population structure and differentiation. Maque is a family of SINE elements which, based on bioinformatic analysis, was suggested to have been active recently in Anopheles gambiae, the major vector of malaria. Here, we report the development of polymorphic Maque insertions as population genetic markers in A. gambiae, and the use of these markers to better characterize divergence on the X chromosome between A. gambiae M and S molecular forms in populations from Burkina Faso and Mali. Our data are consistent with the recent activity of Maque. Phylogenetic analysis suggests that at least two recently active lineages may have a role in mediating genome evolution. We found differences in element insertion frequency and sequence between the M and S populations analysed. Significant differentiation was observed between these two groups across a 6 Mb region at the proximal (centromeric) end of the X chromosome. Locus-specific FST values ranged from 0.14 to 1.00 in this region, yet were not significantly different from zero in more distal locations on the X chromosome; the trend was consistent in populations from both geographical locales suggesting that differentiation is not due to local adaptation. Strong differentiation between M and S at the proximal end of the X chromosome, but not outside this region, suggests the action of selection counteracting limited gene flow between these taxa and supports their characterization as incipient species. [source] Biogeographical patterns of genetic differentiation in dung beetles of the genus Trypocopris (Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analysesJOURNAL OF BIOGEOGRAPHY, Issue 7 2004Loredana Carisio Abstract Aim, To examine the phylogeography and population structure of three dung beetle species of the genus Trypocopris (Coleoptera, Geotrupidae). We wanted to test whether genetic differences and genealogies among populations were in accordance with morphologically described subspecies and we aimed to establish times of divergence among subspecies to depict the appropriate temporal framework of their phylogeographical differentiation. We also wished to investigate the historical demographic events and the relative influences of gene flow and drift on the distribution of genetic variability of the different populations. Location, Europe (mostly Italy). Methods, We collected adult males from dung pats from 15 Italian localities over the period 2000,2002. For sequence analysis, some dried specimens from Albania, Croatia, Slovakia and Spain were also used. We applied cytochrome oxidase I mitochondrial DNA sequencing and the amplified fragment length polymorphism (AFLP) technique to determine whether phylogeographical patterns within the three species support the proposed hypotheses of subspecies designations, and to detect further structure among populations that might mediate diversification. Results and main conclusions, The results show a high concordance between the distribution of mtDNA variation and the main morphological groups recognized as subspecies, which thus may represent independent evolutionary units. The degree of mitochondrial divergence suggests that speciation events occurred during the Pliocene, while diversification of the main subspecific lineages took place in the Pleistocene, from c. 0.3 to 1.5 Ma. Mitochondrial and nuclear data also reveal that there is phylogeographical structuring among populations within each of the main groups and that both contemporary and historical processes determined this pattern of genetic structure. Geographical populations form monophyletic clades in both phylogenetic and network reconstructions. Despite the high levels of intrapopulational diversity, FST values indicate moderate but significant genetic differentiation among populations, and a Bayesian clustering analysis of the AFLP data clearly separates the geographical populations. Nucleotide and gene diversity estimates reveal interspecific differences in the degree of diversification among populations that may be related to the different ecological requirements of the three species. [source] Comparative studies of quantitative trait and neutral marker divergence: a meta-analysisJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2008T. LEINONEN Abstract Comparative studies of quantitative genetic and neutral marker differentiation have provided means for assessing the relative roles of natural selection and random genetic drift in explaining among-population divergence. This information can be useful for our fundamental understanding of population differentiation, as well as for identifying management units in conservation biology. Here, we provide comprehensive review and meta-analysis of the empirical studies that have compared quantitative genetic (QST) and neutral marker (FST) differentiation among natural populations. Our analyses confirm the conclusion from previous reviews , based on ca. 100% more data , that the QST values are on average higher than FST values [mean difference 0.12 (SD 0.27)] suggesting a predominant role for natural selection as a cause of differentiation in quantitative traits. However, although the influence of trait (life history, morphological and behavioural) and