Home About us Contact
|
Home About us Contact | ||
|
|
||
Assignment Tests (assignment + test)
Selected AbstractsPopulation structure and its implications for conservation of the great silver beetle Hydrophilus piceus in BritainFRESHWATER BIOLOGY, Issue 11 2007TREVOR J. C. BEEBEE Summary 1. The great silver water beetle Hydrophilus piceus is one of the largest aquatic insects in Europe. In Britain it is rare and endangered, and confined to a small number of low-lying marshes. Very little is known about the beetle populations in any of these areas, or the connectivity between them. 2. To investigate the population structure of H. piceus in Britain, four polymorphic microsatellite loci were identified and characterized. The genome of this beetle seems to have few microsatellites but contains a high proportion of a larger repeated sequence. 3. All six of the main British populations (Somerset, Lewes, Pevensey, Romney, North Kent and Norfolk) showed substantial genetic diversity at the microsatellite loci. However, estimates of effective population size at one site (Pevensey) were remarkably low, at <10 adults for the period 2004,05. 4. Most of the genetic diversity was partitioned within rather than among the populations, although there was, nevertheless, significant genetic sub-structuring. Almost all population pairwise Fst estimates were significantly different from zero, and there was a clear isolation-by-distance effect. Assignment tests and cluster analyses demonstrated interpopulation relationships largely consistent with their geographical separations. 5. Hydrophilus disperses by flight, and records from moth traps indicated that there was no month in which the beetles never flew, but that flight activity was highest in the spring. 6. The genetic data highlight the need to maintain or regenerate habitat connectivity within flying distance for H. piceus, and to sustain large areas of suitable breeding marshes. [source] Conservation and management implications of fine-scale genetic structure of Gulf sturgeon in the Pascagoula River, MississippiJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2004M. A. Dugo Summary The anadromous Gulf sturgeon occurs along the north central coast of the Gulf of Mexico and is federally listed as threatened. We analyzed fine-scale patterns of Gulf sturgeon population structure, focusing on the Pascagoula River drainage of Mississippi, in reference to movement patterns as determined via telemetry and capture data. We genotyped 361 Gulf sturgeon using eight microsatellite loci including samples from the Pascagoula, Pearl, Escambia, Yellow, Choctawhatchee, and Apalachicola river drainages. Pairwise FST estimates indicated that genetic structure occurs at least at the drainage level. The Pascagoula and Pearl rivers form a western group, demonstrating 100% bootstrap support for a division with drainages to the east. Assignment tests detected non-natal genotypes occurring in all drainages. According to assignment tests, the Pascagoula supports an admixture of individuals, containing minimal influence from drainages to the east (2%) and substantial interaction with the Pearl River (14.1%). The occurrence of Pascagoula River fish in the Pearl was non-reciprocal, observed at 1.1%. After accounting for non-natal genetic diversity within the Pascagoula, there remained a disparity between a pooled Pascagoula group and the only documented spawning site within the drainage located in the Bouie River. We interpret this as an indication of a second genetic stock within the Pascagoula River drainage. Radio telemetry data suggest that spawning likely occurs in the Chickasawhay River, in areas isolated from the Bouie River spawning site by about 350 river kilometers. We emphasize the utility of integrating field and molecular approaches when delineating fine-scale patterns of population structure in anadromous fishes. [source] Genetic and morphometric differentiation among island populations of two Norops lizards (Reptilia: Sauria: Polychrotidae) on independently colonized islands of the Islas de Bahia (Honduras)JOURNAL OF BIOGEOGRAPHY, Issue 7 2007C. F. C. Klütsch Abstract Aim, Anole lizards (Reptilia: Sauria: Polychrotidae) display remarkable morphological and genetic differentiation between island populations. Morphological differences between islands are probably due to both adaptive (e.g. differential resource exploitation and intra- or interspecific competition) and non-adaptive differentiation in allopatry. Anoles are well known for their extreme diversity and rapid adaptive speciation on islands. The main aim of this study was to use tests of morphological and genetic differentiation to investigate the population structure and colonization history of islands of the Islas de Bahia, off the coast of Honduras. Location, Five populations of Norops bicaorum and Norops lemurinus were sampled, four from islands of the Islas de Bahia and one from the mainland of Honduras. Methods, Body size and weight differentiation were measured in order to test for significant differences between sexes and populations. In addition, individuals were genotyped using the amplified fragment length polymorphism technique. Bayesian model-based and assignment/exclusion methods were used to study genetic differentiation between island and mainland populations and to test colonization hypotheses. Results, Assignment tests suggested migration from the mainland to the Cayos Cochinos, and from there independently to both Utila and Roatán, whereas migration between Utila and Roatán was lacking. Migration from the mainland to Utila was inferred, but was much less frequent. Morphologically, individuals from Utila appeared to be significantly different in comparison with all other localities. Significant differentiation between males of Roatán and the mainland was found in body size, whereas no significant difference was detected between the mainland and the Cayos Cochinos. Main conclusions, Significant genetic and morphological differentiation was found among populations. A stepping-stone model for colonization, in combination with an independent migration to Utila and Roatán, was suggested by assignment tests and was compatible with the observed morphological differentiation. [source] Genetic evidence for sex-biased dispersal in resident bottlenose dolphins (Tursiops aduncus)MOLECULAR ECOLOGY, Issue 6 2004Luciana M. Möller Abstract In most mammals males usually disperse before breeding, while females remain in their natal group or area. However, in odontocete cetaceans behavioural and/or genetic evidence from populations of four species indicate that both males and females remain in their natal group or site. For coastal