GENETIC VARIATION IN BROMUS TECTORUM (POACEAE): POPULATION DIFFERENTIATION IN ITS NORTH AMERICAN RANGE

Allelic variation in seedlings from 60 North American populations of the alien annual grass Bromus tectorum was determined at 25 loci using starch gel electrophoresis. Populations were collected from four regions; east of the Rocky Mountains, Nevada and California, the Intermountain West, and British Columbia. Compared to other diploid seed plants, genetic variation within these populations of B. tectorum is low: 4.60% of loci are polymorphic per population, with an average of 1.05 alleles per locus and a mean expected heterozygosity of 0.012. Although 2,141 individuals were analyzed, no heterozygous individuals were detected, and consequently, mean observed heterozygosity is 0.000. Extensive deviations from Hardy-Weinberg expectations were observed at every polymorphic locus due to heterozygote deficiencies. The mean genetic identity (Nei's I) between population pairs was 0.980 and indicates a high level of overall genetic similarity among populations. The among-population component of the total gene diversity is high (G_ST ⁼ 0.478), indicating substantial genetic differentiation among populations. These results are consistent with previous reports for highly self-pollinating plants of low genetic variation and substantial genetic differentiation among populations. Despite the lack of genetic variation as measured by enzyme electrophoresis, this weedy grass has become exceedingly abundant in a diverse array of arid environments throughout much of western North America, perhaps due to phenotypic plasticity.     

Major Histocompatibility Complex (MHC) class II sequence polymorphism in long-finned pilot whale (Globicephala melas) from the North Atlantic

Determining how intra-specific genetic diversity is apportioned among natural populations is essential for detecting local adaptation and identifying populations with inherently low levels of extant diversity which may become a conservation concern. Sequence polymorphism at two adaptive loci (MHC DRA and DQB) was investigated in long-finned pilot whales (Globicephala melas) from four regions in the North Atlantic and compared with previous data from New Zealand (South Pacific). Three alleles were resolved at each locus, with trans-species allele sharing and higher levels of non-synonymous to synonymous substitution, especially in the DQB locus. Overall nucleotide diversities of 0.49?±?0.38% and 4.60?±?2.39% were identified for the DRA and DQB loci, respectively, which are relatively low for MHC loci in the North Atlantic, but comparable to levels previously described in New Zealand (South Pacific). There were significant differences in allele frequencies within the North Atlantic and between the North Atlantic and New Zealand. Patterns of diversity and divergence are consistent with the long-term effects of balancing selection operating on the MHC loci, potentially mediated through the effects of host-parasite coevolution. Differences in allele frequency may reflect variation in pathogen communities, coupled with the effects of differential drift and gene flow.     

Population genetics of bisexual and unisexual populations of the scaly-winged bark louse Echmepteryx hageni (Insecta: Psocoptera)

The scaly-winged bark louse, Echmepteryx hageni, exhibits a unique pattern of co-existence of apparently differnt reproductive modes. Unisexuality is widespread in eastern North America, while sexual populations are restricted to isolated rock out-croppings in southern Illinois and eastern Kentucky. Three of the four nuclear loci examined show greater genetic diversity in the unisexual form compared to the sexual form of E. hageni, in accordance with the pattern previously shown in mitochondrial genetic data. Neutrality tests of the nuclear loci indicate a consistent signal of demographic expansion in asexual populations, but not in sexual populations. There was evidence of inbreeding in the isolated sexual populations at three of the nuclear loci, and one locus had signs of gene specific balancing selection. However, there is no significant genetic differentiation between bisexual and unisexual populations, possibly due to the greater effective population size of nuclear loci relative to mitochondrial loci. The mitochondrial differentiation of E. hageni populations in the northwestern part of their range (Minnesota and Wisconsin) was also not reflected in the nuclear data. We present three hypotheses that may explain the disparity in observed nuclear and mitochondrial genetic diversity between the reproductive forms of E. hageni.     

