Genetic consequences of the ice ages on nurseries of the bat Myotis myotis: a mitochondrial and nuclear survey

Analyses of mitochondrial DNA (mtDNA) control region polymorphism and of variation at 10 nuclear microsatellite loci were used to investigate the mechanisms and genetic consequences of postglacial expansion of Myotis myotis in Europe. Initial sampling consisted of 480 bats genotyped in 24 nursery colonies arranged along a transect of approximately 3000 km. The phylogeographical survey based on mtDNA sequences revealed the existence of major genetic subdivisions across this area, with several suture zones between haplogroups. Such zones of secondary contact were found in the Alps and Rhodopes, whereas other potential barriers to gene flow, like the Pyrenees, did not coincide with genetic discontinuities. Areas of population admixture increased locally the genetic diversity of colonies, which confounded the northward decrease in nucleotide diversity predicted using classical models of postglacial range expansion. However, when analyses were restricted to a subset of 15 nurseries originating from a single presumed glacial refugium, mtDNA polymorphism did indeed support a northwards decrease in diversity. Populations were also highly structured (PhiST = 0.384). Conversely, the same subset of colonies showed no significant latitudinal decrease in microsatellite diversity and much less population structure (FST = 0.010), but pairwise genetic differentiation at these nuclear markers was strongly correlated with increasing geographical distance. Together, this evidence suggests that alleles carried via male bats have maintained enough nuclear gene flow to counteract the effects of recurrent bottlenecks generally associated with recolonization processes. As females are highly philopatric, we argue that the maternally transmitted mtDNA marker better reflects the situation of past, historical gene flow, whereas current levels of gene flow are better reflected by microsatellite markers.     

Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea

Genetic variation was surveyed at nine microsatellite loci and the mitochondrial control region (868 bp) to test for the presence of genetic stock structure in young-of-the-year Atlantic bluefin tuna (Thunnus thynnus thynnus) from the Mediterranean Sea. Bluefin tuna were sampled over a period of 5 years from the Balearic and Tyrrhenian seas in the western basin of the Mediterranean Sea, and from the southern Ionian Sea in the eastern basin of the Mediterranean Sea. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences revealed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for both microsatellite markers and mitochondrial control region sequences (FST=0.0023, P=0.038 and PhiST=0.0233, P=0.000, respectively). Significant genetic differentiation between the Tyrrhenian and Ionian collections was found for both microsatellite and mitochondrial markers (FST=0.0087, P=0.015 and PhiST=0.0367, P=0.030, respectively). These results suggest the possibility of a genetically discrete population in the eastern basin of the Mediterranean Sea.     

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.     

Population genetic structure of Bellamya aeruginosa (Mollusca: Gastropoda: Viviparidae) in China: weak divergence across large geographic distances

Bellamya aeruginosa is a widely distributed Chinese freshwater snail that is heavily harvested, and its natural habitats are under severe threat due to fragmentation and loss. We were interested whether the large geographic distances between populations and habitat fragmentation have led to population differentiation and reduced genetic diversity in the species. To estimate the genetic diversity and population structure of B. aeruginosa, 277 individuals from 12 populations throughout its distribution range across China were sampled: two populations were sampled from the Yellow River system, eight populations from the Yangtze River system, and two populations from isolated plateau lakes. We used seven microsatellite loci and mitochondrial cytochrome oxidase I sequences to estimate population genetic parameters and test for demographic fluctuations. Our results showed that (1) the genetic diversity of B. aeruginosa was high for both markers in most of the studied populations and effective population sizes appear to be large, (2) only very low and mostly nonsignificant levels of genetic differentiation existed among the 12 populations, gene flow was generally high, and (3) relatively weak geographic structure was detected despite large geographic distances between populations. Further, no isolation by linear or stream distance was found among populations within the Yangtze River system and no signs of population bottlenecks were detected. Gene flow occurred even between far distant populations, possibly as a result of passive dispersal during flooding events, zoochoric dispersal, and/or anthropogenic translocations explaining the lack of stronger differentiation across large geographic distances. The high genetic diversity of B. aeruginosa and the weak population differentiation are likely the results of strong gene flow facilitated by passive dispersal and large population sizes suggesting that the species currently is not of conservation concern.     

Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses

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 < or = FST < or = 0.259) could be identified scoring only three loci, while the corresponding number was six for the least differentiated breeds (0.080 < or = FST < or = 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 (> or = 20 animals per population) and fairly variable loci were used.     

