Allelic and genotypic diversity in long-term asexual populations of the pea aphid, Acyrthosiphon pisum in comparison with sexual populations

Many aphid species exhibit geographical variation in the mode of reproduction that ranges from cyclical parthenogenesis with a sexual phase to obligate parthenogenesis (asexual reproduction). Theoretical studies predict that organisms reproducing asexually should maintain higher allelic diversity per locus but lower genotypic diversity than organisms reproducing sexually. To corroborate this hypothesis, we evaluated genotypic and allelic diversities in the sexual and asexual populations of the pea aphid, Acyrthosiphon pisum (Harris). Microsatellite analysis revealed that populations in central Japan are asexual, whereas populations in northern Japan are obligatorily sexual. No mixed populations were detected in our study sites. Phylogenetic analysis using microsatellite data and mitochondrial cytochrome oxidase subunit I (COI) gene sequences revealed a long history of asexuality in central Japan and negated the possibility of the recent origin of the asexual populations from the sexual populations. Asexual populations exhibited much lower genotypic diversity but higher allelic richness per locus than did sexual populations. Asexual populations consisted of a few predominant clones that were considerably differentiated from one another. Sexual populations on alfalfa, an exotic plant in Japan, were most closely related to asexual populations associated with Vicia sativa L. The alfalfa-associated sexual populations harboured one COI haplotype that was included in the haplotype clade of the asexual populations. Available evidence suggests that the sexuality of the alfalfa-associated populations has recently been restored through the northward migration and colonization of alfalfa by V. sativa- associated lineages. Therefore, our results support the theoretical predictions and provide a new perspective on the origin of sexual populations.     

Genetic differentiation and diversity of Acacia koa populations in the Hawaiian Islands

Acacia koa A. Gray (koa) is a leguminous tree endemic to the Hawaiian Islands and can be divided into morphologically distinguishable groups of A. koaia Hillebrand, A. koa and populations that are intermediate between these extremes. The objectives of this investigation were to distinguish among divergent groups of koa at molecular levels, and to determine genetic diversity within and among the groups. Phylogenetic analyses using the ITS/5.8S rDNA and trnK intron sequences did not separate the representative koa types into distinct clusters. An unweighted pair group method with arithmetic mean cluster analysis and principal coordinate analysis, based on allele profiles of 12 microsatellite loci for 215 individual koa samples, separated the population into three distinct clusters consistent with their morphology, A. koaia, A. koa and intermediate forms. There was an average of 8.8 alleles per polymorphic locus (AP) among all koa and koaia individuals. The intermediate populations had the highest genetic diversity (H′ = 1.599), AP (7.9) and total number of unique alleles (21), whereas A. koaia and A. koa showed similar levels of genetic diversity (H′ = 0.965 and 0.943, respectively). No correlation was observed between geographic distance and genetic distance as determined by a Mantel test (r = 0.027, P = 0.91). The data presented here support previous recommendations that morphological variation within koa should be recognized at the subspecific level rather than as distinct species.     

Effects of insularity on genetic diversity within and among natural populations

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.     

Detection and analysis of genetic variation in Hordeum spontaneum populations from Israel using RAPD markers

Randomly amplified polymorphic DNA (RAPD) markers were used to analyse genetic diversity within and between Hordeum spontaneum populations sampled from Israel. Nei's index of genetic differentiation was used to partition diversity into within and between population components. Fifty-seven per cent of the variation detected was partitioned within 10 H. spontaneum populations. Using principal component and multiple regression analysis, part of the variation detected between populations was seen to be associated with certain ecogeographical factors. Fifty-eight per cent of the distribution of the phenotypic frequencies of three RAPD phenotypes detected using a single primer in 20 H. spontaneum populations could be accounted for by four ecogeographical variables, suggesting adaptive variation at certain RAPD loci.     

Genetic diversity and population structure of invasive and native populations of Erigeron canadensis L.