中国桔小实蝇种群的微卫星多态性分析

为了研究桔小实蝇种群的遗传结构,本文采用微卫星分子标记技术,对中国南方9省区、越南和泰国的11个桔小实蝇地理种群共224个个体的遗传多样性水平及种群遗传结构进行了研究。用9对微卫星引物共检测到48个等位基因, 平均每个微卫星位点的等位基因数为5.33个。GENEPOP分析结果表明：11个桔小实蝇种群在9个微卫星位点上的多态位点百分率平均为94.45%。种群的Nei's基因多样性指数平均为0.4371,Shannon信息指数平均为0.7870,表明桔小实蝇种群具有非常丰富的遗传多样性。Nei's遗传多样性分析发现,各地理种群间产生了一定程度的遗传分化,种群间平均遗传分化系数F_st=0.2370。种群间一定程度的遗传分化可能是由地理隔离和基因流障碍（N_em = 0.8049）所引起。UPGMA聚类分析可知, 中国的桔小实蝇地理种群可分为华南支和西南支两大分支,华南分支包括福建、台湾、广东和海南4个种群,西南分支包括四川、云南、广西、贵州和湖南5个种群。由此推测, 中国桔小实蝇种群结构的形成与演变是在地理演化与经贸交流加强这两种因素的影响下不断进行的动态过程。     

栲树天然群体遗传结构的RAPD分析

利用RAPD分子标记对 5个栲树 (CastanopsisfargesiiFranch .)天然群体共计 188个个体的遗传多样性和群体遗传结构进行了分析。 4 1个随机寡核苷酸引物共检测到 385个位点 ,其中多态位点 15 7个 ,占 4 0 .78%。物种水平的Shannon多样性指数I=0 .4 5 97,Nei基因多样度h =0 .2 96。遗传变异分析表明 ,栲树群体的遗传变异主要存在于群体内 ,利用Shannon多样性指数估算的分化 (Hsp_Hpop) /Hsp=0 .0 4 76 ,遗传分化系数Gst =0 .0 4 2 9,分子方差分析 (AMOVA)也证实了这一结论 ,群体内的变异组分占了 94 .97% ,群体间变异只占 5 .0 3%。AMOVA分析结果的显著性检验也表明 ,群体间及群体内个体间均呈现出显著分化 (P <0 .0 0 1)。     

A program to compare genetic differentiation statistics across loci using resampling of individuals and loci

Comparisons of genetic differentiation across populations based on different loci can provide insight into the evolutionary patterns acting on various regions of genomes. Here, we develop a program to statistically compare population genetic differentiation statistics (F(ST) or G'(ST) ) calculated from different loci. The program employs a routine that resamples either or both of individuals and loci and calculates a bootstrap confidence interval in the statistics. Resampling individuals is important when fewer than 25 individuals are sampled per population and when confidence intervals are required for individual loci. Resampling loci provides confidence intervals for sets of loci, such as a set presumed to be neutral, but can be anticonservative if fewer than 20 loci are analysed. We demonstrate the program using previously published data on the genetic differentiation at a major histocompatibility complex locus and at microsatellite loci across 10 populations of the guppy (Poecilia reticulata).     

Selection of high heterozygosity popcorn varieties in Brazil based on SSR markers

We analyzed genetic structure and diversity among eight populations of popcorn, using SSR loci as genetic markers. Our objectives were to select SSR loci that could be used to estimate genetic diversity within popcorn populations, and to analyze the genetic structure of promising populations with high levels of heterozygosity that could be used in breeding programs. Fifty-seven alleles (3.7 alleles per locus) were detected; the highest effective number of alleles (4.21) and the highest gene diversity (0.763) were found for the Umc2226 locus. A very high level of population differentiation was found (F(ST) = 0.3664), with F(ST) for each locus ranging from 0.1029 (Umc1664) to 0.6010 (Umc2350). This analysis allowed us to identify SSR loci with high levels of heterozygosity and heterozygous varieties, which could be selected for production of inbred lines and for developing new cultivars.     