Genetic diversity and differentiation of Kermode bear populations

The Kermode bear is a white phase of the North American black bear that occurs in low to moderate frequency on British Columbia's mid-coast. To investigate the genetic uniqueness of populations containing the white phase, and to ascertain levels of gene flow among populations, we surveyed 10 highly polymorphic microsatellite loci, assayed from trapped bear hairs. A total of 216 unique bear genotypes, 18 of which were white, was sampled among 12 localities. Island populations, where Kermodes are most frequent, show approximately 4% less diversity than mainland populations, and the island richest in white bears (Gribbell) exhibited substantial genetic isolation, with a mean pairwise FST of 0.14 with other localities. Among all localities, FST for the molecular variant underlying the coat-colour difference (A893G) was 0.223, which falls into the 95th percentile of the distribution of FST values among microsatellite alleles, suggestive of greater differentiation for coat colour than expected under neutrality. Control-region sequences confirm that Kermode bears are part of a coastal or western lineage of black bears whose existence predates the Wisconsin glaciation, but microsatellite variation gave no evidence of past population expansion. We conclude that Kermodism was established and is maintained in populations by a combination of genetic isolation and somewhat reduced population sizes in insular habitat, with the possible contribution of selective pressure and/or nonrandom mating.     

Population structure and genetic diversity of trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) above and below natural and man-made barriers in the Russian River,California

The effects of landscape features on gene flow in threatened and endangered species play an important role in influencing the genetic structure of populations. We examined genetic variation of trout in the species Oncorhynchus mykiss at 22 microsatellite loci from 20 sites in the Russian River basin in central California. We assessed relative patterns of genetic structure and variation in fish from above and below both natural (waterfalls) and man-made (dams) barriers. Additionally, we compared sites sampled in the Russian River with sites from 16 other coastal watersheds in California. Genetic variation among the 20 sites sampled within the Russian River was significantly partitioned into six groups above natural barriers and one group consisting of all below barrier and above dam sites. Although the below-barrier sites showed moderate gene flow, we found some support for sub-population differentiation of individual tributaries in the watershed. Genetic variation at all below-barrier sites was high compared to above-barrier sites. Fish above dams were similar to those from below-barrier sites and had similar levels of genetic diversity, indicating they have not been isolated very long from below-barrier populations. Population samples from above natural barriers were highly divergent, with large F _st values, and had significantly lower genetic diversity, indicating relatively small population sizes. The origins of populations above natural barriers could not be ascertained by comparing microsatellite diversity to other California rivers. Finally, below-barrier sites farther inland were more genetically differentiated from other watersheds than below-barrier sites nearer the river’s mouth.     

Gene flow on the ice: genetic differentiation among Adélie penguin colonies around Antarctica

Each summer Adélie penguins breed in large disjunct colonies on ice-free areas around the Antarctic continent. Comprising > 10 million birds, this species represents a dominant feature of the Antarctic ecosystem. The patchy distribution within a large geographical range, natal philopatry and a probable history of refugia, suggest that this species is likely to exhibit significant genetic differentiation within and among colonies. We present data from seven microsatellite DNA loci for 442 individuals from 13 locations around the Antarctic continent. With the exception of one locus, there was no significant genic or genotypic heterogeneity across populations. Pairwise FST values were low with no value > 0.02. When all colonies were compared in a single analysis, the overall FST value was 0.0007. Moreover, assignment tests were relatively ineffective at correctly placing individuals into their respective collection sites. These data reveal a lack of genetic differentiation between Adélie penguin colonies around the Antarctic continent, despite substantial levels of genetic variation. We consider this homogeneity in terms of the dispersal of individuals among colonies and the size of breeding groups and discuss our results in terms of the glacial history of Antarctica.     

Microspatial genetic heterogeneity and gene flow in stray cats (Felis catus L.): a comparison of coat colour and microsatellite loci

We analysed levels of genetic differentiation between nine local urban colonies of stray cats using eight coat colour and nine microsatellite loci. Both types of markers revealed a strong differentiation between colonies (FST = 0.15 and 0.09 for coat colour and microsatellite loci, respectively). Three coat colour loci showed extreme levels of genetic differentiation comparatively to other loci and are strongly suspected to be under divergent selective pressures. Microsatellite loci showed significant heterozygote deficiency within colonies (FIS = 0.14), suggesting that coat colour loci are not appropriate to investigate genetic structure at a fine scale because coat colour allele frequencies are based on Hardy-Weinberg equilibrium. The reported pattern conformed to that predicted from the social structuring of cat colonies: aggressive exclusion of immigrants, inbreeding and very low dispersal rate.     

