Implications of life-history transitions on the population genetic structure of the toxigenic marine dinoflagellate Alexandrium tamarense

Genotypic or phenotypic markers for characterization of natural populations of marine microalgae have typically addressed questions regarding differentiation among populations, usually with reference to a single or few clonal isolates. Based upon a large number of contemporaneous isolates from the same geographical population of the toxigenic species Alexandrium tamarense from the North Sea, we uncovered significant genetic substructure and low but significant multilocus linkage disequilibrium (LD) within the planktonic population. Between the alternative molecular genotyping approaches, only amplified fragment length polymorphism (AFLP) revealed cryptic genetic population substructure by Bayesian clustering, whereas microsatellite markers failed to yield concordant patterns. Both markers, however, gave evidence for genetic differentiation of population subgroups as defined by AFLP. A considerable portion of multilocus LD could be attributed to population subdivision. The remaining LD within population subgroups is interpreted as an indicator of frequency shifts of clonal lineages during vegetative growth of planktonic populations. Phenotypic characters such as cellular content and composition of neurotoxins associated with paralytic shellfish poisoning (PSP) and allelochemical properties may contribute to intra- or inter-annual differentiation of planktonic populations, if clonal lineages that express these characters are selectively favoured. Nevertheless, significant phenotypic differentiation for these characters among the genetically differentiated subgroups was only detected for PSP toxin content in two of the four population subgroups. By integrating the analysis of phenotypic and genotypic characteristics, we developed a conceptual population genetic model to explain the importance of life-cycle dynamics and transitions in the evolutionary ecology of these dinoflagellates.     

Historical influences dominate the population genetic structure of a sedentary marine fish,Atlantic wolffish (Anarhichas lupus), across the North Atlantic Ocean

Genetic variation was assessed in Atlantic wolffish, Anarhichas lupus, across the North Atlantic Ocean using microsatellite and amplified fragment length polymorphism (AFLP) markers. Despite unusual life history attributes such as large benthic eggs, large larvae, a limited pelagic stage and relatively sedentary adults, which suggest potential for strong population structure, range‐wide F_ST values were comparable to other marine fishes (≤0.035). Nevertheless, both significant genetic differentiation among regions and isolation by distance were observed, suggesting limited dispersal in this species. AFLP loci, evaluated on a subset of samples, revealed slightly higher F_ST values, but similar patterns of differentiation and isolation‐by‐distance estimates, compared to microsatellites. The genetic structure of Atlantic wolffish has likely been shaped by its post‐glacial history of recolonization, North Atlantic current patterns and continuity of habitat on continental shelves.     

Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration

Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F_ST up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F_ST above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat.     

Temporal genetic changes between cohorts in a natural population of a marine fish, Diplodus sargus

Temporal changes at 17 allozyme loci in the Diplodus sargus population of Banyuls sur Mer (Mediterranean Sea, France) were monitored within a single population among ten year‐classes (cohorts) sampled over a 6‐month period. The genetic survey was combined with evaluation of the demographic structure of the population by determining variation of abundance between cohorts. The population showed variation in abundance among cohorts ranging from 16 to 214 individuals. Significant divergences in genetic structure were observed between cohorts (P < 0.0001) despite very low values of F_ST (multilocus F_ST over all cohorts = 0.0018). The heterozygosity of each cohort, as well as the F_IS values, was significantly correlated with the abundance of each cohort, with abundant cohorts showing lower heterozygosity and a significant deficit of heterozygotes (positive F_IS values). Finally, multilocus temporal genetic variance (F_k) computed between successive cohorts was higher in low abundance cohorts. Change of heterozygosity between cohorts, distribution of year‐class genetic structure, and change in the genetic structure within a cohort appear to be affected mostly by the abundance of the cohort and are therefore driven by genetic drift. We propose that the Diplodus sargus cohorts are built up from the mixing of families during the pelagic stage or later during recruitment, and that the decrease in heterozygosity leading to a deficit of heterozygotes is characteristic of a Wahlund effect. Such a Wahlund effect would derive from the mixing of the progeny of families made up of few individuals, but exhibiting high fecundity and high variability of reproductive success. Therefore, although cohorts derived from poor recruitment would only group a few families and would exhibit limited deficit of heterozygotes (higher heterozygosity values), they would lead to high genetic drift and appear more divergent (higher mean temporal genetic variance) than cohorts with high abundance. While not demonstrating directly the family structure of marine populations, our survey provides evidence of highly structured populations. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 76 , 9–20.     

