Patterns of population genetic variation in sympatric chiltoniid amphipods within a calcrete aquifer reveal a dynamic subterranean environment

Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km² region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes (=wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete.     

Spatial population genetic structure in Trillium grandiflorum: the roles of dispersal, mating, history, and selection

The roles of the various potential ecological and evolutionary causes of spatial population genetic structure (SPGS) cannot in general be inferred from the extant structure alone. However, a stage-specific analysis can provide clues as to the causes of SPGS. We conducted a stage-specific SPGS analysis of a mapped population of about 2000 Trillium grandiflorum (Liliaceae), a long-lived perennial herb. We compared SPGS for juvenile (J), nonreproductive (NR), and reproductive (R) stages. Fisher's exact test showed that genotypes had Hardy-Weinberg frequencies at all loci and stage classes. Allele frequencies did not differ between stages. Bootstrapped 99% confidence intervals (99%CI) indicate that F-statistic values are indistinguishable from zero, (except for a slightly negative FIT for the R stage). Spatial autocorrelation was used to calculate f the average kinship coefficient between individuals within distance intervals. Null hypothesis 99%CIs for f were constructed by repeatedly randomizing genotypic locations. Significant positive fine-scale genetic structure was detected in the R and NR stages, but not in the J stage. This structure was most pronounced in the R stage, and declined by about half in each remaining stage: near-neighbor f = 0.122, 0.065, 0.027, for R, NR, and J, respectively. For R and NR, the near-neighbor f lies outside the null hypothesis 99%CI, indicating kinship at approximately the level of half-sibs and first cousins, respectively. We also simulated the expected SPGS of juveniles post dispersal, based on measured R-stage SPGS, the mating system, and measured pollen and seed dispersal properties. This provides a null hypothesis expectation (as a 99%CI) for the J-stage correlogram, against which to test the likelihood that post-dispersal events have influenced J-stage SPGS. The actual J correlogram lies within the null hypothesis 99%CI for the shortest distance interval and nearly all other distance intervals indicating that the observed low recruitment, random mating and seed dispersal patterns are sufficient to account for the disappearance of SPSG between the R and the J stages. The observed increase in SPGS between J and R stages has two potential explanations: history and local selection. The observed low total allelic diversity is consistent with a past bottleneck: a possible historical explanation. Only a longitudinal stage-specific study of SPGS structure can distinguish between historical events and local selection as causes of increased structure with increasing life history stage.     

Mitochondrial DNA diversity, population structure, and gender association in the gynodioecious plant Silene vulgaris

A highly variable mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLP) locus is used to assess the population structure of mitochondrial genomes in the gynodioecious plant Silene vulgaris at two spatial scales. Thirteen mtDNA haplotypes were identified within 250 individuals from 18 populations in a 20-km diameter region of western Virginia. The population structure of these mtDNA haplotypes was estimated as thetaST = 0.574 (+/- 0.066 SE) and, surprisingly, genetic differentiation among populations was negatively correlated with geographic distance (Mantel r = -0.246, P < 0.002). Additionally, mtDNA haplotypes were spatially clumped at the scale of meters within one population. Gender in S. vulgaris is determined by an interaction between autosomal male fertility restorers and cytoplasmic male sterility (CMS) factors, and seed fitness is affected by an interaction between gender and population sex ratio; thus, selection acting on gender could influence the distribution of mtDNA RFLP haplotypes. The sex ratio (females:hermaphrodites) varied among mtDNA haplotypes across the entire metapopulation, possibly because the haplotypes were in linkage disequilibrium with different CMS factors. The gender associated with some of the most common haplotypes varied among populations, suggesting that there is also population structure in male fertility restorer genes. In comparison with reports of mtDNA variation from other published studies, we found that S. vulgaris exhibits a large number of mtDNA haplotypes relative to that observed in other species.     

