Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana

Introduced species frequently show geographic differentiation, and when differentiation mirrors the ancestral range, it is often taken as evidence of adaptive evolution. The mouse-ear cress (Arabidopsis thaliana) was introduced to North America from Eurasia 150-200 years ago, providing an opportunity to study parallel adaptation in a genetic model organism. Here, we test for clinal variation in flowering time using 199 North American (NA) accessions of A. thaliana, and evaluate the contributions of major flowering time genes FRI, FLC, and PHYC as well as potential ecological mechanisms underlying differentiation. We find evidence for substantial within population genetic variation in quantitative traits and flowering time, and putatively adaptive longitudinal differentiation, despite low levels of variation at FRI, FLC, and PHYC and genome-wide reductions in population structure relative to Eurasian (EA) samples. The observed longitudinal cline in flowering time in North America is parallel to an EA cline, robust to the effects of population structure, and associated with geographic variation in winter precipitation and temperature. We detected major effects of FRI on quantitative traits associated with reproductive fitness, although the haplotype associated with higher fitness remains rare in North America. Collectively, our results suggest the evolution of parallel flowering time clines through novel genetic mechanisms.     

Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species

Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.     

异色瓢虫不同地理种群的ISSR种群多样性分析

异色瓢虫Harmonia axyridis(Pallas)在亚洲地区是一种重要的捕食性天敌昆虫,但是当引入到欧美后,对当地的物种产生了威胁.本文用ISSR技术对两个中国本地种群和一个引入美国的种群进行了种群多样性以及种群分化的分析.8条ISSR引物共扩增出105条带,其中多态性条带比率为96.19%.Nei's多样性指数、Shannon信息指数、多态性条带比率,在中国种群与美国种群中均非常接近,种群分化不明显(G_(st)=0.042).AMOVA分析显示种群多样性主要来源于种群内部,种群问的基因流非常强(N_m=5.537).基于Nei's多样性构建的聚类结果显示ISSR是一种快速有效的研究异色瓢虫种群多样性关系的技术.     

Population genetics of the wild yeast Saccharomyces paradoxus

Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population structure, and linkage disequilibrium. Synonymous site diversity is approximately 0.3%. Extensive incompatibilities between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species.     

Genetic variation in the widespread lichenicolous fungus Marchandiomyces corallinus

The lichenicolous basidiomycete Marchandiomyces corallinus is widely distributed in North America and Europe, where it commonly is found on a variety of lichens. Theoretically either of these characteristics, a wide geographic range or generalized host ecology, could provide opportunities for genetic differentiation within this species. To determine how genetic variation is partitioned in M. corallinus, 12 fungal isolates were obtained from locations in North America and Europe; at two locations, in Washington County, Maine, and on the Isle of Mull in Scotland, fungi also were isolated from different lichen hosts. Vegetative mycelial compatibility tests were used to determine compatibility groupings from among the isolates; in addition, several PCR amplification products (RAPD, nuITS rDNA) were obtained for each isolate. A number of distinct compatibility groups were recognizable based on geography, not host ecology. In addition compatible isolates always were restricted to either North America or Europe. However RAPD markers indicated that compatible isolates are not always genetically identical. The presence of sequence heterozygosity at specific positions indicated that the isolates are heterokaryotic and a number of distinct haplotypes could be identified based on ITS variation at three separate locations. This type of genetic variation in these fungi suggests that sexual recombination is possible and that genetic differentiation has taken place recently as a result of geographic isolation, not host switching.     

Restriction analysis of an amplified rodA gene fragment to distinguish Aspergillus fumigatus var. ellipticus from Aspergillus fumigatus var. fumigatus

A previous multidisciplinary study indicated that gliotoxin-producing Aspergillus fumigatus Fresen. isolates from silage commodities mostly belonged to its variant A. fumigatus var. ellipticus Raper & Fennell. Sequence analysis revealed the presence of a single nucleotide polymorphism at five positions in a fragment of the rodA gene (coding for a hydrophobin rodletA protein) between Aspergillus fumigatus var. fumigatus and Aspergillus fumigatus var. ellipticus. A method was developed to distinguish these two types of isolates based on restriction analysis of this rodA gene fragment using the HinfI restriction enzyme. In addition, in silico analysis of 113 rodA gene fragments retrieved from GenBank was performed and confirmed the suitability of this method. In conclusion, the method developed in this study allows easy distinction between A. fumigatus var. fumigatus and its variant ellipticus. In combination with the earlier developed PCR-restriction fragment length polymorphism method of Staab et al. (2009, J Clin Microbiol 47: 2079), this method is part of a sequencing-independent identification scheme that allows for rapid distinction between similar species/variants within Aspergillus section Fumigati, specifically A. fumigatus, A. fumigatus var. ellipticus, Aspergillus lentulus Balajee & K.A. Marr, Neosartorya pseudofischeri S.W. Peterson and Neosartorya udagawae Y. Horie, Miyaji & Nishim.     