River drying influences genetic variation and population structure in an Arctic freshwater fish

Conserving biodiversity in an era of rapid climate change requires understanding the mechanisms that influence dispersal, gene flow and, ultimately, species persistence. This information is becoming critical for conserving key species in rapidly warming places such as the Arctic. Arctic freshwater fish not only face warmer conditions, but also the drying of tundra streams due to climate change. Here, we examined population structure, gene flow, and the influence of landscape features on the neutral genetic variation of the Arctic grayling on Alaska’s North Slope. We estimated the number of genetically distinct clusters and determined effective population sizes for and patterns of gene flow among geographic regions. We predicted that river distance, river drying, distance to the coast, and elevational gradient would influence genetic differentiation for Arctic grayling. Bayesian clustering and discriminant analysis of principal components found support for five or six genetic clusters roughly corresponding to downstream and headwater subwatersheds. Estimates of gene flow revealed asymmetric downstream bias. River distance and river dry zones were significantly associated with increasing genetic differentiation among sampling locations despite this species' high dispersal capability and the temporary nature of dry zones. Isolation and downstream-biased dispersal could contribute to high levels of inter-population genetic variation among the headwaters of the North Slope Arctic grayling metapopulation, which might be particularly important for species conservation during rapid climate change. More generally, small, isolated populations might drive particular alleles to higher frequencies due to selection or drift, thus promoting the genetic potential for rapid evolutionary changes under future climate change.

     

Comparative analysis of genetic structure of 2 species of marine fish Dicentrarchus labrax and Dicentrarchus punctatus

We present here the genetic structure existing among five samples of the spotted sea bass Dicentrarchus punctatus, and we compare it to what prevails in the common sea bass D. labrax, a congeneric species sampled on almost the same geographical range. A genetic distance tree inferred from the polymorphism at six microsatellite loci shows a distinct pattern for the two species. D. labrax samples appears to be genetically more homogeneous with a global Fst of 3% as compared to the 10% observed at D. punctatus, indicating a lesser level of gene flow in the latter species. While appearing more differentiated, D. punctatus presents no clear geographical organisation of its genetic variability in opposition to D. labrax samples. This allows us to propose this pair of closely relative species as a good candidate for the study by comparative analysis of the biological and/or historical factors affecting genetic differentiation in marine environment.     

Multiple paternity and population genetic structure in natural populations of the poeciliid fish, Heterandria formosa

Heterandria formosa Agassiz, exhibits internal fertilization, internal brooding of embryos, sperm storage and an extreme level of superfetation. In this study we used microsatellite markers to examine variation among seven populations that exhibited significant variance in their histories of population density. We found that the populations were genetically distinct and that the heterozygosity increased as population density increased. We also examined paternity in three of those populations and found that the number of sires per female and the number of sires per brood increased with population density. Overall, the rates of multiple paternity are quite low relative to other species. The correlations with population density suggest that contact rates play a critical role in the breeding system in this species but the low rates of multiple paternity suggest that females may exert control over fertilization of their ova.     

The genetic structure of the Kuwaiti population

Summary Frequency estimates were determined on seventeen blood group, serum protein, and red-cell enzyme markers on random samples of 193 individuals from two Bedouin tribes in addition to the general population in Kuwait. Genetic heterogeneity between the three communities is evident from the significant differences in allelic distribution of the polymorphic markers.Genetic distance measurements were used to compare the results with the oral history of descent of the two tribal communities. Results were in agreement with tribal history.     

The genetic structure of the Swedish population

Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise F(st)) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS) with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to false conclusions.     

Assessing population genetic structure via the maximisation of genetic distance

Background

The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics.

Methods

In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm) of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set.

Results

The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for F_ST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for F_ST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found.