resident bottlenose dolphins field data suggest that both sexes are philopatric to their natal site. Assignment tests and analyses of relatedness based on microsatellite markers were used to investigate this hypothesis in resident bottlenose dolphins, Tursiops aduncus, from two small coastal populations of southeastern Australia. Mean corrected assignment and mean relatedness were higher for resident females than for resident males. Only 8% of resident females had a lower probability than average of being born locally compared to 33% of resident males. Our genetic data contradict the hypothesis of bisexual philopatry to natal site and suggest that these bottlenose dolphins are not unusual amongst mammals, with females being the more philopatric and males the more dispersing sex. [source] Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crossesANIMAL GENETICS, Issue 4 2002G. Bjřrnstad Assignment tests have been utilized to investigate population classification, measure genetic diversity and to solve forensic questions. Using microsatellite data from 26 loci genotyped in eight horse breeds we examined how population differentiation, number of scored loci, number of scored animals per breed and loci variability affected individual assignment precision applying log likelihood methods. We found that both genetic differentiation and number of scored loci were highly important for recognizing the breed of origin. When comparing two and two breeds, a proportion of 95% of the most differentiated breeds (0.200 , FST , 0.259) could be identified scoring only three loci, while the corresponding number was six for the least differentiated breeds (0.080 , FST , 0.139). An identical proportion of simulated breed crosses, differentiated from their parental breeds by FST estimates in the range 0.050,0.069, was identified when scoring 12 loci. This level of source identification was not obtained for the less differentiated breed crosses. The current data further suggested that population sample size and locus variability were not critical for the assignment precision as long as moderately large sample sizes (, 20 animals per population) and fairly variable loci were used. [source] Genetic differentiation in the urban habitat: the great tits (Parus major) of the parks of Barcelona cityBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010MATS BJÖRKLUND The increase of urban areas has led to a fragmentation of habitats for many forest-living species. Man-made parks might be a solution, but they can also act as sinks that are unable to maintain themselves without immigration from natural areas. Alternatively, parks might act as true metapopulations with extinctions and colonizations. In both cases, we can expect genetic variation to be reduced in the parks compared to the natural habitat. A third alternative is that the parks have sufficient reproduction to maintain themselves. To test these hypotheses, we analysed the pattern of genetic variation in the great tit (Parus major) in 12 parks in central Barcelona, and in an adjacent forest population using microsatellites. Genetic variation was not lower in the parks compared to the forest population, but larger, and gene flow was higher from the town to the forest compared to vice versa. We found a significant genetic differentiation among the parks, with a structure that only partly reflected the geographic position of the parks. Relatedness among individuals within parks was higher than expected by chance, although we found no evidence of kin groups. Assignment tests suggest that some parks are acting as net donors of individuals to other parks. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 9,19. [source] Genetic structure of the European polecat (Mustela putorius) and its implication for conservation strategiesJOURNAL OF ZOOLOGY, Issue 1 2006C. Pertoldi Abstract During the last century, the European polecat Mustela putorius populations in most of Europe declined and survived in fragmented patches, because of habitat alterations and direct persecution. To assess the genetic consequences of the demographic decline and to describe the spatial pattern of genetic diversity, 250 polecats sampled at seven localities from five European countries , Poland, Denmark (southern Denmark and northern Denmark), Spain, Belgium (eastern and western) and the Netherlands , were screened by means of nine microsatellite loci. Genetic diversity estimated by mean expected heterozygosity (HE) and allelic richness (AR) were moderately high within populations [range: 0.50 (northern Denmark) ,HE,0.64 (Poland) and 1.33,AR,7.80] as compared with other carnivores and mustelids. Bottleneck tests suggested that polecat populations in southern Denmark and Poland have declined recently and populations from northern Denmark and the Netherlands have expanded recently, whereas the remaining populations did not show any sign of demographic change. Recent demographic changes could suggest that some of the populations are still not in equilibrium, which could partly explain the relatively high genetic variability observed in polecat populations despite the drastic decline in population size observed in several European countries. A significant heterozygote deficiency [FIS=0.19; 0.01,95% confidence interval (CI),0.32] suggests substructuring within the total European sample. Partitioning of the genetic variation among sampling locations (FST=0.14; 0.06,95% CI,0.23) and pairwise FST between localities (range: 0.01,FST,0.37) without any correlation with the geographic distances between localities were found, suggesting a recent divergence and a restriction of gene flow between populations and the action of genetic drift. An assignment test showed that the Polish and the northern Danish populations were the most unique, whereas the other populations were partially admixed. Factorial component analysis tests indicate a subdivision of the total sample into two distinct groups: one including the samples from Poland and the two Danish localities and the second group comprising the remaining localities investigated. The observed pattern of genetic differentiation is suggested to be due to two main routes of recolonization after the last glacial period. To compare the results obtained with microsatellite data, the most variable region of the mitochondrial DNA (d-loop) was sequenced and different phylogenetic reconstructions and genetic diversity analyses based on nucleotide (,) and haplotype diversity (h) measures within populations were performed using a subsample of populations. The lack of well-defined geographical structure, as well as the reduced level of mitochondrial DNA variability (,: 0.00274±0.00038; h: 