marker type (e.g. microsatellites and allozymes) on the variance of the difference between QST and FST is small, there is much heterogeneity in the data attributable to variation between specific studies and traits. The latter is understandable as there is no reason to expect that natural selection would be acting in similar fashion on all populations and traits (except for fitness itself). We also found evidence to suggest that QST and FST values across studies are positively correlated, but the significance of this finding remains unclear. We discuss these results in the context of utility of the QST,FST comparisons as a tool for inferring natural selection, as well as associated methodological and interpretational problems involved with individual and meta-analytic studies. [source] Population genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of CaliforniaJOURNAL OF FISH BIOLOGY, Issue 2 2010S. M. Plank The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small FST values (,0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep-water channel from the coastal sites, however, was significantly divergent (large FST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size. [source] Fine scale genetic population structure of the freshwater and Omono types of nine-spined stickleback Pungitius pungitius (L.) within the Omono River system, JapanJOURNAL OF FISH BIOLOGY, Issue 2006T. Tsuruta The fine scale geographic population structure of two types of nine-spined stickleback Pungitius pungitius (the widely distributed freshwater type and a local endemic, the Omono type) within the Omono River system, Japan, was investigated. A principal components analysis of allele frequencies and neighbour-joining tree for pair-wise FST values, based on 10 allozyme loci, revealed that the Omono type was comprised of four regional groups with relatively high genetic divergence. This grouping was also supported by hierarchical analysis of molecular variance (AMOVA) with a higher variance component among the regional groups, and by an exact test with significant genotypic differentiation for all sample pairs among the regional groups. Moreover, in the clustering of individuals using the Bayesian method, most of individuals in each regional group were assigned the corresponding cluster. On the other hand, there were less pronounced regional groups of the freshwater type, although AMOVA, exact test for genotypic differentiation and Bayesian analysis indicated genetic divergence between two sampling sites in lower reach of the Omono River and other sites. The results suggest that the Omono type represented an earlier colonization, with subsequent invasion of the freshwater type. [source] Genetic variability and differentiation in red deer (Cervus elaphus) from Scotland and EnglandJOURNAL OF ZOOLOGY, Issue 3 2006S. S. Hmwe Abstract Samples from 69 British red deer Cervus elaphus scoticus from seven populations in Scotland and England were analysed with respect to variability within and differentiation among stocks using 11 polymorphic microsatellite loci and 439 bp of the mitochondrial control region. The results clearly showed the effects of anthropogenic factors on British red deer. On the whole, variability values were within the species' reported range. The island population of Islay, Scotland, however, while showing average microsatellite variability, exhibited no mitochondrial variation at all. One microsatellite locus was monomorphic in three Scottish populations (Islay, Dunachton and Achnacarry). Overall and pairwise FST values indicate considerable differentiation among the populations studied, but Dunachton and Achnacarry, two adjacent populations free from recorded introductions, showed only a little differentiation and were paired in trees based on genetic distances. In terms of variability, no statistically significant differences were observed between island and mainland populations and the overall test of isolation by distance was negative. Possible reasons for the genetic patterns observed, such as differences in human impact on the populations, are discussed. [source] Eastern and Western Poor Cod (Trisopterus minutus capelanus) Populations in the Mediterranean Sea: Evidence from Allozyme and Minisatellite LociMARINE ECOLOGY, Issue 4 2003Valeria Mattiangeli Abstract., Nine allozyme and two minisatellite loci were used to investigate potential genetic differentiation among three samples of Mediterranean poor cod, Trisopterus minutus capelanus, from the Gulf of Lion, the Tuscan Archipelago and the Aegean Sea. Both types of markers showed consistent results, with FST values of 0.0262 and 0.0296 (P < 0.0015, after Bonferroni correction for multiple tests) for allozymes and minisatellites, respectively. Allele frequency heterogeneity tests between pairs of samples showed a clear separation between the two western Mediterranean samples (Gulf of Lion, Tuscan Archipelago) and the eastern one (Aegean Sea). The results indicate that at least two reproductively isolated populations of poor cod occur in the Mediterranean. [source] Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppiesMOLECULAR ECOLOGY, Issue 5 2010EVA-MARIA WILLING