Genetic structure of avian populations--allozymes revisited

Selection on allozymes has sometimes been advanced as one explanation for the low levels of population differentiation detected in avian populations by the use of enzymatic markers. Comparisons of the amount of population subdivision (estimated by FST values or analogous indices) measured by enzymatic and mitochondrial DNA (mtDNA) markers in birds were seen as evidence for this because mtDNA typically produces a more structured picture of population subdivisions. In fact, when taking into account the smaller effective population size of mtDNA, nuclear and mitochondrial markers give concordant results. Some discrepancies still exist, but I suggest that some might originate from different amounts of nuclear vs. mitochondrial gene flow due to partial reproductive isolation. Variable number of tandem repeat (VNTR) loci do not provide a dramatically different picture of population structures in birds compared to allozymes. Although more tests are needed, such as comparing the amount of genetic structure detected in the same populations with allozymes and microsatellites, the low levels of population subdivision measured with allozymes in birds seem to reflect historical and demographic processes and would not appear to result from any peculiarities of bird enzymatic loci.     

Genetic population structure and mobility of two nectar-feeding bats from Venezuelan deserts: inferences from mitochondrial DNA

Glossophaga longirostris and Leptonycteris curasoae are nectar-feeding bats associated with arid zones in northern South America. Despite their close phylogenetic relationship, sympatric condition and niche similarities, morphological and ecological evidence suggest that these species differ in dispersal capabilities. Using mitochondrial DNA, we tested the hypothesis that these species exhibit different levels of population structure that are congruent with their particular movement capabilities. We sequenced a section of the control region of mtDNA for 41 G. longirostris and 42 L. curasoae from 11 zones in Venezuela. Population subdivision in G. longirostris (FST = 0.725) was considerably higher than in L. curasoae (FST = 0.167). L. curasoae individuals shared haplotypes at greater distances (812 km) than G. longirostris (592 km). Our results offer preliminary evidence for one of two possible scenarios, either greater mobility in L. curasoae or a higher degree of female philopatry in G. longirostris.     

Inferring contemporary levels of gene flow and demographic history in a local population of the leaf beetle Gonioctena olivacea from mitochondrial DNA sequence variation

We have studied mitochondrial DNA variation in a local population of the leaf beetle species Gonioctena olivacea, to check whether its apparent low dispersal behaviour affects its pattern of genetic variation at a small geographical scale. We have sampled 10 populations of G. olivacea within a rectangle of 5 x 2 km in the Belgian Ardennes, as well as five populations located approximately along a straight line of 30 km and separated by distances of 3-12 km. For each sampled individual (8-19 per population), a fragment of the mtDNA control region was polymerase chain reaction-amplified and sequenced. Sequence data were analysed to test whether significant genetic differentiation could be detected among populations separated by such relatively short distances. The reconstructed genealogy of the mitochondrial haplotypes was also used to investigate the demographic history of these populations. Computer simulations of the evolution of populations were conducted to assess the minimum amount of gene flow that is necessary to explain the observed pattern of variation in the samples. Results show that migration among populations included in the rectangle of 5 x 2 km is substantial, and probably involves the occurrence of dispersal flights. This appears difficult to reconcile with the results of a previous ecological field study that concluded that most of this species dispersal occurs by walking. While sufficient migration to homogenize genetic diversity occurs among populations separated by distances of a few hundred metres to a few kilometres, distances greater than 5 km results in contrast in strong differentiation among populations, suggesting that migration is drastically reduced on such distances. Finally, the results of coalescent simulations suggest that the star-like genealogy inferred from the mtDNA sequence data is fully compatible with a past demographic expansion. However, a metapopulation structure alone (without the need to invoke a population expansion event) cannot be dismissed as the cause of this star shape.     

Conservation implications of high genetic variation in two closely related and highly threatened species of Crambe (Brassicaceae) endemic to the island of Gran Canaria: C. tamadabensis and C. pritzelii

We used data from 12 allozyme loci for two endemic Brassicaceae from Gran Canaria (the endangered narrow endemic Crambe tamadabensis and its more widespread congener C. pritzelii) to assess whether their genetic diversity patterns reflect their phylogenetic closeness and contrasting population sizes and distribution areas, and to derive conservation implications. Genetic diversity values are high for both species and slightly higher in C. tamadabensis, despite its narrow distribution in north‐western Gran Canaria. At odds with the generally high interpopulation diversity levels reported in Canarian endemics, values of G_ST in C. tamadabensis and C. pritzelii are rather low (0.067 and 0.126, respectively). We construe that the higher genetic structure detected in C. pritzelii is mainly a result of unbalanced allele frequencies and low population sizes at the edges of its distribution. The overall high allozyme variation detected in C. tamadabensis and C. pritzelii is nevertheless compatible with an incipient but consistent genetic differentiation between the two species, modulated by recurrent bottlenecks caused by grazing and drift. Our data suggest that conservation efforts aimed at maintaining the existing genetic connectivity in each species and ex situ conservation of seeds are the best strategies to conserve their genetic diversity.     