0.876±0.028) that was found, has been previously reported in several studies on different carnivores and supports the hypothesis of post-glacial recolonization from southern or eastern refugees of Europe as suggested by the microsatellite data. Implications for conservation strategies of the polecat at the European level are discussed. [source] Low level of gene flow from cultivated beets (Beta vulgaris L. ssp. vulgaris) into Danish populations of sea beet (Beta vulgaris L. ssp. maritima (L.) Arcangeli)MOLECULAR ECOLOGY, Issue 5 2005N. S. ANDERSEN Abstract Gene flow from sugar beets to sea beets occurs in the seed propagation areas in southern Europe. Some seed propagation also takes place in Denmark, but here the crop,wild gene flow has not been investigated. Hence, we studied gene flow to sea beet populations from sugar beet lines used in Danish seed propagation areas. A set of 12 Danish, two Swedish, one French, one Italian, one Dutch, and one Irish populations of sea beets, and four lines of sugar beet were analysed. To evaluate the genetic variation and gene flow, eight microsatellite loci were screened. This analysis revealed hybridization with cultivated beet in one of the sea beet populations from the centre of the Danish seed propagation area. Triploid hybrids found in this population were verified with flow cytometry. Possible hybrids or introgressed plants were also found in the French and Italian populations. However, individual assignment test using a Bayesian method provided 100% assignment success of diploid individuals into their correct subspecies of origin, and a Bayesian Markov chain Monte Carlo (MC MC) approach revealed clear distinction of individuals into groups according to their subspecies of origin, with a zero level of genetic admixture among subspecies. This underlines that introgression beyond the first hybridization is not extensive. The overall pattern of genetic distance and structure showed that Danish and Swedish sea beet populations were closely related to each other, and they are both more closely related to the population from Ireland than to the populations from France, the Netherlands, and Italy. [source] Cytonuclear disequilibrium in a hybrid zone involving deep-sea hydrothermal vent mussels of the genus BathymodiolusMOLECULAR ECOLOGY, Issue 11 2003Y. Won Abstract A hybrid zone involving the deep-sea mussels, Bathymodiolus azoricus and B. puteoserpentis, was recently discovered at Broken Spur hydrothermal vent field (29°10, N, 43°10, W) along an intermediate segment of the Mid-Atlantic Ridge axis. Examination of nuclear (allozymes) and cytoplasmic (mitochondrial DNA) gene markers in a new sample from Broken Spur revealed significant cytonuclear disequilibrium caused by an excess of the parental types (coupling phase) and a deficiency of recombinants (repulsion phase). An assignment test of individual multilocus genotypes also revealed an excess of parental genotypes in the admixed population. These results support the hypothesis that the Broken Spur mussel population comprises a nonequilibrium mixture of parental immigrants and hybrid individuals. [source] Fine-scale population structure and dispersal in Biomphalaria glabrata, the intermediate snail host of Schistosoma mansoni, in VenezuelaMOLECULAR ECOLOGY, Issue 5 2002J. Mavárez Abstract Biomphalaria glabrata is the main intermediate host of Schistosoma mansoni in America and one of the most intensely studied species of freshwater snails, yet very little is known about its population biology. Here, we used seven highly polymorphic microsatellite loci to analyse genetic diversity in the Valencia lake basin, which represents the core of the endemic area for schistosomiasis in Venezuela. Populations were sampled at short spatial scale (a few kilometres), both inside the lake and in ponds or rivers near the lake. Our results indicate that B. glabrata essentially cross-fertilizes, with little variation in selfing rates among populations. Our markers detected considerable genetic variation, with an average heterozygosity of 0.60. More diversity per population was found within than outside the lake, suggesting an influence of connectivity among populations on the levels of genetic diversity. A marked population structure was detected and lake populations were less structured than other populations. Most individuals were assigned to their population of origin using an assignment test. No strong demographic signal (e.g. bottleneck) was detected, though lake populations are likely to experience bottlenecks more frequently than the other populations analysed. Differences in gene flow therefore seem to play an important role in population differentiation and in the restoring of genetic diversity in demographically unstable populations. [source] Microsatellite analysis of North American wapiti (Cervus elaphus) populationsMOLECULAR ECOLOGY, Issue 10 2000Renee O. Polziehn Abstract Eleven populations of wapiti (Cervus elaphus) were analysed for genetic diversity using 12 microsatellite loci. Samples were taken from Vancouver Island, British Columbia; Burwash and French River herds in Ontario; Ya Ha Tinda Ranch, Alberta; and Banff, Elk Island, Jasper, Kootenay, Riding Mountain, Yellowstone and Yoho National Parks. Overall, wapiti populations have on average three to four alleles per locus and an average expected heterozygosity that ranged from 25.75 to 52.85%. The greatest genetic distances were observed between the Vancouver population and all other populations. Using the assignment test, Roosevelt wapiti (C. e. roosevelti Merriam 1897) assigned only to the Vancouver Island population. The distance and assignment values suggest a divergence of the Roosevelt wapiti from other populations and support the subspecific status for the Vancouver Island population. No evidence was found for the existence of unique Eastern wapiti (C. e. canadensis Erxleben 1777) in the Burwash or French River herds in Ontario. The overlapping distribution of genotypes from indigenous populations from Riding Mountain, Elk Island and Yellowstone National Parks suggests that wapiti were once a continuous population before settlers decimated their numbers. The lack of differentiation between these populations raises questions about the status of Manitoban (C. e.manitobensis Millais 1915) and Rocky Mountain (C. e.nelsoni Bailey 1935) subspecies. [source] Isolation by distance, based on microsatellite data, tested with spatial autocorrelation (spaida) and assignment test (spassign)MOLECULAR ECOLOGY RESOURCES, Issue 1 2004Snćbjörn Pálsson Abstract spassign and spaida are two small programs useful to detect isolate by distance of microsatellite loci. The programs are written