Molecular genetic variation and population structure in morphologically differentiated cave and surface populations of the freshwater amphipod Gammarus minus

Gammarus minus is an important component of surface spring and cave ecosystems throughout Appalachia, and is a useful indicator of the hydrology and gene flow in freshwater communities. Gammarus minus populations occupying large cave passages (> 2 km) are usually troglomorphic, having reduced eyes, fewer ommatidia, larger body size, longer antennae, and reduced pigmentation relative to surface populations. We surveyed five cave stream and 10 surface spring populations for DNA sequence variation in the cytochrome c oxidase I (COI) and internal transcribed spacer 1 (ITS-1) genes with an aim towards characterizing phylogeographical structure and comparing the nature of genetic variation in cave vs. surface populations. Although standing variation at both loci was rather low within populations, a significant degree of divergence and spatial structuring of populations was observed. Levels of genetic variation within cave and spring populations differed substantially, with caves harbouring significantly less variation at the COI locus than surface springs. Codon usage bias was significantly lower in caves, indicating that cave streams harbour smaller and/or more recently colonized populations. Overall these data indicate limited gene flow among populations and suggest that the cave populations sampled in this study are prone to bottlenecks, possibly due to larger temperature fluctuations and more frequent incidence of drought conditions associated with these particular cave habitats.     

孑遗植物桫椤种群遗传变异的RAPD分析

应用 RAPD标记分析了桫椤分布在海南尖峰岭及霸王岭 ,广东塘朗山、黑石顶及大西山孑遗种群的遗传变异。 2 8个引物共检测到 1 1 8个位点 ,其中多态位点 33个 ,多态位点比率 2 7.97%。Shannon多样性、Nei遗传分化和分子方差分析 ( AMOVA)结果一致显示尖峰岭种群遗传多样性最大 ,霸王岭种群次之、塘郎山种群第三 ,黑石顶种群第四 ,而大西山种群最小。种群的遗传变异主要发生在种群间 ;Shannon指数测出的种群间遗传多样性所占比率为 79.1 0 % (基于表型频率 )和 77.85 % (基于基因频率 ) ,Nei基因分化系数 ( Gst)达 80 .69% ,分子方差分析也表明种群分化极为显著 ( Φst=0 .82 86,P<0 .0 0 1 )。桫椤的种内遗传多样性水平很低 ,种内 Shannon多样性仅为 0 .0 641 (基于表型频率 )和 0 .1 1 2 4 (基于基因频率 ) ,总基因多样性只有 0 .0 770。另外 ,Jaccard相似性系数的 UPGMA分析结果显示 5个种群分为两个分支 :尖峰岭种群和霸王岭种群组成一分支 ;黑石顶、塘郎山和大西山种群组成另一分支 ,并且三者中前两者的遗传关系更为密切。聚类分析结果还得到主成分分析的支持。根据桫椤种群的遗传变异特点 ,初步探讨了保护策略。     

Mechanisms of population differentiation in seabirds

Despite recent advances in population genetic theory and empirical research, the extent of genetic differentiation among natural populations of animals remains difficult to predict. We reviewed studies of geographic variation in mitochondrial DNA in seabirds to test the importance of various factors in generating population genetic and phylogeographic structure. The extent of population genetic and phylogeographic structure varies extensively among species. Species fragmented by land or ice invariably exhibit population genetic structure and most also have phylogeographic structure. However, many populations (26 of 37) display genetic structure in the absence of land, suggesting that other barriers to gene flow exist. In these populations, the extent of genetic structure is best explained by nonbreeding distribution: almost all species with two or more population-specific nonbreeding areas (or seasons) have phylogeographic structure, and all species that are resident at or near breeding colonies year-round have population genetic structure. Geographic distance between colonies and foraging range appeared to have a weak influence on the extent of population genetic structure, but little evidence was found for an effect of colony dispersion or population bottlenecks. In two species (Galapagos petrel, Pterodroma phaeopygia, and Xantus's murrelet, Synthliboramphus hypoleucus), population genetic structure, and even phylogeographic structure, exist in the absence of any recognizable physical or nonphysical barrier, suggesting that other selective or behavioural processes such as philopatry may limit gene flow. Retained ancestral variation may be masking barriers to dispersal in some species, especially at high latitudes. Allopatric speciation undoubtedly occurs in this group, but reproductive isolation also appears to have evolved through founder-induced speciation, and there is strong evidence that parapatric and sympatric speciation occur. While many questions remain unanswered, results of the present review should aid conservation efforts by enabling managers to predict the extent of population differentiation in species that have not yet been studied using molecular markers, and, thus, enable the identification of management units and evolutionary significant units for conservation.     