Genetic variation and population structure of the mosquito Anopheles jeyporiensis in southern China

Genetic differentiation among populations of Anopheles jeyporiensis was examined using 76 mtDNA COII sequences from 16 sites throughout southern China and northern Vietnam. The COII sequences are AT-rich (74.58%) and reveal high levels of diversity with 39 of 685 sites polymorphic and 50 different haplotypes present. Genetic variation is high within populations and significant geographical structure was detected at both population and regional levels. In the larger samples, the distributions of haplotypes suggest recent population expansion.     

Range‐wide genetic homogeneity in the California sea mussel (Mytilus californianus): a comparison of allozymes,nuclear DNA markers,and mitochondrial DNA sequences

We tested for genetic differentiation among six populations of California sea mussels (Mytilus californianus) sampled across 4000 km of its geographical range by comparing patterns of variation at four independent types of genetic markers: allozymes, single‐copy nuclear DNA markers, and DNA sequences from the male and female mitochondrial genomes. Despite our extensive sampling and genotyping efforts, we detected no significant differences among localities and no signal of isolation by distance suggesting that M. californianus is genetically homogeneous throughout its range. This concordance differs from similar studies on other mytilids, especially in the role of postsettlement selection generating differences between exposed coastal and estuarine habitats. To assess if this homogeneity was due to M. californianus not inhabiting estuarine environments, we reviewed studies comparing allozymes with other classes of nuclear DNA markers. Although both types of markers gave broadly consistent results, there was a bias favouring studies in which allozymes were more divergent than DNA markers (nine to three) and a disproportionate number of these cases involved marine taxa (seven). Furthermore, allozymes were significantly more heterogeneous than DNA markers in three of the four studies that sampled coastal and estuarine habitats. We conclude that the genetic uniformity exhibited by M. californianus may result from a combination of extensive gene flow and the lack of exposure to strong selective gradients across its range.     

Genetic relationships among populations of wild resident, and wild and hatchery anadromous brook charr

To determine the genetic relationship of anadromous and resident life-history types within and among drainages, and compare several hatchery strains to their progenitor populations, brook charr Salvelinus fontinalis were examined for allozyme and mitochondrial DNA variation. Greater genetic similarity of sympatric anadromous and resident charr was found compared to similar life-history forms allopatrically, suggesting the two life-history types are not reproductively isolated. Low divergence among the mtDNA haplotypes suggests that the two life-history types are members of the same evolutionary lineage. Population differentiation from mtDNA data exceeded that from estimates based on allozymes. Genetic deviations from expectations suggest that the hatchery strains were derived from few individuals.     

Genetic population structure of the German cockroach, Blattella germanica: Absence of geographical variation

The genetic structure of 31 populations of the German cockroach, Blattella germanica (L.), located in two French cities 900 km apart, was estimated by enzyme gel electrophoresis. A set of 41 loci was analysed. Eight loci (4 Est, 3 Lap and 1 Got) were polymorphic. Diversity was estimated at different geographical levels: the overall population, between cities and within a city. Hierarchical F-statistics indicated significant genetic differentiation between all populations and among populations within each city, but no differentiation between cities. F_ST values for populations within each city and for the overall sample were substantially dissimilar. In addition, a cluster analysis did not separate populations according to their geographical origin but according to the predominance of either of the two alternative Est-4 alleles. The results of this analysis point to the absence of genetic differentiation on a large geographical scale: no large-scale geographical distance effect was detected. However, we evidenced strong genetic substructuring on a local scale, within cities.     