Abstract Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise FST values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. FST outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations [source] Local selection and population structure in a deep-sea fish, the roundnose grenadier (Coryphaenoides rupestris)MOLECULAR ECOLOGY, Issue 2 2010THOMAS A. WHITE Abstract Local populations within a species can become isolated by stochastic or adaptive processes, though it is most commonly the former that we quantify. Using presumably neutral markers we can assess the time-dependent process of genetic drift, and thereby quantify patterns of differentiation in support of the effective management of diversity. However, adaptive differences can be overlooked in these studies, and these are the very characteristics that we hope to conserve by managing neutral diversity. In this study, we used 16 hypothetically neutral microsatellite markers to investigate the genetic structure of the roundnose grenadier in the North Atlantic. We found that one locus was a clear outlier under directional selection, with FST values much greater than at the remaining loci. Differentiation between populations at this locus was related to depth, suggesting directional selection, presumably acting on a linked locus. Considering only the loci identified as neutral, there remained significant population structure over the region of the North Atlantic studied. In addition to a weak pattern of isolation by distance, we identified a putative barrier to gene flow between sample sites either side of the Charlie-Gibbs Fracture Zone, which marks the location where the sub-polar front crosses the Mid-Atlantic Ridge. This may reflect a boundary across which larvae are differentially distributed in separate current systems to some extent, promoting differentiation by drift. Structure due to both drift and apparent selection should be considered in management policy. [source] Genome scan in the mosquito Aedes rusticus: population structure and detection of positive selection after insecticide treatmentMOLECULAR ECOLOGY, Issue 2 2010MARGOT PARIS Abstract Identification of genes involved in local adaptation is particularly challenging for species functioning as a network of interconnected populations undergoing frequent extinctions,recolonizations, because populations are submitted to contrasted evolutionary pressures. Using amplified fragment length polymorphism markers, population genetic structure of the mosquito Aedes rusticus was analysed in five geographical areas of the French Rhône-Alpes region. We included a number of sites that were treated with the bio-insecticide Bacillus thuringiensis israelensis (Bti) for more than 15 years. Analysis of molecular variance revealed that most of the genetic variability was found within populations (96%), with no significant variation among geographical areas, although variation among populations within areas (4%) was significant. The global genetic differentiation index FST was low (0.0366 ± 0.167). However, pairwise FST values were significant and no isolation-by-distance at the regional level was observed, suggesting a metapopulation structure in this species. Bti -treatment had no effect on genetic structure and on within-population genetic diversity. Potential signatures of positive selection associated with Bti -treatment were detected for five loci, even though toxicological bioassays performed on field-collected larvae showed no significant difference in mortality between Bti -treated and nontreated sites. The difficulty of detecting moderate resistance in field-collected larvae together with possible differential persistence of toxins in the environment may explain our inability to detect a toxicological response to Bti in treated sites. The evidence for positive selection occurring at several genomic regions suggests a first step towards Bti resistance in natural mosquito populations treated with this bio-insecticide. Furthermore, this signal was detectable using genomic tools before any toxicological evidence for resistance could be identified. [source] Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian PeninsulaMOLECULAR ECOLOGY, Issue 20 2008A. GERALDES Abstract The role of the Y chromosome in speciation is unclear. Hybrid zones provide natural arenas for studying speciation, as differential introgression of markers may reveal selection acting against incompatibilities. Two subspecies of the European rabbit (Oryctolagus cuniculus) form a hybrid zone in the Iberian Peninsula. Previous work on mitochondrial DNA (mtDNA), Y- and X-linked loci revealed the existence of two divergent lineages in the rabbit genome and that these lineages are largely subspecies-specific for mtDNA and two X-linked loci. Here we investigated the geographic distribution of the two Y chromosome lineages by genotyping two diagnostic single nucleotide polymorphisms in a sample of 353 male rabbits representing both subspecies, and found that Y chromosome lineages are also largely subspecies-specific. We then sequenced three autosomal loci and discovered considerable variation in levels of differentiation at these loci. Finally, we compared estimates of population differentiation