in C and are available for Linux and Windows system at http://www.hi.is/~snaebj/programs.html. spaida calculates two estimates of spatial autocorrelation, Moran's I and Geary's c, first by assuming the infinite allele model, and second by assuming a stepwise mutational model. spassign calculates the assignment probabilities of an individuals genotype to the location where it was sampled and compares probabilities of assignment to other locations. Genetic distances among regions based on the overall differences in likelihoods are calculated. [source] Infraspecific variation and phylogeography of the high-polyploid Iberian endemic Anthoxanthum amarum Brot. (Poaceae; Pooideae) assessed by random amplified polymorphic DNA markers (RAPDs) and morphologyBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2007MANUEL PIMENTEL High morphological and ecological diversity has been observed in the north-west Iberian Peninsula endemic Anthoxanthum amarum Brot., for which two different morphotypes (northern and southern) have been described on the basis of qualitative traits and geographical origin. In the present study, a combined molecular and morphological method was applied to ten populations of this species with the following aims: (1) to assess whether the variation observed was taxonomically meaningful; (2) to assess the influence of the environment on the variation in the morphological characters; and (3) to track the potential phylogeographical information deduced from our random amplified polymorphic DNA marker (RAPD) data in order to draw inferences about the past history of this species in the north-west Iberian Peninsula. To achieve these aims, 26 macromorphological characters were recorded in 279 specimens, and 77 RAPD phenotypes were identified in the 79 plants studied. The association analyses performed using the morphological and molecular data showed that no clear separation existed between the morphs, and a strong correlation between qualitative characters and the environment was detected. Moreover, both the multivariate analyses and the assignment test based on RAPD data revealed that the genetic variation was hierarchically structured, and three genetically distinct groups could be identified. Two of these clusters might correspond to different expansion routes proposed in the literature for different plant species in the north-west Iberian Peninsula. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 179,192. [source] Long-distance dispersal of seeds in the fire-tolerant shrub Banksia attenuataECOGRAPHY, Issue 4 2009Tianhua He Long-distance dispersal (LDD) of seeds enables alleles, individuals and species of plants to (re)colonize suitable but remote habitats. Banksia attenuata is a long-lived resprouting shrub restricted to dune crests in fire-prone sclerophyll shrublands of the Eneabba sandplain, southwestern Australia. Highly polymorphic microsatellite DNA genetic markers and population assignment tests were employed to identify LDD immigrants among 788 individuals from 27 stands of B. attenuata comprising a metapopulation. Of the 487 (61.8% of the total) individuals unambiguously assigned to a unique source population, 27 (5.5%) were identified as immigrants by assignment to a known population other than that from which they were sampled, while the remaining 460 were assigned to the population from which they were sampled. The distance between source and sink populations for these immigrants ranged from 0.2 to 2.6,km, averaging 1.4,km, and broadly trending in the direction of seasonal winds. These results suggest that B. attenuata has similar long-distance seed dispersal properties as its co-occurring shorter-lived and fire-sensitive congener, B. hookeriana, despite fewer, larger and less mobile seeds. The frequency and distance of LDD for seeds observed in both species (5.5,6.8%) helps explain the persistence of populations on these geographically isolated dunes, where they are subject to local extinction from recurrent fire and severe summer drought, and will remain important under predicted climate change conditions. Analysis also revealed that species richness of the functional group to which B. attenuata belongs was positively correlated with the number of immigrants identified per dune, and such correlation was likely driven by environmental properties of the dunes, particularly water availability. [source] Genetic pattern of the recent recovery of European otters in southern FranceECOGRAPHY, Issue 2 2008Xavier Janssens We investigated how landscape affects the population genetic structure and the dispersal of the elusive European otter Lutra lutra in a contemporary colonization context, over several generations and at the level of hydrographic basins. Our study area included 10 basins located in the Cévennes National Park (CNP), at the southern front of the natural otter recovery in France. Each basin comprised 50 to 300 km of permanent rivers that were surveyed for otter presence from 1991 to 2005. Faecal samples collected in 2004 and 2005 in this area were genotyped at 9 microsatellite loci, resulting in the identification of 70 genetically distinct individuals. Bayesian clustering methods were used to infer genetic structure of the populations and to compare recent gene flow to the observed colonization. At the regional level, we identified 2 distinct genetic clusters (NE and SW; FST=0.102) partially separated by ridges, suggesting that the CNP was recolonized by 2 genetically distinct otter populations. At the basin level, the genetic distance between groups of individuals in different basins was positively correlated to the mean slope separating these basins. The probable origins and directions of individual movements (i.e. migration between clusters and basin colonization inside clusters) were inferred from assignment tests. This approach shows that steep and dry lands can stop, impede or divert the dispersal of a mobile carnivore such as the otter. [source] Do dams increase genetic diversity in brown trout (Salmo trutta)?ECOLOGY OF FRESHWATER FISH, Issue 4 2006Microgeographic differentiation in a fragmented river Abstract , Local genetic differentiation may potentially arise in recently fragmented populations. Brown trout is a polytypic species exhibiting substantial genetic differentiation, which may evolve in few generations. Movement (semi-)barriers in rivers may cause fragmentation, isolation and genetic differentiation in fish. In the Mĺna River (28 km) flowing from the alpine Lake Mřsvatn to the boreal Lake Tinnsjř, construction of four hydropower dams during the period 1906,1957 have fragmented the previously (since last Ice Age) continuous wild resident brown trout