群体遗传结构中的基因流

群体遗传结构上的差异是遗传多样性的一种重要体现,对群体遗传结构的研究已有较久的历史,而其中的基因流研究近些年来越来越受到重视。它对群体遗传学、进化生物学、保护生物学、生态学有着极其重要的作用。虽然传统的群体遗传学能估测基因流大小,但它的精确性还有很大局限性。随着生物技术的进步,对基因流的研究逐渐向分子水平过渡,应用蛋白质电泳技术、分子标记技术(RAPD、RFLP、VNTR、ISSR、DNA测序等)方法对群体间基因流的流动水平进行了深入细致的研究。通过综述群体遗传结构的几种模式:陆岛模式、海岛模式、阶石模式、距离隔离模式、层次模式,以及在群体遗传结构的几种模式基础上的基因流的研究方法、作用、地位和近些年来研究者的研究成果,并指出了这些方法的局限性。     

The interplay of dispersal limitation,rivers, and historical events shapes the genetic structure of an Amazonian frog

Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a ～6‐km transect, to evaluate dispersal ability, and between paired bank populations along a ～65‐km stretch of the Approuague river, to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale, and conclude that the species has a restricted dispersal ability that is probably tied to its life‐history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river, and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is the result of restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life‐history traits comparable with A. andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 356–373.     

Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum

The Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of the D-loop mitochondrial region, samples collected at four different locations in the Southern Ocean, three in the Atlantic and one in the Pacific sector. Sampling was replicated in two different years at two locations. Sequence analysis showed a remarkably high polymorphism, with 110 haplotypes over the 256 investigated specimens, and about 80% of haplotypes occurring only once. Neutrality tests indicated that all samples were not at mutation-drift equilibrium, and suggested a past population expansion. This result was supported by the presence of a star-like topology in the D-loop gene tree, and by results of mismatch distribution. The start of the expansion was dated, using a specifically calibrated clock, between 111 and 126 thousand years ago. This value corresponds to the start of the cooling period that led to the last glaciation peak, and is in close agreement with a recently suggested range expansion for pelagic Antarctic ecosystems. Analysis of molecular variation indicated a small, though highly significant, value of differentiation between samples. This result, together with the lack of association between clades and geographical locations, indicates a weak population structure for the species.     

Patchy population structure in a short-distance migrant: evidence from genetic and demographic data

Species often occur in subdivided populations as a consequence of spatial heterogeneity of the habitat. To describe the spatial organization of subpopulations, existing theory proposes three main population models: patchy population, metapopulation and isolated populations. These models differ in their predicted levels of connectivity among subpopulations, and in the risk that a subpopulation will go extinct. However, spatially discrete subpopulations are commonly considered to be organized as metapopulations, even though explicit tests of metapopulation assumptions are rare. Here, we test predictions of the three models on the basis of demographic and genetic data, a combined approach so far surprisingly little used in mobile organisms. From 2002 to 2005, we studied nine subpopulations of the wetland-restricted reed bunting ( Emberiza schoeniclus ) in the southeastern part of the Canton Zurich (Switzerland), from which local declines of this species have been reported. Here, wetlands are as small as 2.7 ha and separated through intensively used agricultural landscapes. Demographic data consisted of dispersal of colour-banded individuals among subpopulations, immigration rates and extinction-/recolonization dynamics. Genetic data were based on the distribution of genetic variability and gene flow among subpopulations derived from the analysis of nine microsatellite loci. Both demographic and genetic data revealed that the patchy population model best described the spatial organization of reed bunting subpopulations. High levels of dispersal among subpopulations, high immigration into the patchy population, and genetic admixture suggested little risk of extinction of both subpopulations and the entire patchy population. This study exemplifies the idea that spatially discrete subpopulations may be organized in ways other than a metapopulation, and hence has implications for the conservation of subpopulations and species.     