between rabbit subspecies at 26 markers and found a surprising bimodal distribution of FST values. The vast majority of loci showed little or no differentiation between rabbit subspecies while a few loci, including the SRY gene, showed little or no introgression across the hybrid zone. Estimates of population differentiation for the Y chromosome were surprisingly high given that there is male-biased dispersal in rabbits. Taken together, these data indicate that there is a clear dichotomy in the rabbit genome and that some loci remain highly differentiated despite extensive gene flow following secondary contact. [source] The Bassian Isthmus and the major ocean currents of southeast Australia influence the phylogeography and population structure of a southern Australian intertidal barnacle Catomerus polymerus (Darwin)MOLECULAR ECOLOGY, Issue 8 2008KATHERINE L. YORK Abstract Southern Australia is currently divided into three marine biogeographical provinces based on faunal distributions and physical parameters. These regions indicate eastern and western distributions, with an overlap occurring in the Bass Strait in Victoria. However, studies indicate that the boundaries of these provinces vary depending on the species being examined, and in particular on the mode of development employed by that species, be they direct developers or planktonic larvae dispersers. Mitochondrial DNA sequence analysis of the surf barnacle Catomerus polymerus in southern Australia revealed an east,west phylogeographical split involving two highly divergent clades (cytochrome oxidase I 3.5 ± 0.76%, control region 6.7 ± 0.65%), with almost no geographical overlap. Spatial genetic structure was not detected within either clade, indicative of a relatively long-lived planktonic larval phase. Five microsatellite loci indicated that C. polymerus populations exhibit relatively high levels of genetic divergence, and fall into four subregions: eastern Australia, central Victoria, western Victoria and Tasmania, and South Australia. FST values between eastern Australia (from the eastern mitochondrial DNA clade) and the remaining three subregions ranged from 0.038 to 0.159, with other analyses indicating isolation by distance between the subregions of western mitochondrial origin. We suggest that the east,west division is indicative of allopatric divergence resulting from the emergence of the Bassian land-bridge during glacial maxima, preventing gene flow between these two lineages. Subsequently, contemporary ecological conditions, namely the East Australian, Leeuwin, and Zeehan currents and the geographical disjunctions at the Coorong and Ninety Mile Beach are most likely responsible for the four subregions indicated by the microsatellite data. [source] Potential selection in native grass populations by exotic invasionMOLECULAR ECOLOGY, Issue 8 2006BRIAN A. MEALOR Abstract Ecological impacts of invasive plant species are well documented, but the genetic response of native species to invasive dominance has been often overlooked. Invasive plants can drastically alter site conditions where they reach dominance, potentially exerting novel selective pressures on persistent native plant populations. Do native plant populations in old exotic invasions show evidence of selection when compared to conspecific populations in adjacent, noninvaded areas? We employ amplified fragment length polymorphism (AFLP) analysis to screen a large number of loci from two native grass species (Hesperostipa comata (Trin. & Rupr.) Barkworth and Sporobolus airoides Torr.) that occur in old infestations of the invasive forb Acroptilon repens. We then compare observed locus by locus FST values with distributions of FST estimated from simulation models under expectation of neutrality. We also compare the proportion of loci possibly linked to selection and those not linked to selection which exhibit parallel trends in divergence between two community types (invaded, noninvaded). Few loci (H. comata, 2.6%; S. airoides, 8.7%) in the two native grasses may be linked to genes under the influence of selection. Also, loci linked to selection showed a greater portion of parallel trends in divergence than neutral loci. Genetic similarities between community types were less than genetic similarity within community types suggesting differentiation in response to community alteration. These results indicate that a small portion of scored AFLP loci may be linked to genes undergoing selection tied to community dominance by an invasive species. We propose that native plants in communities dominated by exotic invasives may be undergoing natural selection. [source] Genetic variation and relationships among eight Indian riverine buffalo breedsMOLECULAR ECOLOGY, Issue 3 2006SATISH KUMAR Abstract Twenty-seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy,Weinberg equilibrium were observed for 26 locus-breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of FST index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour-joining tree constructed from chord distances, multidimensional scaling (MDS) display of FST values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800,2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes. [source] Low