Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise F_ST and exact tests identified weak (global F_ST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects.     

Effects of habitat fragmentation, population size and demographic history on genetic diversity: the Cross River gorilla in a comparative context

In small and fragmented populations, genetic diversity may be reduced owing to increased levels of drift and inbreeding. This reduced diversity is often associated with decreased fitness and a higher threat of extinction. However, it is difficult to determine when a population has low diversity except in a comparative context. We assessed genetic variability in the critically endangered Cross River gorilla (Gorilla gorilla diehli), a small and fragmented population, using 11 autosomal microsatellite loci. We show that levels of diversity in the Cross River population are not evenly distributed across the three genetically identified subpopulations, and that one centrally located subpopulation has higher levels of variability than the others. All measures of genetic variability in the Cross River population were comparable to those of the similarly small mountain gorilla (G. beringei beringei) populations (Bwindi and Virunga). However, for some measures both the Cross River and mountain gorilla populations show lower levels of diversity than a sample from a large, continuous western gorilla population (Mondika, G. gorilla gorilla). Finally, we tested for the genetic signature of a bottleneck in each of the four populations. Only Cross River showed strong evidence of a reduction in population size, suggesting that the reduction in size of this population was more recent or abrupt than in the two mountain gorilla populations. These results emphasize the need for maintaining connectivity in fragmented populations and highlight the importance of allowing small populations to expand.     

草鱼野生群体遗传变异的微卫星分析

利用12个微卫星标记, 对来自长江水系(邗江、吴江、九江、石首、木洞和万州)、珠江水系(肇庆)和黑龙江水系(嫩江)的8个草鱼野生地理群体进行了遗传多样性及遗传结构等分析。遗传多样性分析显示, 12个微卫星位点均为高度多态位点(PIC=0.755~0.930), 8个草鱼野生群体显示出较高的遗传多样性水平(Ho=0.839~0.893), 其中长江水系的6个群体和肇庆群体的多样性水平高于嫩江群体。瓶颈效应分析显示, 嫩江、肇庆群体及2个长江上游群体(木洞、万州)近期出现了瓶颈效应, 群体数量发生下降。群体间遗传分化指数F^ST及AMOVA分析显示, 群体间出现极显著遗传分化(P<0.01), 整体分化水平较低(F^ST<0.05)。遗传距离分析结果显示, 长江水系的6个群体与肇庆群体遗传距离较近, 与嫩江群体较远; 基于此的UPGMA聚类树显示, 长江水系下游、中游和上游的群体依次聚类, 然后与肇庆群体聚类, 最后与嫩江群体聚类, 遗传距离与地理距离呈现出较强的正相关性。遗传结构分析显示, 所有样本被划分为5个理论群, 肇庆和嫩江群体中个体的遗传结构相对独立, 而长江上游、中游和下游群体中个体的遗传结构则存在一定程度的混杂。综上所述, 中国草鱼野生资源具有较高的遗传多样性, 地理群体间存在遗传分化, 具有进一步遗传改良的潜力; 但部分群体出现的瓶颈效应也需要引起重视。     

Census vs. effective population size in chinook salmon: large- and small-scale environmental perturbation effects

Population viability has often been assessed by census of reproducing adults. Recently this method has been called into question and estimation of the effective population size (Ne) proposed as a complementary method to determine population health. We examined genetic diversity in five populations of chinook salmon (Oncorhynchus tshawytscha) from the upper Fraser River watershed (British Columbia, Canada) at 11 microsatellite loci over 20 years using DNA extracted from archived scale samples. We tested for changes in genetic diversity, calculated the ratio of the number of alleles to the range in allele size to give the statistic M, calculated Ne from the temporal change in allele frequency, used the maximum likelihood method to calculate effective population size (NeM), calculated the harmonic mean of population size, and compared these statistics to annual census estimates. Over the last two decades population size has increased in all five populations of chinook examined; however, Ne calculated for each population was low (81-691) and decreasing over the time interval measured. Values of NeM were low, but substantially higher than Ne calculated using the temporal method. The calculated values for M were generally low (M < 0.70), indicating recent population reductions for all five populations. Large-scale historic barriers to migration and development activities do not appear to account for the low values of Ne; however, available spawning area is positively correlated with Ne. Both Ne and M estimates indicate that these populations are potentially susceptible to inbreeding effects and may lack the ability to respond adaptively to stochastic events. Our findings question the practice of relying exclusively on census estimates for interpreting population health and show the importance of determining genetic diversity within populations.     