Genetic heterogeneity of the tropical abalone (Haliotis asinina) revealed by RAPD and microsatellite analyses

Genetic heterogeneity of the tropical abalone, Haliotis asinina was examined using randomly amplified polymorphic DNA (RAPD) and microsatellite analyses. One hundred and thirteen polymorphic RAPD fragments were generated. The percentage of polymorphic bands of H. asinina across overall primers was 85.20%. The average genetic distance of natural samples within the Gulf of Thailand (HACAME and HASAME) was 0.0219. Larger distance was observed when those samples were compared with HATRAW from the Andaman Sea (0.2309 and 0.2314). Geographic heterogeneity and F(ST) analyses revealed population differentiation between H. asinina from the Gulf of Thailand and the Andaman Sea (p < 0.0001). Three microsatellite loci (CUHas1, CUHas4 and CUHas5) indicated relatively high genetic diversity in H. asinina (total number of alleles = 26, 5, 23 and observed heterozygosity = 0.84, 0.42 and 0.33, respectively). Significant population differentiation was also found between samples from different coastal regions (p < 0.0001). Therefore, the gene pool of natural H. asinina in coastal Thai waters can be genetically divided to 2 different populations; the Gulf of Thailand (A) and the Andaman Sea (B).     

Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data

The relative roles of natural selection and direct environmental induction, as well as of natural selection and genetic drift, in creating clinal latitudinal variation in quantitative traits have seldom been assessed in vertebrates. To address these issues, we compared molecular and quantitative genetic differentiation between six common frog (Rana temporaria) populations along an approximately 1600 km long latitudinal gradient across Scandinavia. The degree of population differentiation (QST approximately 0.81) in three heritable quantitative traits (age and size at metamorphosis, growth rate) exceeded that in eight (neutral) microsatellite loci (FST = 0.24). Isolation by distance was clear for both neutral markers and quantitative traits, but considerably stronger for one of the three quantitative traits than for neutral markers. QST estimates obtained using animals subjected to different rearing conditions (temperature and food treatments) revealed some environmental dependency in patterns of population divergence in quantitative traits, but in general, these effects were weak in comparison to overall patterns. Pairwise comparisons of FST and QST estimates across populations and treatments revealed that the degree of quantitative trait differentiation was not generally predictable from knowledge of that in molecular markers. In fact, both positive and negative correlations were observed depending on conditions where the quantitative genetic variability had been measured. All in all, the results suggest a very high degree of genetic subdivision both in neutral marker genes and genes coding quantitative traits across a relatively recently (< 9000 years) colonized environmental gradient. In particular, they give evidence for natural selection being the primary agent behind the observed latitudinal differentiation in quantitative traits.     

Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci

Global climate fluctuated considerably throughout the Pliocene and Pleistocene, influencing the evolutionary history of a wide range of species. Using both mitochondrial sequences and microsatellites, we have investigated the evolutionary consequences of such environmental fluctuation for the patterns of genetic variation in the common warthog, sampled from 24 localities in Africa. In the sample of 181 individuals, 70 mitochondrial DNA haplotypes were identified and an overall nucleotide diversity of 4.0% was observed. The haplotypes cluster in three well-differentiated clades (estimated net sequence divergence of 3.1-6.6%) corresponding to the geographical origins of individuals (i.e. eastern, western and southern African clades). At the microsatellite loci, high polymorphism was observed both in the number of alleles per locus (6-21), and in the gene diversity (in each population 0.59-0.80). Analysis of population differentiation indicates greater subdivision at the mitochondrial loci (FST=0.85) than at nuclear loci (FST=0.20), but both mitochondrial and nuclear loci support the existence of the three warthog lineages. We interpret our results in terms of the large-scale climatic fluctuations of the Pleistocene.     

Genetic diversity and structure in a natural Elymus caninus population from Denmark based on microsatellite and isozyme analyses

 Genetic diversity in a natural Elymus caninus population from Denmark was assessed using isozyme and microsatellite markers. A total of 119 individuals from 46 maternal plants were assayed. Microsatellite loci are shown to display higher levels of variation than isozyme loci. The mean number of alleles per locus was 1.04 for isozymes and 1.38 for microsatellites. The percentage of polymorphic loci for isozymes and microsatellites was 4.7% and 23.6% across the maternal plant, respectively. The genetic diversity at population level was 0.1 for isozymes, and 0.63 for microsatellites. The mean genetic diversity at maternal plant level was 0.027 for isozyme loci and 0.117 for microsatellite loci. The average of total allozyme diversity (H_T) was 0.22. The average of total microsatellite diversity was 0.56. Isozyme and microsatellite variation showed the same pattern of differentiation between maternal plants. More than 75% total genetic diversity was found among maternal plants. About 25% total genetic diversity was detected within maternal plants. Ten (22.7%) maternal plants produced heterozygous offspring at allozyme loci, and 30 (68.2%) maternal plants gave heterozygous offspring at microsatellite loci. Both types of markers revealed a relatively high genetic diversity in this population. Received November 7, 2000 Accepted February 15, 2001     