小蓬草入侵地和原产地种群的遗传多样性和种群结构 外来入侵植物对全球生物多样性造成了危害。小蓬草(Erigeron canadensis L.)是危害最为严重的外来农业杂草之一,代表了洲际入侵的典型例子。本研究利用10个多态性SSR位点,分别对采自中国江苏和浙江省的入侵地和采自美国阿拉巴马州的原产地各5个种群、共计312个植株的基因型进行了遗传多样性和遗传结构分析。结果表明,江苏省和浙江省的入侵种群显示出与阿拉巴马州原产地种群相似的遗传多样性,表明入侵期间没有严重的遗传瓶颈。利用STRUCTURE对种群结构的分析结果显示,种群之间分化较低,在原产地和入侵范围内均只仅检测到两个基因群。在入侵种群中观察到的遗传多样性较高,表明在入侵初期可能存在多次引入或引入了遗传背景不同的繁殖体。上述研究为阐明小蓬草这一全球有害杂草在中国东部的入侵动态提供了新的证据。在防除实践中,应注意防范小蓬草入侵种群和本地种群之间的种子基因流传播,阻止除草剂抗性植株的引入和扩散。     

Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species

Determining true genetic dissimilarity between individuals is an important and decisive point for clustering and analysing diversity within and among populations, because different dissimilarity indices may yield conflicting outcomes. We show that there are no acceptable universal approaches to assessing the dissimilarity between individuals with molecular markers. Different measures are relevant to dominant and codominant DNA markers depending on the ploidy of organisms. The Dice coefficient is the suitable measure for haploids with codominant markers and it can be applied directly to (0,1)-vectors representing banding profiles of individuals. None of the common measures, Dice, Jaccard, simple mismatch coefficient (or the squared Euclidean distance), is appropriate for diploids with codominant markers. By transforming multiallelic banding patterns at each locus into the corresponding homozygous or heterozygous states, a new measure of dissimilarity within locus was developed and expanded to assess dissimilarity between multilocus states of two individuals by averaging across all codominant loci tested. There is no rigorous well-founded solution in the case of dominant markers. The simple mismatch coefficient is the most suitable measure of dissimilarity between banding patterns of closely related haploid forms. For distantly related haploid individuals, the Jaccard dissimilarity is recommended. In general, no suitable method for measuring genetic dissimilarity between diploids with dominant markers can be proposed. Banding patterns of diploids with dominant markers and polyploids with codominant markers represent individuals' phenotypes rather than genotypes. All dissimilarity measures proposed and developed herein are metrics.     

Plant species diversity and composition of experimental grasslands affect genetic differentiation of Lolium perenne populations

Contrasting hypotheses exist about the relationship between plant species diversity and genetic diversity. However, experimental data of species diversity effects on genetic differentiation among populations are lacking. To address this, Lolium perenne was sown with an equal number of seeds in 78 experimental grasslands (Jena Experiment) varying in species richness (1, 2, 4, 8 to 16) and functional group richness and composition (1-4; grasses, legumes, small herbs, tall herbs). Population sizes were determined 4years after sowing, and single-nucleotide polymorphism (SNP) DNA markers based on bulk samples of up to 100 individuals per population were applied. Genetic distances between the field populations and the initially sown seed population increased with sown species richness. The degree of genetic differentiation from the original seed population was largely explained by actual population sizes, which suggests that genetic drift was the main driver of differentiation. Weak relationships among relative allele frequencies and species diversity or actual population sizes, and a positive correlation between actual population sizes and expected heterozygosity also supported the role of genetic drift. Functional composition had additional effects on genetic differentiation of L. perenne populations, indicating a selection because of genotype-specific interactions with other species. Our study supports that genetic diversity is likely to be lower in plant communities with a higher number of interspecific competitors. Negative effects of species richness on population sizes may increase the probability of genetic drift, and selection because of genotype-specific interactions depending on species and genotypic community composition may modulate this relationship.     

Genetic diversity of north Okhotsk Sea chum salmon populations with natural and artificial reproduction

The variability of 32 enzyme loci was studied in chum salmon populations with different types of reproduction—natural, mixed, and artificial—in some Magadan Region rivers. Among the populations studied, the values of mean heterozygosity and allele number per locus did not differ significantly. We found evidence of definite temporal stability of the populations, and also found that their genetic variability was expressed only slightly but still remained in spite of periodic egg transplantations between rivers. Statistically significant spatial genetic differentiation of the populations accounted for 0.55 to 0.76% of the total variation and the mean inter-year differentiation accounted for 0.30% of the total. Significant temporal (seasonal) genetic subdivision was revealed in chum salmon of the Tauy River. The populations of the Okhotsk Sea coast are very similar genetically to the east Sakhalin populations. The industrial chum salmon population founded and reproduced artificially in the Kulkuty River preserves the genetic similarity of the donor Yama River chum salmon. In the industrial population, we observed a tendency toward reduction of genetic variation over time. The contribution of the Yama population to the gene pool of the Ola chum salmon, (both by natural reproduction and by farming) is small in spite of many large-scale transplantations. However, the consequences of those transplantations are revealed by means of linkage disequilibrium analysis.     

Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neighboring joining tree distinguished the modern from the original populations. The F_ST‐outlier identified several genes putatively involved in the genetic differentiation between the two groups, such as stature and growth, behavior, and adaptability to local environments. The ROH islands within both the original and the modern populations overlapped with QTL associated with relevant traits. In modern Brown (Brown Swiss and Italian Brown), ROH islands harbored candidate genes associated with milk production traits, in evident agreement with the artificial selection conducted to improve this trait in these populations. In original Brown (Original Braunvieh and Braunvieh), we identified candidate genes related with fat deposition, confirming that breeding strategies for the original Brown populations aimed to produce dual‐purpose animals. Our study highlighted the presence of several genomic regions that vary between Brown populations, in line with their different breeding histories.     

Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: implications for their classification

The genetic diversity and relationships amongst the dromedary (Camelus dromedarius) populations are poorly documented. Four recognized Kenyan dromedary breeds (Somali, Turkana, Rendille, Gabbra) and dromedary from Pakistan and the Arabian Peninsula (Saudi Arabia, United Arab Emirates) were studied using 14 microsatellite loci. Phylogenetic analysis showed that Kenyan dromedaries are distinct from Arabian and Pakistani populations. Expected heterozygosity and allelic diversity values indicate that Kenyan dromedaries are less diverse than non-Kenyan populations. With the exception of the Somali population, the Kenyan dromedaries are poorly differentiated (average FST=0.009), with only one to two loci separating the Gabbra, Rendille and Turkana populations studied (P < 0.05). Individual assignments were performed using the maximum likelihood method. A correct breed assignment of only 39-48% was observed for the Kenyan dromedaries, using an allocation stringency of a log of the odds ratio >2. Our results do not support the present classification of the indigenous Kenyan dromedary into four distinct breeds based on socio-geographical criteria. Instead, our results point to just two separate genetic entities, the Somali and a group including the Gabbra, Rendille and Turkana populations.     

Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) with isozymes and RAPD markers

The knowledge of population structure and genetic diversity of wild relatives of rice is needed to investigate their evolutionary history and potential use in breeding programs. Very little is known about the wild rice species ( Oryza spp.), particularly those that are native to South America. A study using isozyme and RAPD markers was conducted to estimate the level of genetic diversity of four South American wild rice populations ( Oryza glumaepatula ) recently collected in the Amazon forest and western Brazil rivers. F -statistics and genetic diversity parameters calculated from isozyme and RAPD markers indicated high values for inbreeding coefficients and differentiation among the four populations. In agreement with this, a pattern of greater variation between than within populations was observed with both types of markers. These findings were corroborated by an AMOVA analysis, which indicated that a large portion of the total genetic variation was attributed to regional divergence. The partition of the AMOVA analysis among populations showed that most of the genetic diversity was due to differences among populations. This distribution pattern of genetic variation of O. glumaepatula populations is in agreement with the expectation for an autogamous species and provides important baseline data for conservation and collection strategies for this species.     

中国与欧洲高卢蜜环菌的遗传多样性

高卢蜜环菌(Armillaria gallica)为北半球广布种,不同大陆间的菌株遗传相似性和多样性水平能反映出该种在洲际大陆尺度上的地理遗传变异关系。作者用ISSR(inter-simple sequence repeat)分子标记技术,对从中国和欧洲收集到的高卢蜜环菌79个菌株进行了遗传多样性分析。用6个ISSR引物扩增得到210个位点,其中多态性位点(频率<0.95)为202个,占96.2%,平均每个引物多态位点多达33.6个,表明ISSR标记在蜜环菌中存在较高的多态性。根据非加权类平均法(UPGMA)聚类分析,中国53个菌株中的49个在0.773的相似性水平上聚成了中国类群(China group);而欧洲26个菌株遗传分化较大,分别在0.775和0.763的相似性水平上聚成了欧洲类群A(Europe group A)和B(Europe group B);2个欧洲类群间的相似性水平仅为0.738,而欧洲类群A与中国类群间的相似性却达到了0.770;两个大陆均有少数菌株表现出较为明显的遗传分化,个别菌株的种内遗传相似性甚至低于蜜环菌种间的遗传相似性。结果表明,中欧两个大陆间的A.gallica菌株因地理隔离已经表现出明显的遗传分化,处于异域物种形成过程中;欧洲大陆的菌株遗传分化更为明显,可能是两个大陆A.gallica菌株的起源地。     

Genetic diversity and gene flow within and between two different habitats of Primula merrilliana (Primulaceae), an endangered distylous forest herb in eastern China