Population genetic structure of mahogany (Swietenia macrophylla King, Meliaceae) across the Brazilian Amazon, based on variation at microsatellite loci: implications for conservation

Mahogany (Swietenia macrophylla, Meliaceae) is the most valuable and intensively exploited Neotropical tree. No information is available regarding the genetic structure of mahogany in South America, yet the region harbours most of the unlogged populations of this prized hardwood. Here we report on the genetic diversity within and the differentiation among seven natural populations separated by up to 2100 km along the southern arc of the Brazilian Amazon basin. We analysed the variation at eight microsatellite loci for 194 adult individuals. All loci were highly variable, with the number of alleles per locus ranging from 13 to 27 (mean = 18.4). High levels of genetic diversity were found for all populations at the eight loci (mean HE = 0.781, range 0.754-0.812). We found moderate but statistically significant genetic differentiation among populations considering both estimators of FST and RST, theta = 0.097 and rho = 0.147, respectively. Estimates of theta and rho were significantly greater than zero for all pairwise population comparisons. Pairwise rho-values were positively and significantly correlated with geographical distance under the isolation-by-distance model. Furthermore, four of the populations exhibited a significant inbreeding coefficient. The finding of local differentiation among Amazonian mahogany populations underscores the need for in situ conservation of multiple populations of S. macrophylla across its distribution in the Brazilian Amazon. In addition, the occurrence of microgeographical genetic differentiation at a local scale indicates the importance of maintaining populations in their diverse habitats, especially in areas with mosaics of topography and soil.     

The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences

Glycine soja, also called wild soybean, is the wild ancestor of domesticated soybean (Glycine max), and one of the world's major cultivated crops. Wild soybean is a valuable resource for the breeding of cultivated soybean and harbors useful genes or agronomic traits. To use and conserve this valuable resource, we conducted a study to evaluate the genetic diversity and population structure of wild soybean using the sequencing data of two nuclear loci (AF105221 and PhyB) and one chloroplast locus (trnQ-rps16) of more than 600 individuals representing 53 populations throughout the natural distribution range. The results showed that most of the variation was found within the populations and groups, but significant genetic differentiation was also detected among different eco-geographical groups. Correlations between genetic and geographical distance at all the loci were consistent with the isolation by distance gene flow model. G. soja exhibited the highest genetic diversity in middle and downstream of Yangzi River (MDYR) region, followed by North East China (NEC), and was the lowest in North West China (NWC). We concluded that both in situ and ex situ conservation strategies required for wild soybean populations, especially which are native to MDYR and NEC regions.     

Genetic variation within and among populations of Arabidopsis thaliana.

We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.     

Deeply divergent lineages of the widespread New Zealand amphipod Paracalliope fluviatilis revealed using allozyme and mitochondrial DNA analyses

1. We evaluated the population genetic structure of the common New Zealand amphipod Paracalliope fluviatilis using eight allozyme loci, and the mitochondrial cytochrome oxidase c subunit I (COI) gene locus. Morphological analyses were also conducted to evaluate any phenotypic differences. Individuals belonging to P. fluviatilis were collected from a total of 14 freshwater fluvial habitats on the North and South Islands, New Zealand. 2. We found evidence for strong genetic differentiation among locations (Wright's F_ST > 0.25), and fixed differences (non‐shared alleles) at two of the eight allozyme loci indicating the possibility of previously unknown species. Analysis of a 545‐bp fragment of the COI locus was mostly congruent with the allozyme data and revealed the same deeply divergent lineages (sequence divergences up to 26%). 3. Clear genetic breaks were identified between North Island and South Island populations. North Island populations separated by <100 km also showed genetic differences between east and west draining watersheds (sequence divergence >12%). Accordingly, present‐day dispersal among hydrologically isolated habitats appears minimal for this taxon. 4. Although population differences were clearly shown by allozyme and mtDNA analyses, individuals were morphologically indistinguishable. This suggests that, as in North American and European taxa (e.g. Hyalella and Gammarus), morphological conservatism may be prevalent among New Zealand's freshwater amphipods. We conclude that molecular techniques, particularly the COI gene locus, may be powerful tools for resolving species that show no distinctive morphological differences.     

Isolation and characterization of EST‐derived microsatellite loci from the fungal wheat pathogen Phaeosphaeria nodorum

Eleven polymorphic microsatellite loci and one minisatellite locus originating from expressed sequence tag (EST) libraries of Phaeosphaeria (syn. Stagonospora) nodorum were isolated and characterized. The satellite markers were used to genotype isolates from field populations collected in China, North America and South Africa. The number of alleles per locus ranged from two to 15. Genotype diversity ranged from 87.5 to 95.3 and gene diversity from 0.1 to 0.8. The variable levels of polymorphism within and among populations of P. nodorum renders these 12 satellite loci ideal markers for population genetic analysis of P. nodorum.     