A simple method of removing the effect of a bottleneck and unequal population sizes on pairwise genetic distances

In this paper, we derive the expectation of two popular genetic distances under a model of pure population fission allowing for unequal population sizes. Under the model, we show that conventional genetic distances are not proportional to the divergence time and generally overestimate it due to unequal genetic drift and to a bottleneck effect at the divergence time. This bias cannot be totally removed even if the present population sizes are known. Instead, we present a method to estimate the divergence times between populations which is based on the average number of nucleotide differences within and between populations. The method simultaneously estimates the divergence time, the ancestral population size and the relative sizes of the derived populations. A simulation study revealed that this method is essentially unbiased and that it leads to better estimates than traditional approaches for a very wide range of parameter values. Simulations also indicated that moderate population growth after divergence has little effect on the estimates of all three estimated parameters. An application of our method to a comparison of humans and chimpanzee mitochondrial DNA diversity revealed that common chimpanzees have a significantly larger female population size than humans.     

The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus)

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.     

Genetic diversity and hierarchical population structure of a rare autotetraploid plant,Aster kantoensis (Asteraceae)

We sampled 17 populations of a rare autotetraploid Aster kantoensis (Asteraceae) from three river systems located in central Japan, and studied them for allelic variation at 22 enzyme loci. There was no significant correlation between the actual population size and three genetic diversity parameters, suggesting that the effective population size was very small even for the large populations, i.e., even large populations may still have a high probability of being of recent origin and remain influenced by the founder effect. Compared to other autotetraploid species, the total genetic variation of A. kantoensis is small. The number of alleles and gene diversity of a population were not significantly different among the river systems, although the percentage of polymorphic loci was different. Genetic differentiation among river systems was larger than between populations within the river systems, thereby indicating that gene flow between river systems is small, especially between the Kinu River system and Tama or Sagami River systems.     

Population structure and gene flow in the Sheepnose mussel (Plethobasus cyphyus) and their implications for conservation

North American freshwater mussel species have experienced substantial range fragmentation and population reductions. These impacts have the potential to reduce genetic connectivity among populations and increase the risk of losing genetic diversity. Thirteen microsatellite loci and an 883 bp fragment of the mitochondrial ND1 gene were used to assess genetic diversity, population structure, contemporary migration rates, and population size changes across the range of the Sheepnose mussel (Plethobasus cyphyus). Population structure analyses reveal five populations, three in the Upper Mississippi River Basin and two in the Ohio River Basin. Sampling locations exhibit a high degree of genetic diversity and contemporary migration estimates indicate that migration within river basins is occurring, although at low rates, but there is no migration is occurring between the Ohio and Mississippi river basins. No evidence of bottlenecks was detected, and almost all locations exhibited the signature of population expansion. Our results indicate that although anthropogenic activity has altered the landscape across the range of the Sheepnose, these activities have yet to be reflected in losses of genetic diversity. Efforts to conserve Sheepnose populations should focus on maintaining existing habitats and fostering genetic connectivity between extant demes to conserve remaining genetic diversity for future viable populations.     

Genetic Structure of Wild Bonobo Populations: Diversity of Mitochondrial DNA and Geographical Distribution

Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species’ range. In 136 effective samples from different individuals (range: 7–37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation.     

Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences

Molecular genetic data were used to investigate population sizes and ages of Eleutherodactylus (Anura: Leptodactylidae), a species-rich group of small leaf-litter frogs endemic to Central America. Population genetic structure and divergence was investigated for four closely related species surveyed across nine localities in Costa Rica and Panama. DNA sequence data were collected from a mitochondrial gene (ND2) and a nuclear gene (c-myc). Phylogenetic analyses yielded concordant results between loci, with reciprocal monophyly of mitochondrial DNA haplotypes for all species and of c-myc haplotypes for three of the four species. Estimates of genetic differentiation among populations (FST) based upon mitochondrial data were always higher than nuclear-based FST estimates, even after correcting for the expected fourfold lower effective population size (Ne) of the mitochondrial genome. Comparing within-population variation and the relative mutation rates of the two genes revealed that the Ne of the mitochondrial genome was 15-fold lower than the estimate of the nuclear genome based on c-myc. Nuclear FST estimates were approximately 0 for the most proximal pairs of populations, but ranged from 0.5 to 1.0 for all other pairs, even within the same nominal species. The nuclear locus yielded estimates of Ne within localities on the order of 105. This value is two to three orders of magnitude larger than any previous Ne estimate from frogs, but is nonetheless consistent with published demographic data. Applying a molecular clock model suggested that morphologically indistinguishable populations within one species may be 107 years old. These results demonstrate that even a geologically young and dynamic region of the tropics can support very old lineages that harbour great levels of genetic diversity within populations. The association of high nucleotide diversity within populations, large divergence between populations, and high species diversity is also discussed in light of neutral community models.     