Understanding whether and how different habitats shape population genetics is a fundamental question and a specific goal for evolutionary and conservation biology research. This study examined genetic diversity and gene flow within and between mountain and foothill habitats of Primula merrilliana, an endangered distylous forest herb in eastern China. Eleven population characteristics, including area, size and density variation, from the two habitats were also investigated. Mountain populations had significantly higher mean genetic diversity than foothill populations, which may be explained by stronger self‐incompatibility breeding system, more opportunity to use elevational shifts to track suitable sites under conditions of climate change and more heterogeneous environments in the former habitat, rather than by the differences of population size, gene flow and genetic drift intensity between them. Genetic analysis revealed that two distinct lineages, corresponding to the two habitats, diverged at China's ‘Last Glaciation’ (11 700–67 500 yr BP), suggesting this divergence was probably triggered by warmer climates during inter‐ (or post‐) glacial periods. Low unidirectional gene flow from mountain to foothill habitats, chiefly by seed dispersal, played a more important role in overall gene flow between habitats than within‐habitat gene flow. Within habitats, pollen contributes more substantially to gene flow than seed dispersal, especially in foothill habitats, possibly due to higher individual density and larger population sizes. These results have implications for the conservation in this and similar landscape areas and indicate the need to protect suitable habitats with wide elevational spans and sufficient size to permit ecological and elevational shifts in response to climatic changes. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 172–189.     

Genetic analysis of fish genomes and populations: allozyme variation within and among Atlantic salmon from Downeast rivers of Maine

Analysis of genetic variation within and among samples of naturally produced Atlantic salmon ( n  = 372) from 7 Maine (U.S.A.) and one Canadian river were conducted based on 54 allozyme loci. Eight of the 54 loci proved polymorphic, and estimated heterozygosities ( H _S) based on all loci ranged from 0·012 to 0·026 (mean = 0·021, s . e . = 0·002). Only one of 56 tests revealed genotypic proportions that deviated significantly from Hardy–Weinberg expectations. Genetic distances ( D ) between samples ranged from 0·002 to 0·022. No obvious association existed between genetic and geographic distances. Cluster analysis of genetic distances revealed the Dennys River sample as the most differentiated when all samples were included in the analysis, though bootstrap support of the cluster analysis was generally weak. G ‐tests revealed significant differences in allele frequencies among samples at five of the polymorphic loci, and the G ‐value summed over all loci also indicated significant differences among samples. F _ST values indicated that 3·4% of the total genetic diversity was due to variability among samples, while 96·6% was due to variability within samples. These results indicate that the Atlantic salmon analyzed in this study had levels of genetic variability and differentiation among samples comparable to native populations from other areas collected across a similar geographic range.     

A puzzle with many pieces: the genetic structure and diversity of Phaeocystis antarctica Karsten (Prymnesiophyta)

Strong ocean current systems characterize the Southern Ocean. The genetic structure of marine phytoplankton species is believed to depend mainly on currents. Genetic estimates of the relatedness of populations of phytoplankton species therefore should provide a proxy showing to what extent different geographic regions are interconnected by the ocean current systems. In this study, spatial and temporal patterns of genetic diversity were studied in the circumpolar prymnesiophyte Phaeocystis antarctica Karsten using seven nuclear microsatellite loci. Analyses were conducted for 86 P. antarctica isolates sampled around the Antarctic continent between 1982 and 2007. The results revealed high genetic diversity without single genotypes recurring even among isolates within a bloom or originating from the same bucket of water. Populations of P. antarctica were significantly differentiated among the oceanic regions. However, some geographically distant populations were more closely related to each other than they were to other geographically close populations. Temporal haplotype turnover within regions was also suggested by the multilocus fingerprints. Our data suggest that even within blooms of P. antarctica genetic diversity and population sizes are large but exchange between different regions can be limited. Positive and significant inbreeding coefficients hint at further regional substructure of populations, suggesting that patches, once isolated from one another, may not reconnect. These data emphasize that even for planktonic species in a marine ecosystem that is influenced by strong currents, significant breaks in gene flow may occur.     