gene flow but high genetic diversity in the threatened Mallorcan midwife toad Alytes muletensisMOLECULAR ECOLOGY, Issue 11 2005F. J. L. KRAAIJEVELD-SMIT Abstract We investigated fine-scale genetic structuring in the rare and vulnerable Mallorcan midwife toad Alytes muletensis using eight polymorphic microsatellite markers. The current range of this amphibian is restricted to some 19 sites of which six are derived from reintroductions, all located in the mountain ranges of Mallorca. We sampled tadpoles from 14 pools covering 10 natural sites and two reintroduction sites for microsatellite DNA analyses. Relatively high levels of genetic variation were found in most pools (HE = 0.38,0.71, allelic richness = 2.6,6.2). Only at one pool has the population recently gone through a bottleneck. Dispersal between pools in different torrents does not occur whereas downstream dispersal between pools within the same torrent does happen at low frequencies. This occasional exchange of individuals does not lead to neighbouring pools in the same torrent being panmictic. This can be concluded because all FST values (0.12,0.53) differ significantly from zero and structure analyses identified neighbouring pools as separate populations. Furthermore, assignment and migration tests showed little exchange between neighbouring pools. If upstream locations or complete torrents go extinct, they are unlikely to be recolonized naturally. For conservation purposes, reintroductions of tadpoles to sites where local extinctions have occurred may therefore be advisable. [source] Genetic structure of avian populations , allozymes revisitedMOLECULAR ECOLOGY, Issue 10 2000P.-A. Crochet Abstract Selection on allozymes has sometimes been advanced as one explanation for the low levels of population differentiation detected in avian populations by the use of enzymatic markers. Comparisons of the amount of population subdivision (estimated by FST values or analogous indices) measured by enzymatic and mitochondrial DNA (mtDNA) markers in birds were seen as evidence for this because mtDNA typically produces a more structured picture of population subdivisions. In fact, when taking into account the smaller effective population size of mtDNA, nuclear and mitochondrial markers give concordant results. Some discrepancies still exist, but I suggest that some might originate from different amounts of nuclear vs. mitochondrial gene flow due to partial reproductive isolation. Variable number of tandem repeat (VNTR) loci do not provide a dramatically different picture of population structures in birds compared to allozymes. Although more tests are needed, such as comparing the amount of genetic structure detected in the same populations with allozymes and microsatellites, the low levels of population subdivision measured with allozymes in birds seem to reflect historical and demographic processes and would not appear to result from any peculiarities of bird enzymatic loci. [source] Microsatellite DNA markers for the study of horseshoe crab (Limulus polyphemus) population structureMOLECULAR ECOLOGY RESOURCES, Issue 3 2004TIM L. KING Abstract Twenty-two microsatellite DNA loci were identified and characterized for horseshoe crabs (Limulus polyphemus) collected from two Atlantic coast and one Gulf of Mexico site. These markers revealed a high degree of genetic diversity (8,35 alleles per locus), heterozygosity (25.0% to 100.0%), and allelic heterogeneity (69.8% of comparisons). Considerable regional differentiation was observed as genetic distances (chord) ranged between 0.25 and 0.45, and all FST values (0.014,0.092) were significant. These preliminary findings are consistent with patterns of regional differentiation observed using allozyme variation and contradictory to findings of limited gene flow reported for sequence variation at the mitochondrial DNA COI region. [source] Isolation and characterization of novel tetranucleotide microsatellite DNA markers for the spotted salamander, Ambystoma maculatumMOLECULAR ECOLOGY RESOURCES, Issue 1 2003S. E. Julian Abstract Fifteen tetranucleotide microsatellite loci were identified and characterized for spotted salamanders (Ambystoma maculatum) collected from three vernal pools in the south-eastern USA. These markers revealed a high degree of genetic diversity (7,32 alleles per locus), heterozygosity (31.6,86.3%) and allelic heterogeneity (91% of comparisons were statistically significant). Considerable differentiation among populations was observed as genetic distances (chord) ranged between 0.50 and 0.65, and all FST values (0.08,0.14) were statistically significant. Moreover, genotypic assignment tests correctly classified all individuals to their respective collection. These markers should prove useful for investigating fine-scale population structure and mating system. [source] Polymorphic Alu insertions in five North-West Italian populationsAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 4 2007A. Santovito We analyzed the frequencies of eight human polymorphic Alu insertion loci in population samples from five towns in North-West Italy: Postua, Cavaglià, Biella, Torino, and Genova. All loci under scrutiny were found to be polymorphic in