Genetic variation and population structure in native Americans

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.     

Conservation genetics of Amorpha georgiana (Fabaceae), an endangered legume of the Southeastern United States

Amorpha georgiana (Fabaceae) is an endangered legume species found in longleaf pine savannas in the Southeastern United States. Approximately 900 individuals and 14 populations remain, most of which are concentrated in North Carolina. Eleven microsatellite loci were used to explore genetic diversity, population structure and recent population bottlenecks using genotypic data from 132 individuals collected at ten different localities. Although A. georgiana is quite rare, it exhibited high levels of genetic diversity (17.7 alleles/locus; H _o = 0.65, H _E = 0.75). Most of the genetic variation was found within rather than between populations of this species. The single remaining Georgia population was well differentiated from populations of the Carolinas ( F _ST > 0.1), which had weaker structure among them ( F _ST < 0.1). Only a geographically disjunct population showed strong evidence of a recent population bottleneck, perhaps due to a recent founder event. Hybridization with A. herbacea was also detected. For conservation management plans, A. georgiana populations in each geographic region (North Carolina, South Carolina and Georgia) plus a disjunct population in North Carolina (Holly Shelter) should be treated as separate management units for which in situ conservation, including habitat restoration and use of prescribed burns, should ensure persistence of this species and preservation of its evolutionary potential.     

利用SSR分子标记分析秦岭冷杉自然居群的遗传多样性

利用10对SSR引物对濒危植物秦岭冷杉(Abies chensiensis)6个自然居群的120个个体进行了遗传多样性研究,旨在分析秦岭冷杉6个自然居群的遗传多样性、遗传结构及基因流变化.研究结果表明,120个个体在10个位点上共检测到149个等位基因,平均每个位点的等位基因数(A)为14.9,每个位点的有效等位基因数(e)为7.7,每个位点的平均预期杂合度(He)和平均观察杂合度(Ho)分别为0.841和0.243,Shannon多样性指数(Ⅰ)为2.13,自然居群杂合性基因多样度的比率(FsT)为6.7％,居群间的基因流(Nm)为3.45.利用Mantel检测到自然居群的遗传距离与地理距离间无显著相关性(r=0.490 6,P＞0.05).秦岭冷杉自然居群的遗传多样性水平较低,遗传变异主要存在于居群内部.结合研究数据、实地调查及相关资料,推测秦岭冷杉自然居群间基因流较原来增大可能是因为居群间发生了远交衰退.     

GENETIC VARIABILITY OF GELIDIUM CANARIENSIS (RHODOPHYTA) DETERMINED BY ISOZYME ELECTROPHORESIS1

The populations of Gelidium canariensis (Grunow) Seoane-Camba from the Canary Islands were analyzed for genetic variability by isozyme electrophoresis in 1989 and 1990. Each population was divided into sporophytic and gametophytic subpopulations. Twenty-three to 27 putative alleles corresponding to 22 gene loci were analyzed. Sev-enteen loci were monomorphic in all six subpopulations, and five were polymorphic in at least one subpopulation. Significant deviations from Hardy-Weinberg equilibrium were found. The amount of genetic variability (percentage of polymorphic loci, mean number of alleles per locus, and average gene diversity) of haploid subpopulations was lower than that of diploid subpopulations. No correlation between genetic distance and geographical distance was found. Low genetic differentiation between sporophytic and gametophytic subpopulations of the same locality was obsewed in two populations. The low genetic diversity and genetic differentiation suggest that the genetic structure of the populations of G. canariensis from the Canary Islands is due to a combination of founder effects and the predominance of asexual reproduction. Initial differences in gene frequencies may have persisted because of insufficient time to reach a higher level of differentiation.     

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.     