population. Samples from the two lakes (N = 40) and six sites in the river (N = 30) isolated at different times were analysed at nine microsatellite loci. All populations showed substantial genetic variation (mean number of alleles per locus 5.3,8.9, observed heterozygosity 0.57,0.65 per population, overall Fst = 0.032). Pairwise multilocus Fst estimates indicated no significant differentiation between populations in the two lakes, and no or little differentiation in the lower river (Fst = 0.0035,0.0091). The microgeographic differentiation among wild resident trout at these sites was less than expected based on similar previous studies. However, results from the upper river, in particular the site immediately below the Lake Mřsvatn outlet and dam, indicated isolation (Fst > 0.035). Calculation of genetic distances and assignment tests corroborated these results, as did a significant correlation between years of isolation (since dam construction) and Fst. The population structuring is most likely a result of fragmentation by dams, which has increased overall genetic diversity. This increased local differentiation may be caused by natural selection, but more likely by genetic drift in small, recently fragmented populations. Increased local genetic diversity by genetic drift does not justify conservation measures aiming at preserving genetic diversity. [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] Population genetics suggests effectiveness of habitat connectivity measures for the European tree frog in SwitzerlandJOURNAL OF APPLIED ECOLOGY, Issue 4 2009Sonia Angelone Summary 1.,Governmental authorities in many countries financially support the implementation of habitat connectivity measures to enhance the exchange of individuals among fragmented populations. The evaluation of the effectiveness of such measures is crucial for future management directions and can be accomplished by using genetic methods. 2.,We retraced the population history of the European tree frog in two Swiss river valleys (Reuss and Thur), performed comprehensive population sampling to infer the genetic structure at 11 microsatellite markers, and used first-generation migrant assignment tests to evaluate the contemporary exchange of individuals. 3.,Compared with the Thur valley, the Reuss valley has lost almost double the number of breeding sites and exhibited a more pronounced genetic grouping. However, similar numbers of contemporary migrants were detected in both valleys. In the Reuss valley, 81% of the migration events occurred within the identified genetic groups, whereas in the Thur valley migration patterns were diffuse. 4.,Our results show that the connectivity measures implemented in the Reuss valley facilitated effective tree frog migration among breeding sites within distances up to 4 km. Nevertheless, the Reuss valley exhibited high genetic differentiation, which reflected the impact of barriers to tree frog movement such as the River Reuss. By contrast in the Thur valley, a larger number of breeding sites have been preserved and high admixture indicated exchange of individuals at distances up to 16 km. 5.,Synthesis and applications. We show that genetic methods can substantiate the effectiveness of connectivity measures taken in conservation management at the landscape scale. We urge responsible authorities from both river valleys to continue implementing connectivity measures and to create a dense network of breeding sites, as spatial gaps of 8 km are rarely traversed by tree frogs. [source] Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samplesJOURNAL OF APPLIED ECOLOGY, Issue 4 2006MICHAEL M. HANSEN Summary 1Gene flow from domesticated to wild populations is a major threat to wild salmonid fish. However, few studies have addressed how populations could be restored after admixture has occurred. We analysed the prospects for restoring the previously intensively stocked brown trout population of the Skjern River, Denmark, by identifying remaining non-admixed individuals to be used for supportive breeding. 2We analysed microsatellite DNA markers in historical (1940,50s) and contemporary (1992,2004) samples from the Skjern River system, from the strain of domesticated trout previously used for stocking, and from the neighbouring Storĺ River. We analysed admixture proportions to estimate the genetic contribution by domesticated trout. We identified non-admixed trout using assignment tests, and further analysed the possible sources of indigenous trout by estimating contemporary migration among populations. 3Genetic differentiation between the historical Storĺ and Skjern river populations was low (,ST = 0·004), suggesting considerable gene flow in the past. The contemporary Skjern and Storĺ river populations and a supportive breeding brood stock were strongly admixed, but some non-admixed individuals nevertheless remained in the wild-caught samples. In addition, two resident populations in isolated tributaries were found to be indigenous. The indigenous anadromous individuals from the Skjern River were unlikely to have been recruited from either the isolated tributary populations or the neighbouring Storĺ River and were presumably derived from unidentified spawning sites in the river system. 4All but one non-admixed anadromous Skjern River trout were females, which we ascribed to sampling bias. Moreover, all non-admixed fish were late-spawning (January,February) whereas the majority of all trout caught for the study were ripe by November,December. The difference in spawning time could be an important factor delaying complete admixture of domesticated and indigenous trout. 5Synthesis and applications. This study demonstrates the feasibility of restoring populations that have been admixed with exogenous individuals, by identifying non-admixed individuals using genetic markers. However, the results also highlight the problem that numbers of identified non-admixed individuals may be small, necessitating identification of nearby, closely related populations that can be incorporated into breeding programmes. [source] Conservation and management implications of fine-scale genetic structure of Gulf sturgeon in the Pascagoula River, MississippiJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2004M. A. Dugo Summary The anadromous Gulf sturgeon occurs along the north central coast of the Gulf of Mexico and is federally listed as threatened. We analyzed fine-scale patterns of Gulf sturgeon population structure, focusing on the Pascagoula River drainage of Mississippi, in reference to movement patterns as determined via telemetry and capture data. We genotyped 361 Gulf sturgeon using eight microsatellite loci including samples from