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

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Evaluation of a remnant lake sturgeon population’s utility as a source for reintroductions in the Ohio River system

The selection of an appropriate source population may be crucial to the long-term success of reintroduction programs. Appropriate source populations often are those that originate from the same genetic lineage as native populations. However, source populations also should exhibit high levels of genetic diversity to maximize their capacity to adapt to variable environmental conditions. Finally, it is preferable if source populations are genetically representative of historical lineages with little or no contamination from non-native or domesticated stocks. Here, we use nuclear (microsatellite) and cytoplasmic (mitochondrial control region) markers to assess the genetic suitability of a potential source population inhabiting the White River in Indiana: the last extant lake sturgeon population in the Ohio River drainage. The White River population exhibited slightly lower levels of genetic diversity than other lake sturgeon populations. However, the population’s two private microsatellite alleles and three private haplotypes suggest a unique evolutionary trajectory. Population assignment tests revealed only two putative migrants in the White River, indicating the population has almost completely maintained its genetic integrity. Additionally, pairwise F _ST estimates indicated significant levels of genetic divergence between the White River and seven additional lake sturgeon populations, suggesting its genetic distinctiveness. These data indicate that the White River population may be the most suitable source population for future lake sturgeon reintroductions throughout the Ohio River drainage. Furthermore, the White River population appears to be a reservoir of unique genetic information and reintroduction may be a necessary strategy to ensure the persistence of this important genetic lineage.     

Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.     

Population size and fragmentation thresholds for the maintenance of genetic diversity in the herbaceous endemic Scutellaria montana (Lamiaceae)

Abstract.-The level and distribution of genetic variation is thought to be affected primarily by the size of individual populations and by gene flow among populations. Although the effects of population size have frequently been examined, the contributions of regional gene flow to levels of genetic variation are less well known. Here I examine the effects of population size and the number of neighboring populations (metapopulation density) on the distribution and maintenance of genetic diversity in an endemic herbaceous perennial. Reductions in the proportion of polymorphic loci and the effective number of alleles per locus were apparent for many populations with a census size of less than 100 individuals, but no effects of population size on levels of inbreeding were detected. I assess the effects of regional population density on levels of diversity and inbreeding using stepwise regression analysis of metapopulation diameter (i.e., the size of a circle within which population density is estimated). This procedure provides a spatially explicit evaluation of the effects of metapopulation size on population genetic parameters and indicates the critical number of neighboring populations (fragmentation threshold) for the regional maintenance of genetic diversity. Stepwise regression analyses revealed fragmentation thresholds at two levels; at a scale of 2 km, where small metapopulations resulted in greater levels of selfing or sibling mating, and at a scale of 8 km, where metapopulation size was positively associated with higher levels of genetic diversity. I hypothesize that the smaller fragmentation threshold may reflect higher levels of selfing in isolated populations because of the absence of pollinators. The larger threshold probably indicates the maximum distance over which pollen dispersal rates are high enough to counteract genetic drift. This study demonstrates that the regional distribution of populations can be an important factor for the long-term maintenance of genetic variation.     

Role of recent and old riverine barriers in fine-scale population genetic structure of Geoffroy's tamarin (Saguinus geoffroyi) in the Panama Canal watershed

The role of physical barriers in promoting population divergence and genetic structuring is well known. While it is well established that animals can show genetic structuring at small spatial scales, less well-resolved is how the timing of the appearance of barriers affects population structure. This study uses the Panama Canal watershed as a test of the effects of old and recent riverine barriers in creating population structure in Saguinus geoffroyi, a small cooperatively breeding Neotropical primate. Mitochondrial sequences and microsatellite genotypes from three sampling localities revealed genetic structure across the Chagres River and the Panama Canal, suggesting that both waterways act as barriers to gene flow. F-statistics and exact tests of population differentiation suggest population structure on either side of both riverine barriers. Genetic differentiation across the Canal, however, was less than observed across the Chagres. Accordingly, Bayesian clustering algorithms detected between two and three populations, with localities across the older Chagres River always assigned as distinct populations. While conclusions represent a preliminary assessment of genetic structure of S. geoffroyi, this study adds to the evidence indicating that riverine barriers create genetic structure across a wide variety of taxa in the Panama Canal watershed and highlights the potential of this study area for discerning modern from historical influences on observed patterns of population genetic structure.     