Variation on islands: major histocompatibility complex (Mhc) polymorphism in populations of the Australian bush rat

Loss of genetic variation in small, isolated populations is commonly observed at neutral or nearly neutral loci. In this study, the loss of genetic variation was assessed in island populations for a locus of major histocompatibility complex (Mhc), a locus shown to be under the influence of balancing selection. A total of 36 alleles was found at the second exon of RT1.Ba in 14 island and two mainland populations of Rattus fuscipes greyii. Despite this high overall diversity, a substantial lack of variation was observed in the small island populations, with 13 islands supporting only one to two alleles. Two populations, Waldegrave and Williams Islands, showed moderately high levels of heterozygosity (52-56%) which were greater than expected under neutrality, suggesting the action of balancing selection. However, congruence between the level of variation at this Mhc locus and in previous allozyme electrophoresis and mitochondrial DNA studies highlights the dominant influence of genetic drift and population factors, such as bottlenecks and structuring in the founding population, in the loss of genetic variation in these small, isolated populations.     

Ecological-genomic diversity of microsatellites in wild barley,Hordeum spontaneum,populations in Jordan

We analyzed the ecological-genomic diversity of microsatellites of wild barley, Hordeum spontaneum (C. Koch) Thell., at 18 loci in 306 individuals of 16 populations from Jordan across a southward transect of increasing aridity. The 18 microsatellites revealed a total of 249 alleles, with an average of 13.8 alleles per locus (range 3-29), with nonrandom distribution. The proportion of polymorphic loci per population averaged 0.91 (range 0.83-1.00); gene diversity, He, averaged 0.512 (range 0.38-0.651). We compared the number of alleles of the 18 loci to those found in Israel populations by Turpeinen et al. Out of the 280 alleles, 138 (49.3%) were unique (i.e. occurred in only one of the countries). The percentage of unique alleles in Jordan and Israel populations was 43.0% and 17.9%, respectively, suggesting that Jordan is an important center of origin and diversity of wild barley. Estimates of mean gene diversity were highest in the populations collected near the Golan Heights, such as Shuni North, Shuni South and Jarash. Sixty nine percent of the microsatellite variation was partitioned within populations and 31% between populations. Associations between ecogeographical values and gene diversity were established for eight microsatellite loci. The cluster produced by simple sequence repeat (SSR) data is mostly coincidence with the result of the dendrogram of the Spalax ehrenbergi superspecies of subterranean mole rats in Jordan based on allozyme gene loci. The major soil type in the wild barley habitat of each ecological group was different. Stepwise multiple regression analysis indicated that the variance of gene diversity was explained by altitude (R(2) = 0.362**). These observations suggest that microsatellites are at least partly adaptive and subject to natural selection.     

黑头酸臭蚁微卫星标记的分离与开发(英文)

【目的】本研究旨在分离黑头酸臭蚁Tapinoma melanocephalum基因组微卫星标记,确定这些微卫星位点的多态性。【方法】使用454 GS-FLX焦磷酸测序技术开发来自中国华南陆地和岛屿的11个黑头酸臭蚁地理种群基因组微卫星位点。从随机设计的100对微卫星引物中筛选出10对引物,用于确定黑头酸臭蚁4个地理种群［东澳岛(DAD)、荷包岛(HBD)、梅州(MZ)和山咀(SJ)］10个微卫星位点的多态性,分析种群遗传多样性和种群分化。【结果】从11个黑头酸臭蚁地理种群基因组中成功开发和分离10对微卫星引物。在DAD, HBD, MZ和SJ 4个地理种群中,10个微卫星位点中7个有高多态性,这10个位点均显著偏离Hardy-Weinberg平衡;每个位点的等位基因数量(A)是3.50~9.00个,每个地理种群每个位点等位基因丰富度(A_R)在1.992~12.938之间。岛屿地理种群(DAD和HBD)的AR和预期杂合度(H_E)与大陆地理种群(MZ和SJ)的相比差异不显著。4个地理种群均显示高水平遗传分化(F_ST=0.15969);HBD和MZ种群与其他配对地理种群相比,遗传分化较高(F_ST=0.185),基因流较低,说明这两个种群基因流被限制。此外,遗传变异来自种群内个体之间。【结论】筛选新的微卫星位点能够为研究黑头酸臭蚁种群结构和繁殖结构提供有效工具,以深入了解其传播机制。