the Pascagoula, Pearl, Escambia, Yellow, Choctawhatchee, and Apalachicola river drainages. Pairwise FST estimates indicated that genetic structure occurs at least at the drainage level. The Pascagoula and Pearl rivers form a western group, demonstrating 100% bootstrap support for a division with drainages to the east. Assignment tests detected non-natal genotypes occurring in all drainages. According to assignment tests, the Pascagoula supports an admixture of individuals, containing minimal influence from drainages to the east (2%) and substantial interaction with the Pearl River (14.1%). The occurrence of Pascagoula River fish in the Pearl was non-reciprocal, observed at 1.1%. After accounting for non-natal genetic diversity within the Pascagoula, there remained a disparity between a pooled Pascagoula group and the only documented spawning site within the drainage located in the Bouie River. We interpret this as an indication of a second genetic stock within the Pascagoula River drainage. Radio telemetry data suggest that spawning likely occurs in the Chickasawhay River, in areas isolated from the Bouie River spawning site by about 350 river kilometers. We emphasize the utility of integrating field and molecular approaches when delineating fine-scale patterns of population structure in anadromous fishes. [source] Genetic and morphometric differentiation among island populations of two Norops lizards (Reptilia: Sauria: Polychrotidae) on independently colonized islands of the Islas de Bahia (Honduras)JOURNAL OF BIOGEOGRAPHY, Issue 7 2007C. F. C. Klütsch Abstract Aim, Anole lizards (Reptilia: Sauria: Polychrotidae) display remarkable morphological and genetic differentiation between island populations. Morphological differences between islands are probably due to both adaptive (e.g. differential resource exploitation and intra- or interspecific competition) and non-adaptive differentiation in allopatry. Anoles are well known for their extreme diversity and rapid adaptive speciation on islands. The main aim of this study was to use tests of morphological and genetic differentiation to investigate the population structure and colonization history of islands of the Islas de Bahia, off the coast of Honduras. Location, Five populations of Norops bicaorum and Norops lemurinus were sampled, four from islands of the Islas de Bahia and one from the mainland of Honduras. Methods, Body size and weight differentiation were measured in order to test for significant differences between sexes and populations. In addition, individuals were genotyped using the amplified fragment length polymorphism technique. Bayesian model-based and assignment/exclusion methods were used to study genetic differentiation between island and mainland populations and to test colonization hypotheses. Results, Assignment tests suggested migration from the mainland to the Cayos Cochinos, and from there independently to both Utila and Roatán, whereas migration between Utila and Roatán was lacking. Migration from the mainland to Utila was inferred, but was much less frequent. Morphologically, individuals from Utila appeared to be significantly different in comparison with all other localities. Significant differentiation between males of Roatán and the mainland was found in body size, whereas no significant difference was detected between the mainland and the Cayos Cochinos. Main conclusions, Significant genetic and morphological differentiation was found among populations. A stepping-stone model for colonization, in combination with an independent migration to Utila and Roatán, was suggested by assignment tests and was compatible with the observed morphological differentiation. [source] Microgeographic population structure of brook charr: a comparison of microsatellite and mark-recapture dataJOURNAL OF FISH BIOLOGY, Issue 3 2003B. K. Adams Polymorphism at five microsatellite genetic markers (genotyped n = 496) and mark-recapture tagging data (tagged n = 9813) were used to define the population structure of brook charr, Salvelinus fontinalis from the Indian Bay watershed, Newfoundland, Canada. Despite the absence of physical barriers to migration among lakes, both genetic and tagging data suggest that brook charr in each lake represent reproductively isolated populations. Exact tests comparing allele frequencies, , (global value = 0·063), Rst (global value = 0·052), individual assignment tests, and Nei's genetic distance provided congruent estimates of population subdivision in agreement with the tagging data (only 2·2% of recaptures were lake-to-lake). The genetic structure of the brook charr populations corresponded with the geographic structure of the drainage basin on a qualitative level, although linear distance over water was not significantly correlated with the tagging data or the genetic distance measures. The agreement between the tagging and the genetic data suggest that microsatellite markers can be useful tools for defining real biological units. The results also suggest that brook charr exhibit microgeographic population structure at the watershed scale, and that this is the scale at which conservation and management of this salmonid might best be implemented. [source] Use of micreosatellite markers for identification of indigenous brown trout in a geographical region heavily influenced by stocked domensticated troutJOURNAL OF FISH BIOLOGY, Issue 5 2001N. G. Fritzner Based on estimates of genetic differentiation between populations, assignment tests and analysis of isolation by distance, stocked populations of brown trout Salmo trutta of Funen Island, Denmark, had been genetically affected by domesticated trout, whereas the stocking of wild exogenous trout into one of the rivers had little or no impact. At the same time, there were clear indications of remaining indigenous gene pools in the Funen populations. The management implications of these findings are discussed and changes in trout release activity are recommended to avoid further mixing of trout gene pools. [source] Rolling stones and stable homes: social structure, habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris)MOLECULAR ECOLOGY, Issue 4 2010KIMBERLY R. ANDREWS Abstract Spinner dolphins (Stenella longirostris) exhibit different social behaviours at two regions in the Hawaiian Archipelago: off the high volcanic islands in the SE archipelago they form dynamic groups with ever-changing membership, but in the low carbonate atolls in the NW archipelago they form long-term stable groups. To determine whether these environmental and social differences influence population genetic structure, we surveyed spinner dolphins throughout the Hawaiian Archipelago with mtDNA control