Spatial and demographic population genetic structure in Catasetum viridiflavum across a human-disturbed habitat

Spatial and temporal genetic structures were examined across sites on islands and mainland (continuous forest) populations of an epiphytic orchid, Catasetum viridiflavum, using 17 polymorphic allozyme loci. I tested whether patches on islands or at mainland sites comprised small local populations or a large population. Low among population differentiation was observed across the landscape suggesting that the species-specific pollinator and tiny wind-dispersed seeds maintain interconnections among distant patches. Temporal genetic structure among stage classes, and among breeding individuals are important components of the maintenance of genetic variation in this orchid. The natural history of this species including small breeding populations, probable high frequency of mating among relatives, and the high rates of seed movement among sites contribute to the high FIS. These data show that physically isolated patches in this epiphytic orchid comprise a single larger genetic population, which is independent of the physical distances among sites. Although quite different in ecological and life history characteristics, the genetic structure of this orchid demonstrates a pattern similar to temperate and tropical trees in fragmented landscapes.     

Spatial genetic structure of a small rodent in a heterogeneous landscape

Gene flow in natural populations may be strongly influenced by landscape features. The integration of landscape characteristics in population genetic studies may thus improve our understanding of population functioning. In this study, we investigated the population genetic structure and gene flow pattern for the common vole, Microtus arvalis, in a heterogeneous landscape characterised by strong spatial and temporal variation. The studied area is an intensive agricultural zone of approximately 500 km² crossed by a motorway. We used individual-based Bayesian methods to define the number of population units and their spatial borders without prior delimitation of such units. Unexpectedly, we determined a single genetic unit that covered the entire area studied. In particular, the motorway considered as a likely barrier to dispersal was not associated with any spatial genetic discontinuity. Using computer simulations, we demonstrated that recent anthropogenic barriers to effective dispersal are difficult to detect through analysis of genetic variation for species with large effective population sizes. We observed a slight, but significant, pattern of isolation by distance over the whole study site. Spatial autocorrelation analyses detected genetic structuring on a local scale, most probably due to the social organisation of the study species. Overall, our analysis suggests intense small-scale dispersal associated with a large effective population size. High dispersal rates may be imposed by the strong spatio-temporal heterogeneity of habitat quality, which characterises intensive agroecosystems.     

Genetic analysis of the population structure of socially organized oystercatchers (Haematopus ostralegus) using microsatellites

On the island of Schiermonnikoog (The Netherlands), the breeding population of oystercatchers can be divided into two groups: 'residents' and 'leapfrogs', based on their distinct social characteristics and limited probabilities of status change between breeding seasons. In order to investigate whether this social organization has caused local genetic differentiation, leapfrogs and residents were compared at eight polymorphic microsatellite loci. No significant genetic subdivision between residents and leapfrogs was observed (theta = 0.0000; 95% confidence interval (CI), -0.0027-0.0033), indicating that the oystercatcher population on the island of Schiermonnikoog has to be considered as one panmictic unit. Investigation of three additional locations in the northern part of The Netherlands did not reveal significant genetic population subdivision either (theta = -0.0005; 95% CI, -0.0045-0.0037), despite the fact that adult osytercatchers show extreme fidelity to their breeding localities. These results indicate panmixis and considerable levels of gene flow within the northern part of The Netherlands. Thus, the results from genetical analyses do not seem to be in agreement with observational data on the dispersal behaviour of breeding individuals. It is argued that the lack of population structure, locally on Schiermonnikoog as well as across larger geographical distances, is to be attributed to high levels of gene flow through dispersal of juvenile birds.     

基于mtDNA-COI基因序列的雷氏按蚊分子群体遗传结构研究

【目的】探讨我国雷氏按蚊Anopheles lesteri的群体差异和分化程度。【方法】采用PCR方法, 从分子水平鉴别了采自我国和韩国的雷氏按蚊共9个群体139个样本, 扩增其线粒体DNA细胞色素氧化酶亚基Ⅰ基因, 并进行序列测定和分析。【结果】本研究共获得49个单倍型, 各单倍型呈高水平的平行演化, 来自云南群体的单倍型显示是扩张的源头。分子变异等级分析(AMOVA)的计算结果显示, 群体内变异占总变异的比例（64.95%）大于群体间（35.05%）, FST值为0.3504, 各群体间出现遗传分化。Mantel检验结果显示基因流水平与地理距离呈负相关关系（R²＝0.1322）, 群体遗传结构符合距离隔离模型。【结论】雷氏按蚊韩国和辽宁群体与其他分布地群体间差异大, 已出现明显分化, 我国其他分布地群体间的遗传差异小。