Specialization to cold‐water upwellings may facilitate gene flow in seabirds: new evidence from the Peruvian pelican Pelecanus thagus (Pelecaniformes: Pelecanidae)

Recent research has shown that tropical seabirds specialized to feed on cold water upwellings exhibit low population genetic differentiation and high gene flow across large geographic distances. This pattern is opposite to the general pattern of differentiation reported for tropical seabirds, and led us to hypothesize that specialization to cold‐water upwellings facilitates gene flow between colonies. As a test of this hypothesis we characterized population differentiation and gene flow across the range of the Peruvian pelican Pelecanus thagus, an upwelling specialist endemic to the Humboldt Current, using an 838 base pair segment of the mitochondrial control region and seven microsatellite loci. In support of our hypothesis we report genetic panmixia across the geographic range of this species and inferred high gene flow between colonies. The high dispersal propensity of upwelling specialist seabirds (adults and/or juveniles) may reduce loss of genetic diversity during population declines, and increase the ability of these species to colonize new islands.     

Genetic variability in natural populations of Arabidopsis thaliana in northern Europe

Ten populations of the model plant Arabidopsis thaliana were collected along a north-south gradient in Norway and screened for microsatellite polymorphisms in 25 loci and variability in quantitative traits. Overall, the average levels of genetic diversity were found to be relatively high in these populations, compared to previously published surveys of within population variability. Six of the populations were polymorphic at microsatellite loci, resulting in an overall proportion of polymorphic loci of 18%, and a relatively high gene diversity for a selfing species (HE = 0.06). Of the overall variability, 12% was found within populations. Two of six polymorphic populations contained heterozygous individuals. Both FST and phylogenetic analyses showed no correlation between geographical and genetic distances. Haplotypic diversity patterns suggested postglacial colonization of Scandinavia from a number of different sources. Heritable variation was observed for many of the studied quantitative traits, with all populations showing variability in at least some traits, even populations with no microsatellite variability. There was a positive association between variability in quantitative traits and microsatellites within populations. Several quantitative traits exhibited QST values significantly less than FST, suggesting that selection may be acting to retard differentiation for these traits.     

海南岛中华蜜蜂遗传多样性的微卫星DNA分析

为了解海南岛中华蜜蜂Apis cerana cerana的遗传多样性和遗传结构及其与大陆种群的关系, 本研究应用10个微卫星DNA标记对海南岛11个地点627个蜂群的627头工蜂样本和大陆2个地点102个蜂群的102头工蜂样本进行了分析。结果表明： 海南岛中华蜜蜂遗传多样性较高, 单个位点检测到等位基因5～17个; 各种群平均等位基因数为4.5～7.0个, 平均杂合度为0.59～0.65。海南岛中华蜜蜂在10个位点上表现出相似遗传结构, 文昌和屯昌种群在AT101位点的等位基因频率较特殊。岛内 岛外中华蜜蜂的遗传分化系数F_ST范围为0.06～0.13; 文昌、 屯昌种群分别同海南岛内其他9个种群的F_ST（0.06～0.12）大于这9个种群间的FST（0～0.05）。海南岛中华蜜蜂同邻近大陆种群发生了明显的遗传分化; 除文昌、 屯昌种群发生中等程度的分化外, 海南岛内其他种群之间遗传分化较小。本研究结果对海南岛中华蜜蜂资源的保护和合理利用具有重要的指导意义。     

The effects of sample size on population genetic diversity estimates in song sparrows Melospiza melodia

To empirically determine the effects of sample size on commonly used measures of average genetic diversity, we genotyped 200 song sparrows Melospiza melodia from two populations, one genetically depauperate (n=100) and the other genetically diverse (n=100), using eight microsatellite loci. These genotypes were used to randomly create 10,000 datasets of differing sizes (5 to 50) for each population to determine what the effects of sample size might be on several estimates of genetic diversity (number of alleles per locus, average observed heterozygosity, and unbiased average expected heterozygosity) in natural populations of conservation concern. We found that at small sample sizes of 5 to 10 individuals, estimates of unbiased heterozygosity outperformed those based on observed heterozygosity or allelic diversity for both low- and high-diversity populations. We also found that when comparing across populations in which different numbers of individuals were sampled, rarefaction provided a useful way to compare estimates of allelic diversity. We recommend that standard errors should be reported for all diversity estimators, especially when sample sizes are small. We also recommend that at least 20 to 30 individuals be sampled in microsatellite studies that assess genetic diversity when working in a population that has an unknown level of diversity. However, research on critically endangered populations (where large sample sizes are impossible or extremely difficult to obtain) should include measures of genetic diversity even if sample sizes are less than ideal. These estimates can be useful in assessing the genetic diversity of the population.     