Seed bank influences on genetic diversity in the rare annual Clarkia springvillensis (Onagraceae)

The potential for seed banks to significantly affect the genetic structure of populations was recognized nearly two decades ago. However, there has been little empirical work that examines the problem. In this study, we explore the possibility that the seed bank of a rare annual, Clarkia springvillensis, could act as a buffer against the genetic consequences of small population size. We examined the adult and seed bank cohort in three natural populations. The seed bank was surveyed by collecting soil cores twice during the growing season: postgermination and post seed set. The genetic constitution of the adults and seed bank cohort was determined by examining eight polymorphic isozyme loci via starch gel electrophoresis. The total genetic diversity in the seed bank (Ht = 0.355) was significantly higher than in the adults (Ht = 0.260). Additionally, Fst estimates of genetic differentiation among populations showed significantly less differentiation among population seed banks (Fst = 0.008) than among adults (Fst = 0.045). These results are in agreement with the expectation that seed banks would act to maintain genetic diversity in populations as well as have the effect of slowing differentiation of populations.     

Assessment of the genetic diversity among Glyptosternum maculatum, an endemic fish of Yarlung Zangbo River, Tibet, China using SSR markers

The genetic diversity of Glyptosternum maculatum populations from Nyang River, Lhasa River, and Shetongmon Reach of Yarlung Zangbo River was assessed using six microsatellite markers. Overall, the genetic diversity across the three populations was low. The Shetongmon population exhibited the highest level of genetic diversity in terms of number of alleles and effective alleles, heterozygosity, and polymorphic information content value, followed by the Nyang population and Lhasa population. The analysis of molecular variance demonstrated that almost the variation (86.64%) occurred within populations. The differentiation among populations was not significant, and population structure was weak. These results revealed that three natural populations of G. maculatum are not genetically differentiated and the large disparity of living altitude did not caused genetic differentiation between different populations. Our observations will help identify the genetic relationship among populations to understand the genetic diversity of G. maculatum.     

Genetic diversity and structure of natural fragmented Chamaecyparis obtusa populations as revealed by microsatellite markers

The genetic diversity and population structure of hinoki (Chamaecyparis obtusa) in Japan were investigated by examining the distribution of alleles at 13 microsatellite loci in 25 natural populations from Iwaki in northern Japan to Yakushima Island in southern Japan. On average, 26.9 alleles per locus were identified across all populations and 4.0% of the genetic variation was retained among populations (G _ST = 0.040). According to linkage disequilibrium analysis, estimates of effective population size and detected evidence of bottleneck events, the genetic diversity of some populations may have declined as a result of fragmentation and/or over-exploitation. The central populations located in the Chubu district appear to have relatively large effective population sizes, while marginal populations, such as the Yakushima, Kobayashi and Iwaki populations, have smaller effective population sizes and are isolated from the other populations. Microsatellite analysis revealed the genetic uniqueness of the Yakushima population. Although genetic differentiation between populations was low, we detected a gradual cline in the genetic structure and found that locus Cos2619 may be non-neutral with respect to natural selection.     

Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.     

Elevated genetic diversity of mitochondrial genes in asexual populations of Bark Lice ('Psocoptera': Echmepteryx hageni)

Asexual reproduction is commonly thought to be associated with low genetic diversity in animals. Echmepteryx hageni (Insecta: 'Psocoptera') is one of several psocopteran species that are primarily parthenogenetic, but also exists in small, isolated sexual populations. We used mitochondrial DNA sequences to investigate the population history and genealogical relationships between the sexual and asexual forms of this species. The asexual population of E. hageni exhibits extremely high mitochondrial haplotype diversity (H=0.98), whereas the sexual forms had significantly lower haplotypic diversity (H=0.25, after correcting for sample size). This diversity in asexuals represents one the greatest genetic diversities reported for asexual animals in the literature. Nucleotide diversities were also higher in asexual compared to sexual populations (π=0.0071 vs. 0.00027). Compared to other reported estimates of π in insects, asexual nucleotide diversity is high, but not remarkably elevated. Three hypotheses might explain the elevated genetic diversity of asexual populations: (i) larger effective population size, (ii) greater mutation rate or (iii) possible recent origin of sexuals. In addition, phylogeographic analysis revealed little geographic structure among asexual E. hageni, although specimens from the upper Midwest form a single clade and are genetically differentiated. The mismatch distribution and neutrality tests indicate a historical population size increase, possibly associated with expansion from glacial refugia.