Microsatellite analysis of population structure and genetic differentiation within and between populations of the root vole, Microtus oeconomus in the Netherlands

Eight microsatellite markers for the root vole (Microtus oeconomus) were developed to assess the amount of genetic variation for nine Dutch root vole populations from four different regions, and to evaluate the degree of differentiation and isolation. All eight microsatellite loci were found to be highly variable with observed heterozygosity values ranging from 0.61 to 0.82. These values are similar to those observed for more distant populations from Norway, Finland and Germany. Therefore, the populations seem not particularly depauperate of genetic variation at the microsatellite level. Genetically, the Dutch populations were found to have diverged considerably. Pairwise comparisons of all populations studied revealed FST values significantly greater than zero for most comparisons. However, the magnitude of these values considerably depends on the compared population pair. The level of differentiation between local populations within Dutch regions is generally significantly lower than the differentiation between Dutch regions. The level of differentiation between Dutch regions, however, is not significantly different from that between populations of larger geographical distance. This implies that the regional Dutch populations are both isolated from each other and from other European populations. The observation that even local populations show low but significant genetic differentiation may be indicative for progressive isolation of these populations.     

Genetic diversity among populations and size classes of buckeyes (Aesculus: Hippocastanaceae) examined with multilocus VNTR probes

 Little is known about genetic variation in members of the genus Aesculus (Hippocastanaceae), in particular A. flava (yellow buckeye) and A. glabra (Ohio buckeye). Here, three synthetic DNA probes (composed of tandemly repeated, core sequences) that reveal alleles at multiple variable-number tandem-repeat (VNTR) loci in these two species were used to investigate: 1) levels of genetic variation in one stand of A. flava and three isolated stands of A. glabra; 2) whether the stands of A. glabra are genetically differentiated from one another; 3) whether there has been selection for more heterozygous individuals through time in one stand each of A. flava and A. glabra; and 4) whether a possible genetic bottleneck had occurred during the formation of either species of Aesculus. First, variation of VNTR genetic markers within and among three populations of A. glabra separated by 60–180 km was examined. In each one hectare (ha) population, 22 individuals were randomly sampled. Among the three populations, the mean number of bands scored per individual was 80.35 and the average number of estimated loci surveyed was 54.17. Mean similarity and estimated heterozygosity within populations ranged from 0.634 to 0.743 and from 0.342 to 0.486, respectively. The mean similarity across populations was 0.657, while the mean estimated heterozygosity across populations was 0.484 for A. glabra. The most isolated site was the most genetically differentiated as indicated by differences in levels of similarity, heterozygosity, and Fst value comparisons. In a separate experiment, genetic variation in 22 large (reproductively mature; dbh > 8 cm) individuals was compared with that in 22 small (not yet reproductive; dbh < 1 cm) individuals collected within one ha stands for both A. flava and A. glabra. Mean similarity values among large versus small individuals of A. flava were 0.665 versus 0.662, while for A. glabra the corresponding values were 0.686 versus 0.691, respectively. Permutation tests of these similarity data detected no evidence for size class genetic differentiation in either species (both p-values > 0.050). Further, permutation tests for the number of bands per individual (average band number should be higher in more heterozygous individuals) detected no significant differences between size classes for either species. Thus, evidence of pronounced inbreeding and/or selection altering population genetics within small relative to large individuals was not detected. In addition, comparable similarity and heterozygosity values between these two closely related species (which still maintain an active zone of hybridization) suggests that either: 1) no extreme genetic bottleneck has accompanied the formation of these species from a common ancestor; or 2) signs of such a bottleneck have largely been eliminated. These studies demonstrate the utility of multilocus VNTR DNA probes for investigating genetic variation within and among plant populations, between size classes within a population, and between closely related species. Received May 15, 1998 Accepted September 11, 2001     

Genetic diversity, population structure, and conservation of Sophora moorcroftiana (Fabaceae), a shrub endemic to the Tibetan Plateau

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the middle reaches of Yarlung Zangbo River in Tibet. It is an important species to fix sand dunes and to avoid the formation of shifting sands; therefore, its progressive over-exploitation may enhance land desertification. The levels and distribution of genetic variability of this species were evaluated from 10 natural populations at 24 loci encoding 13 enzymes, using allozyme analysis by starch gel electrophoresis. Data obtained revealed moderate levels of genetic variation within populations (Pp=27.5%, Ap=1.5, Hep=0.122) and a considerable divergence among populations (FST=0.199). Significant positive correlations (r2=0.49, p<0.05; r2=0.46, p<0.05) were found between elevation and both mean number of alleles per locus (A) and gene diversity (He) in the studied populations of S. moorcroftiana. Lower genetic diversity in lower elevation populations might be due to the negative effects of human pressures and habitat fragmentation, to adaptation to high altitudes as a consequence of a peripatric speciation process, or to directional gene flow along the river basin from the source populations located in the west at higher altitudes. The evaluation of the degree of threat has led to the inclusion of this species in the category of EN ("endangered"), and conservation strategies for this endemic species are discussed on the basis of these findings.