Conclusion

This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy-Weinberg and linkage equilibrium, performs well under different simulated scenarios and with real data. Therefore, it could be a useful tool to determine genetically homogeneous groups, especially in those situations where the number of clusters is high, with complex population structure and where Hardy-Weinberg and/or linkage equilibrium are present.     

Effects of population structure on genetic association studies

Population-based case-control association is a promising approach for unravelling the genetic basis of complex diseases. One potential problem of this approach is the presence of population structure in the samples. Using the Collaborative Study on the Genetics of Alcoholism (COGA) single-nucleotide polymorphism (SNP) datasets, we addressed three questions: How can the degree of population structure be quantified, and how does the population structure affect association studies? How accurate and efficient is the genomic control method in correcting for population structure? The amount of population structure in the COGA SNP data was found to inflate the p-value in association tests. Genomic control was found to be effective only when the appropriate number of markers was used in the control group in order to correctly calibrate the test. The approach presented in this paper could be used to select the appropriate number of markers for use in the genomic control method of correcting population structure.     

Extensive population genetic structure in the giraffe

Background  

A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation.     

The genetic structure of fish: differences in the intraspecific distribution of biochemical genetic variation between marine, anadromous, and freshwater species

Biochemical genetic markers have been increasingly used for inferences on the population genetic structure of various fish, but little attention has been paid to relative differences in the distribution of variability within species in different groups of fish. Nested gene diversity analyses of multiple locus electrophoretic data from the literature for 19 species (6 marine species, 4 anadromous salmonids, and 9 freshwater species (5 salmonids)), mainly from Scandinavia and North America, show that (i) average heterozygosity is higher in marine species than in freshwater species, (ii) the average fraction of the total gene diversity allocated between localities increases in the order marine (1.6%), anadromous (3.7%), and freshwater species (29.4%), and (iii) the fraction of the total gene diversity associated with differences between geographic clusters of localities is generally smaller than that between localities within clusters. This finding is consistent with that the differentiation observed in most species is of postglacial origin, and that the timespan available since deglaciation has been too short to result in the accumulation of substantial differences between clusters.     

The genetic structure of the Lithuanian wolf population

Lithuanian wolves form part of the larger Baltic population, the distribution of which is continuous across the region. In this paper, we evaluate the genetic diversity of the Lithuanian wolf population using mitochondrial DNA analysis and 29 autosomal microsatellite loci. Analysis of the mtDNA control region (647 bp) revealed 5 haplotypes distributed among 29 individuals and high haplotype diversity (0.658). Two haplotypes were distributed across the country, whilst the others were restricted to eastern Lithuania. Analysis of microsatellites revealed high heterozygosity (H_E=0.709) and no evidence for a recent bottleneck. Using detection of first generation migrants, four individuals appeared to assign better with populations genetically differentiated from those resident in Lithuania. These immigrants were males carrying rare mitochondrial haplotypes and were encountered in the eastern part of the country, this indicates that Lithuania is subject to immigration from differentiated populations. Additionally, we did not detect any signs of recent hybridisation with dogs.     

Multilocus sequence typing reveals high genetic diversity and epidemic population structure for the fish pathogen Yersinia ruckeri

Yersinia ruckeri is the causative agent of enteric redmouth in fish and one of the major bacterial pathogens causing losses in salmonid aquaculture. Previously typing methods, including restriction enzyme analysis, pulsed-field gel electrophoresis and multilocus enzyme electrophoresis (MLEE) have indicated a clonal population structure. In this work, we describe a multilocus sequence typing (MLST) scheme for Y.ruckeri based on the internal fragment sequence of six housekeeping genes. This MLST scheme was applied to 103 Y.ruckeri strains from diverse geographic areas and hosts as well as environmental sources. Sequences obtained from this work were deposited and are available in a public database (http://publmst.org/yruckeri/). Thirty different sequence types (ST) were identified, 21 of which were represented by a single isolate, evidencing high genetic diversity. ST2 comprised more than one-third of the isolates and was most frequently observed among isolates from trout. Two major clonal complexes (CC) were identified by eBURST analysis showing a common evolutionary origin for 94 isolates forming 21 STs into CC1 and for 6 isolates of 6 STs in the CC2. It was also possible to associate some unique ST with isolates from recent outbreaks in vaccinated salmonid fish.     