region sequences and 10 microsatellite loci (n = 505). F -statistics, Bayesian cluster analyses, and assignment tests revealed population genetic separations between most islands, with less genetic structuring among the NW atolls than among the SE high islands. The populations with the most stable social structure (Midway and Kure Atolls) have the highest gene flow between populations (mtDNA ,ST < 0.001, P = 0.357; microsatellite FST = ,0.001; P = 0.597), and a population with dynamic groups and fluid social structure (the Kona Coast of the island of Hawai'i) has the lowest gene flow (mtDNA 0.042 < ,ST < 0.236, P < 0.05; microsatellite 0.016 < FST < 0.040, P < 0.001). We suggest that gene flow, dispersal, and social structure are influenced by the availability of habitat and resources at each island. Genetic comparisons to a South Pacific location (n = 16) indicate that Hawaiian populations are genetically depauperate and isolated from other Pacific locations (mtDNA 0.216 < FST < 0.643, P < 0.001; microsatellite 0.058 < FST < 0.090, P < 0.001); this isolation may also influence social and genetic structure within Hawai'i. Our results illustrate that genetic and social structure are flexible traits that can vary between even closely-related populations. [source] The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservationMOLECULAR ECOLOGY, Issue 18 2007MENG-HUA LI Abstract We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian-based clustering approach, we identified a genetic distinctness between populations of modern commercial origin and those of native origin. Our data suggested that northern European Russia represents the most heavily colonized area by modern commercial cattle. Further genetic mixture analyses based on individual assignment tests found that native Red Steppe cattle were also employed in the historical breeding practices in Eastern Europe, most probably for incorporating their strong and extensive adaptability. In analysis of molecular variance, within-population differences accounted for ~90% of the genetic variation. Despite some correspondence between geographical proximity and genetic similarity, genetic differentiation was observed to be significantly associated with the difference in breeding purpose among the European populations (percentage of variance among groups and significance: 2.99%, P = 0.02). Our findings give unique genetic insight into the historical patterns of cattle breeding practices in the former Soviet Union. The results identify the neighbouring Near Eastern regions such as the Balkan, the Caucasus and Ukraine, and the isolated Far Eastern Siberia as areas of ,genetic endemism', where cattle populations should be given conservation priority. The results will also be of importance for cost-effective management of their future utilization. [source] Fine-scale spatial genetic structure and dispersal among spotted salamander (Ambystoma maculatum) breeding populationsMOLECULAR ECOLOGY, Issue 2 2007KELLY R. ZAMUDIO Abstract We examined fine-scale genetic variation among breeding aggregations of the spotted salamander (Ambystoma maculatum) to quantify dispersal, interpopulation connectivity and population genetic structure. Spotted salamanders rely on temporary ponds or wetlands for aggregate breeding. Adequate breeding sites are relatively isolated from one another and field studies suggest considerable adult site fidelity; therefore, we expected to find population structure and differentiation at small spatial scales. We used microsatellites to estimate population structure and dispersal among 29 breeding aggregations in Tompkins County, New York, USA, an area encompassing 1272 km2. Bayesian and frequency-based analyses revealed fine-scale genetic structure with two genetically defined demes: the North deme included seven breeding ponds, and the South deme included 13 ponds. Nine ponds showed evidence of admixture between these two genetic pools. Bayesian assignment tests for detection of interpopulation dispersal indicate that immigration among ponds is common within demes, and that certain populations serve as sources of immigrants to neighbouring ponds. Likewise, spatial genetic correlation analyses showed that populations , 4.8 km distant from each other show significant genetic correlation that is not evident at higher scales. Within-population levels of relatedness are consistently larger than expected if mating were completely random across ponds, and in the case of a few ponds, within-population processes such as inbreeding or reproductive skew contribute significantly to differentiation from neighbouring ponds. Our data underscore the importance of these within-population processes as a source of genetic diversity across the landscape, despite considerable population connectivity. Our data further suggest that spotted salamander breeding groups behave as metapopulations, with population clusters as functional units, but sufficient migration among demes to allow for potential rescue and recolonization. Amphibian habitats are becoming increasingly fragmented and a clear understanding of dispersal and patterns of population connectivity for taxa with different ecologies and life histories is crucial for their conservation. [source] Genetic enrichment of the arctic clonal plant Saxifraga cernua at its southern periphery via the alpine sexual Saxifraga sibiricaMOLECULAR ECOLOGY, Issue 11 2006MAXIM V. KAPRALOV Abstract Isolation of populations at the margins of a species range may lead to decreasing genetic diversity via genetic drift and inbreeding. Hybridization between peripheral populations of two species can, however, counteract genetic impoverishment. The mainly clonal, polyploid plant Saxifraga cernua has a wide arctic distribution but also extends southwards into alpine sites. In the Ural Mountains, its peripheral distribution overlaps with that of its sexually reproducing, diploid relative Saxifraga sibirica, and fertile polyploids of more or less intermediate appearance are found in this overlap zone. We used amplified fragment length polymorphism (AFLP) analysis to address the potential impact of interspecific gene flow on genetic diversity in the peripheral populations. A total of 149 plants from 17 populations along a 1650 km south,north gradient were analysed for 253 markers. The results suggest that three Middle Ural populations containing fertile and morphologically more or less intermediate plants have been affected by hybridization. All of these plants formed a strongly supported (100%) group with S. cernua in a neighbour-joining tree, but their AFLP phenotypes assigned either to S. cernua or to artificial (simulated) F1 hybrids between S. cernua