药食同源植物薤白的谱系地理学研究

对我国14个地区的药食同源植物薤白（Allium macrostemon）的叶绿体基因片段（psbA-trnH、rps16和trnL-F）与核基因片段（ITS）进行测序分析,揭示薤白的遗传变异分布式样、单倍型地理分布格局,并推断其在第四纪冰期的避难所。结果表明：薤白叶绿体基因（cpDNA）遗传多样性低于核基因（nrDNA）遗传多样性（cpDNA：H_T=0.868;nrDNA：H_T=0.890）。cpDNA和nrDNA的分子变异分析（AMOVA）结果显示：薤白遗传变异主要发生在居群间（cpDNA：92.84%;nrDNA：98.40%）,存在遗传分化（cpDNA：N_st=0.918,G_st=0.866,F_st=0.928;nrDNA：N_st=0.984,G_st=0.855,F_st=0.984）,且N_st均大于G_st,表明该物种具有明显的谱系地理结构。在薤白居群中,共检测到11个叶绿体单倍型和14个nrDNA基因型;单倍型网络图及地理分布图表明,叶绿体单倍型H3、核DNA基因型H1频率最高,位于网络结构图的中心位置,可能为古老单倍型。此外,冰期避难所假说认为遗传多样性高、拥有古老单倍型和较多特有单倍型的区域可能是该物种的冰期避难所,因此推测薤白在第四纪冰期时可能在大盘山、天水和通化地区存在多个冰期避难所。这些分析可为类似草本植物的进化提供参考,丰富对东亚草本植物分子系统与生物地理学的认识。     

In defence of model‐based inference in phylogeography

Recent papers have promoted the view that model‐based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model‐based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model‐based inference in population genetics.     

SMALL POPULATION GENETIC VARIABILITY AT LOCI UNDER STABILIZING SELECTION

Genetic variability at a locus under stabilizing selection in a finite population is investigated using analytic methods and computer simulations. Three measures are examined: the number of alleles k, heterozygosity H, and additive genetic variance Vg. A nearly-neutral theory results. The composite parameter S = NV_M/V_s (where N is the population size, V_M the variance of new mutant allelic effects and V_s the weakness of stabilizing selection) figures prominently in the results. The equilibrium heterozygosity is similar to that of strictly neutral theory, H = 4N_μc/ (1 + 4N_μc), except that μ_c = where c is about 0.5. Simulations corroborate except for very low N. Genetic variability attains similar equilibrium values at both a “lone” locus and at an “embedded” locus. This agrees with my earlier work concerning molecular clock rates. These results modify the neutralist interpretation of data concerning genetic variability and genetic distances between populations. Low H values are proportional not to N but to . This may explain the narrow observed range of H among species. Heterozygosities need not be highly correlated to genetic variances. Genetic variances are not highly dependent on population size except in very small populations which are difficult to sample without bias because the smallest populations go extinct the fastest. Nearly neutral evolution will not be easily distinguished from strictly neutral theory under the Hudson-Kreitman-Aguade inter-/intraspecific variation ratio test, since a similar effective mutation rate holds for genetic distances and D = 2μ_ct, where . As with strictly neutral theory, comparisons across loci should show D and H to be positively correlated because of the shared μ_c. But unlike neutral theory, for a given locus, comparisons across species should show D and H to be negatively correlated. There is no obvious threshold of population size below which genetic variability inevitably declines. Extinction depends on both genetic variation and natural selection. Neither theory nor observation presently indicates the measure of genetic variability (k, H, V_G or other) that best indicates vulnerability of a small population to extinction.     

Random genetic drift during cyclical ameiotic parthenogenesis

The classical models of population genetics assume sexual reproduction and do not apply to organisms in which parthenogenetic reproduction is alternated with sexual recombination. Under cyclic parthenogenesis, variation in rates or frequencies of parthenogenetic reproduction among clones produces selection that is independent of processes occurring in the sexual phases.In this paper I examine how selection during cyclic parthenogenesis influences random genetic drift and leads to a loss of variance among clones. To illustrate these effects, computer simulations are presented demonstrating the response of effective clone number and equilibrium clone diversity to selection and mutation.     

New chloroplast primers for intraspecific variation in Dicranum scoparium Hedw. (Dicranaceae) and amplification success in other bryophyte species

Primers for four loci that amplify cpDNA regions have been designed for population genetic analyses in Dicranum scoparium Hedw. and compared with trnL(UAA)5'exon-trnF. All loci showed intraspecific variation with a number of haplotypes ranging between two and six. trnH-psbA(Dic) showed an intercontinental disjunction, but no variability within the four Swiss populations surveyed, whereas the three remaining loci displayed intrapopulation variability in at least one population (rps19-rpl2, rpoB, trnT-rps4). These primers were additionally tested on 22 bryophytes and three fern species. The primers amplified mostly in mosses and liverworts, but less well in ferns, pointing to their evolutionary distance from the bryophytes.