Population genetic structure and effective population size of ayu (Plecoglossus altivelis), an amphidromous fish

The temporal and spatial population genetic structure of ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae), an amphidromous fish, was examined using analysis of variation at six microsatellite DNA loci. Intracohort genetic diversities, as measured by the number of alleles and heterozygosity, were similar among six cohorts (2001–2006) within a population (Nezugaseki River), with the mean number of alleles per cohort ranging from 11·0 to 12·5 and the expected heterozygosity ranging from 0·74 to 0·77. Intrapopulational genetic diversities were also similar across the three studied populations along the 50 km coast, with the mean number of alleles and the expected heterozygosity ranging from 11·33 to 11·67 and from 0·75 to 0·76, respectively. The authors observed only one significant difference in pair-wise population differentiation ( F _ST-value) between the cohorts within a population and among three populations. Estimates of the effective population size ( N _e) based on maximum-likelihood method yielded small values (ranging from 94·8 to 135·5), whereas census population size ranged from c. 4800 to 24 000. As a result, the ratio of annual effective population sizes to census population size ( N _e/ N ) ranged from 0·004 to 0·023. These estimates of N _e/ N agree more closely with estimates for marine fishes than that of the larger estimates for freshwater fishes. The present study suggests that ayu which is highly fecund and shows low survival during the early life stages is also characterized by having low value of N _e/ N , similar to marine species with a pelagic life cycle.     

Stochastic population dynamics and life-history variation in marine fish species

Abstract We examined whether differences in life-history characteristics can explain interspecific variation in stochastic population dynamics in nine marine fish species living in the Barents Sea system. After observation errors in population estimates were accounted for, temporal variability in natural mortality rate, annual recruitment, and population growth rate was negatively related to generation time. Mean natural mortality rate, annual recruitment, and population growth rate were lower in long-lived species than in short-lived species. Thus, important species-specific characteristics of the population dynamics were related to the species position along the slow-fast continuum of life-history variation. These relationships were further associated with interspecific differences in ecology: species at the fast end were mainly pelagic, with short generation times and high natural mortality, annual recruitment, and population growth rates, and also showed high temporal variability in those demographic traits. In contrast, species at the slow end were long-lived, deepwater species with low rates and reduced temporal variability in the same demographic traits. These interspecific relationships show that the life-history characteristics of a species can predict basic features of interspecific variation in population dynamical characteristics of marine fish, which should have implications for the choice of harvest strategy to facilitate sustainable yields.     

Isozymes,plant population genetic structure and genetic conservation

Summary The exploration, conservation and use of the genetic resources of plants is a contemporary issue which requires a multidisciplinary approach. Here the role of population genetic data, particularly those derived from electrophoretic analysis of protein variation, is reviewed. Measures of the geographic structure of genetic variation are used to check on sampling theory. Current estimates justify the contention that alleles which have a highly localised distribution, yet are in high frequency in some neighbourhoods, represent a substantial fraction of the variation. This class, which is the most important class in the framing of sampling strategies, accounts for about 20–30% of variants found in 12 plant species. The importance of documenting possible coadapted complexes and gene-environment relationships is discussed. Furthermore, the genetic structure of natural populations of crop relatives might suggest the best structure to use in the breeding of crops for reduced vulnerability to pest and disease attack, or for adaptation to inferior environments. The studies reported to date show that whilst monomorphic natural populations do occur, particularly in inbreeding colonisers, or at the extreme margins of the distribution, polymorphism seems to be the more common mode. It is stressed here that the genetic resources of the wild relatives of crop plants should be systematically evaluated. These sources will supplement, and might even rival, the primitive land races in their effectiveness in breeding programmes. We may look forward to a wider application of gel electrophoresis in the evaluation of plant genetic resources because this technique is currently the best available for detecting genetic differences close to the DNA level on samples of reasonable size.     

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。