and S. sibirica in multilocus assignment tests. The three populations were highly diverse with virtually every plant representing a distinct AFLP phenotype, providing additional evidence for formation of later-generation hybrids and/or backcrossing to S. cernua. In contrast, other peripheral populations of S. cernua were typically monoclonal, suggesting that hybridization with S. sibirica can increase genetic diversity in S. cernua at its southern periphery. [source] Differential patterns of hybridization and introgression between the swallowtails Papilio machaon and P. hospiton from Sardinia and Corsica islands (Lepidoptera, Papilionidae)MOLECULAR ECOLOGY, Issue 6 2003R. Cianchi Abstract Proportions of hybridization and introgression between the swallowtails Papilio hospiton, endemic to Sardinia and Corsica, and the holarctic Papilio machaon, were characterized using nine fully diagnostic and two differentiated allozyme loci and a mitochondrial DNA marker. Very low frequencies of F1 hybrids were detected in both Sardinia (0,4%, average 1.4%) and Corsica (0,3%, average 0.5%), as well as of first generation backcrosses (B1). No F2 were observed, in agreement with the hybrid breakdown detected in laboratory crosses. In spite of this minimal current gene exchange, specimens carrying introgressed alleles were found in high proportions in P. machaon but in lower proportions in P. hospiton. Introgression apparently occurred through past hybridization and repeated backcrossing, as evidenced by hybrid index scores and Bayesian assignment tests. Levels of introgression were low (0,1%) at two sex-linked loci and mitochondrial DNA, limited (0.4,2%) at three autosomal loci coding for dimeric enzymes, and high (up to 43%) at four autosomal loci coding for monomeric enzymes. Accordingly, selective filters are acting against foreign alleles, with differential effectiveness depending on the loci involved. The low levels of introgression at sex-linked loci and mitochondrial DNA are in agreement with Haldane's rule and suggest that introgression in P. machaon proceeds mainly through males, owing to a lower fitness of hybrid females. Papilio machaon populations showed higher levels of introgression in Sardinia than in Corsica. The role of reinforcement in the present reproductive isolation between P. machaon and P. hospiton is examined, as well as the evolutionary effects of introgressive hybridization between the two species. [source] Characteristics of sex-biased dispersal and gene flow in coastal river otters: implications for natural recolonization of extirpated populationsMOLECULAR ECOLOGY, Issue 3 2002G. M. Blundell Abstract River otters (Lontra canadensis) were extirpated from much of their historic distribution because of exposure to pollution and urbanization, resulting in expansive reintroduction programmes that continue today for this and other species of otters worldwide. Bioaccumulation of toxins negatively affects fecundity among mustelids, but high vagility and different dispersal distances between genders may permit otter populations to recover from extirpation caused by localized environmental pollution. Without understanding the influence of factors such as social structure and sex-biased dispersal on genetic variation and gene flow among populations, effects of local extirpation and the potential for natural recolonization (i.e. the need for translocations) cannot be assessed. We studied gene flow among seven study areas for river otters (n = 110 otters) inhabiting marine environments in Prince William Sound, Alaska, USA. Using nine DNA microsatellite markers and assignment tests, we calculated immigration rates and dispersal distances and tested for isolation by distance. In addition, we radiotracked 55 individuals in three areas to determine characteristics of dispersal. Gender differences in sociality and spatial relationships resulted in different dispersal distances. Male river otters had greater gene flow among close populations (within 16,30 km) mostly via breeding dispersal, but both genders exhibited an equal, low probability of natal dispersal; and some females dispersed 60,90 km. These data, obtained in a coastal environment without anthropogenic barriers to dispersal (e.g. habitat fragmentation or urbanization), may serve as baseline data for predicting dispersal under optimal conditions. Our data may indicate that natural recolonization of coastal river otters following local extirpation could be a slow process because of low dispersal among females, and recolonization may be substantially delayed unless viable populations occurred nearby. Because of significant isolation by distance for male otters and low gene flow for females, translocations should be undertaken with caution to help preserve genetic diversity in this species. [source] Source population of dispersing rock-wallabies (Petrogale lateralis) idengified by assignment tests on multilocus genotypic dataMOLECULAR ECOLOGY, Issue 12 2001M. D. B. Eldridge Abstract The ability to confidently idengify or exclude a population as the source of an individual has numerous powerful applications in molecular ecology. Several alternative assignment methods have recently been developed and are yet to be fully evaluated with empirical data. In this study we tested the efficacy of different assignment methods by using a translocated rock-wallaby (Petrogale lateralis) population, of known provenance. Specimens from the translocated population (n = 43), its known source population (n = 30) and four other nearby populations (n = 19,32) were genotyped for 11 polymorphic microsatellite loci. The results idengified Bayesian clustering, frequency and Bayesian methods as the most consistent and accurate, correctly assigning 93,100% of individuals up to a significance threshold of P = 0.01. Performance was variable among the distance-based methods, with the Cavalli-Sforza and Edwards chord distance performing best, whereas Goldstein et al.'s (,µ)2 consistently performed poorly. Using Bayesian clustering, frequency and Bayesian methods we then attempted to determine the source of rock-wallabies which have recently recolonized an outcrop (Gardners) 8 km from the nearest rock-wallaby population. Results indicate that the population at Gardners originated via a recent dispersal event from the eastern end of Mt. Caroline. This is only the second published record of dispersal by rock-wallabies between habitat patches and is the longest movement recorded to date. Molecular techniques and methods of analysis are now available to allow detailed studies of dispersal in rock-wallabies and should also be possible for many other taxa. [source] | ||||||||||||||||||||||||||||