Genetic differentiation of neutral markers and quantitative traits in predominantly selfing metapopulations: confronting theory and experiments with Arabidopsis thaliana

The comparison of the genetic differentiation of quantitative traits (QST) and molecular markers (FST) can inform on the strength and spatial heterogeneity of selection in natural populations, provided that markers behave neutrally. However, selection may influence the behaviour of markers in selfing species with strong linkage disequilibria among loci, therefore invalidating this test of detection of selection. We address this issue by monitoring the genetic differentiation of five microsatellite loci (FST) and nine quantitative traits (QST) in experimental metapopulations of the predominantly selfing species Arabidopsis thaliana, that evolved during eight generations. Metapopulations differed with respect to population size and selection heterogeneity. In large populations, the genetic differentiation of neutral microsatellites was much larger under heterogeneous selection than under uniform selection. Using simulations, we show that this influence of selection heterogeneity on FST can be attributable to initial linkage disequilibria among loci, creating stronger genetic differentiation of QTL than expected under a simple additive model with no initial linkage. We found no significant differences between FST and QST regardless of selection heterogeneity, despite a demonstrated effect of selection on QST values. Additional data are required to validate the role of mating system and linkage disequilibria in the joint evolution of neutral and selected genetic differentiation, but our results suggest that FST/QST comparisons can be conservative tests to detect selection in selfing species.     

Genetic differentiation between Apis cerana cerana populations from Damen Island and adjacent mainland in China

Geographic isolation interrupted gene flow between populations leading to population differentiation during the long evolutionary period. In this paper, 33 colonies from Damen Island and 100 colonies from adjacent mainland populations, Juxi and Chixi, were analyzed with both mitochondrial tRNA^leu-COII sequences and five microsatellite loci. The results showed that Apis cerana cerana population from Damen Island significantly differentiated from its adjacent mainland populations. In addition, Damen Island population showed a lower level of genetic diversity in terms of the number of mitochondrial haplotypes while both island and mainland populations showed a low level of genetic diversity with mutilocus analysis. The divergent small island population A.c. cerana might probably have suffered inbreeding and genetic drift as well as limited gene flow across the strait. Our data provides useful information for management and preservation for the Damen Island population.     

Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus)

Genetic analyses of bird subspecies designated as conservation units can address whether they represent units with independent evolutionary histories and provide insights into the evolutionary processes that determine the degree to which they are genetically distinct. Here we use mitochondrial DNA control region sequence and six microsatellite DNA loci to examine phylogeographical structure and genetic differentiation among five North American grasshopper sparrow (Ammodramus savannarum) populations representing three subspecies, including a population of the endangered Florida subspecies (A. s. floridanus). This federally listed taxon is of particular interest because it differs phenotypically from other subspecies in plumage and behaviour and has also undergone a drastic decline in population size over the past century. Despite this designation, we observed no phylogeographical structure among populations in either marker: mtDNA haplotypes and microsatellite genotypes from floridanus samples did not form clades that were phylogenetically distinct from variants found in other subspecies. However, there was low but significant differentiation between Florida and all other populations combined in both mtDNA (FST = 0.069) and in one measure of microsatellite differentiation (theta = 0.016), while the non-Florida populations were not different from each other. Based on analyses of mtDNA variation using a coalescent-based model, the effective sizes of these populations are large (approximately 80,000 females) and they have only recently diverged from each other (< 26,000 ybp). These populations are probably far from genetic equilibrium and therefore the lack of phylogenetic distinctiveness of the floridanus subspecies and minimal genetic differentiation is due most probably to retained ancestral polymorphism. Finally, levels of variation in Florida were similar to other populations supporting the idea that the drastic reduction in population size which has occurred within the last 100 years has not yet had an impact on levels of variation in floridanus. We argue that despite the lack of phylogenetic distinctiveness of floridanus genotypes the observed genetic differentiation and previously documented phenotypic differences justify continued designation of this subspecies as a protected population segment.