all samples, with the two exceptions of locus A25 in Postua, which was fixed for the absence of the Alu element, and APO in Genova, where the Alu insertion was fixed. Heterozigosity values were highly variable in all loci. FST values for all loci indicate that most of the variability is found within populations, while between population variability is lower. In the multidimensional scaling (MDS) analysis plot, the studied populations are separated from the main group represented by European populations. The Postua sample is set apart also from neighboring towns as Cavaglià and Biella, confirming previous observations of the demographic isolation of this population. Am. J. Hum. Biol. 19:589,592, 2007. © 2007 Wiley-Liss, Inc. [source] Genetic differentiation in pointing dog breeds inferred from microsatellites and mitochondrial DNA sequenceANIMAL GENETICS, Issue 1 2008D. Parra Summary Recent studies presenting genetic analysis of dog breeds do not focus specifically on genetic relationships among pointing dog breeds, although hunting was among the first traits of interest when dogs were domesticated. This report compares histories with genetic relationships among five modern breeds of pointing dogs (English Setter, English Pointer, Epagneul Breton, Deutsch Drahthaar and German Shorthaired Pointer) collected in Spain using mitochondrial, autosomal and Y-chromosome information. We identified 236 alleles in autosomal microsatellites, four Y-chromosome haplotypes and 18 mitochondrial haplotypes. Average FST values were 11.2, 14.4 and 13.1 for autosomal, Y-chromosome microsatellite markers and mtDNA sequence respectively, reflecting relatively high genetic differentiation among breeds. The high gene diversity observed in the pointing breeds (61.7,68.2) suggests contributions from genetically different individuals, but that these individuals originated from the same ancestors. The modern English Setter, thought to have arisen from the Old Spanish Pointer, was the first breed to cluster independently when using autosomal markers and seems to share a common maternal origin with the English Pointer and German Shorthaired Pointer, either via common domestic breed females in the British Isles or through the Old Spanish Pointer females taken to the British Isles in the 14th and 16th centuries. Analysis of mitochondrial DNA sequence indicates the isolation of the Epagneul Breton, which has been formally documented, and shows Deutsch Drahthaar as the result of crossing the German Shorthaired Pointer with other breeds. Our molecular data are consistent with historical documents. [source] Population structure, genetic variation and morphological diversity in indigenous sheep of EthiopiaANIMAL GENETICS, Issue 6 2007S. Gizaw Summary We investigated genetic and morphological diversity and population structure of 14 traditional sheep populations originating from four ecological zones in Ethiopia (sub-alpine, wet highland, sub-humid lowland and arid lowland). All animals (n = 672) were genotyped for 17 microsatellite markers and scored for 12 morphological characters. The sheep were initially classified as fat-tailed (11 populations), thin-tailed (one population) and fat-rumped sheep (two populations). These classifications are thought to correspond to three consecutive introduction events of sheep from the Near-East into East Africa. For the 14 populations, allelic richness ranged from 5.87 to 7.51 and expected heterozygosity (HE) from 0.66 to 0.75. Genetic differentiations (FST values) between all pairs of populations, except between sub-alpine populations, were significantly different from zero (P < 0.001). Cluster analysis of morphological characters and a dendrogram constructed from genetic distances were broadly consistent with the classification into fat-tailed, thin-tailed and fat-rumped sheep. Bayesian cluster analysis using microsatellite markers indicated that there has been further genetic differentiation after the initial introduction of sheep into Ethiopia. Investigation of factors associated with genetic variation showed that an isolation-by-distance model, independently of other factors, explained most of the observed genetic variation. We also obtained a strong indication of adaptive divergence in morphological characters, patterns of morphological variation being highly associated with ecology even when the effect of neutral genetic divergence (FST) was parcelled out in partial Mantel tests. Using a combination of FST values, Bayesian clustering analysis and morphological divergence, we propose a classification of Ethiopian sheep into six breed groups and nine breeds. [source] Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphismsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2005E.M. Ibeagha-Awemu Summary Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (Fit) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to 6.1%. The breeds were moderately differentiated (Fst = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the Fst value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub-clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub-clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds. [source] | ||||||||||||||||||||||||||||