The structure of allozyme and leaf shape variation in isolated, range-margin populations of the shrub Hippocrepis emerus (Leguminosae)

We investigated allozyme variation and phenotypic variation in leaf shape in 15 populations of the shrub Hippocrepis emerus (Leguminosae) from the three isolated, regional populations in Scandinavia and analysed patterns of differentiation and the hierarchical structuring of diversity on different geographic scales There are pronounced geographic differences between the Norwegian and Swedish isolates of the species and most of the polymorphic allozyme loci show reciprocal fixation in the two isolates The Scandinavian populations of H emerus are not only disjunct on a macrogeographic scale but also show considerable disjunction within regions Within the Oland regional population, a central group of populations shows low levels of Inter-population differentiation the Gotland group of populations is related to this core group of Oland populations The geographically marginal populations on Oland are spatially isolated and show a higher degree of divergence between populations than does the central group of Oland populations We interpret genetic divergence between the marginal populations in terms of genetic drift - as a result of historical fluctuations in habitat availability and population size     

Genetic differentiation in natural populations of a Keystone Bunchgrass (<Emphasis Type="Italic">Aristida stricta</Emphasis>) across its native range

Aristida stricta Michx. (Poaceae) is a perennial bunchgrass native to the Southeastern Coastal Plain of North America where it is a keystone species in the longleaf pine savannas and slash pine flatwoods from southeastern North Carolina to Florida, and westward to the coast of Mississippi. We examined genetic relationships within and among ten populations of A. stricta by using eight inter-simple sequence repeat (ISSR) markers to generate band frequency data for 32 individuals from each sampled population. An analysis of molecular variance showed that 38% of the variation resided among populations while 62% was attributable to variation within populations. Grouping the populations by habitat or by geographic location did not show significant differentiation between the groups. Overall, pair-wise geographic and genetic distances were not correlated. Data indicate that while individuals within each population are genetically diverse, there seemingly are barriers to gene flow across populations leading to their divergence. Each population contains several exclusive loci suggesting that limited gene flow and/or genetic drift are likely leading to this pattern of localization. Our results, coupled with those of the previous studies that presented evidence for local adaptation and phenotypic differences among populations, suggest that there is sufficient differentiation among populations of this species to warrant: (1) maintenance of the existing genetic diversity at individual sites, and (2) use of local seed and plant sources for conservation projects.     

Reproductive biology and genetic structure in Lloydia serotina

Concern regarding the conservation status of small, isolated populations of the arctic-alpine plant species Lloydia serotina prompted research to establish the status and performance of this species in Wales, in comparison with large populations in its more typical alpine habitat. Relationships between reproductive strategies and genetic variation were investigated in a number of populations, representing a wide habitat, geographic and population size range. In all populations, vegetative reproduction predominates over sexual reproduction, but seed produced is viable and germinates readily under controlled conditions. Smaller, peripheral populations produced fewer flowers and seeds than the larger ones, but all populations studied supported significant percentages (>30%) of male plants, due to either the occurrence of androdioecy in this species or to a resource limited breeding system. Analysis of allozyme variation in sixteen populations from North America, the European Alps and Wales showed lower levels of genetic variation in smaller populations which averaged 1.1–1.2 alleles per locus and 10–20% of loci polymorphic, whereas larger populations averaged 1.4 alleles per locus and 30–40% polymorphic loci. This applied especially to the most northerly and southerly populations in North America, suggesting the occurrence of genetic drift in these small, peripheral populations. F-statistics suggest relatively high levels of differentiation among smaller populations, even among those closely related geographically, but genetic variation has been retained in all but one population, possibly due to infrequent sexual reproduction by long lived clones. RAPD analysis of four small populations in Wales provided further evidence of clonal growth and possible inbreeding dominating a mixed mating reproductive system with consequent genetic structuring in these populations.     

Divergence Among an International Population of Trichophyton tonsurans Isolates

Trichophyton tonsurans is a widely distributed pathogen that demonstrates a significant degree of genetic and phenetic heterogeneity. To date, the degree of genetic relatedness among geographically segregated isolates has not been explored. This investigation evaluates the extent of genetic variation among an international population of T. tonsurans isolates and examines the relatedness of isolates within and between countries. Molecular strain typing was performed on 198 isolates obtained from 14 countries. A mixed-marker strategy utilizing 27 sequence variations in 13 gene loci was applied to all isolates and cluster analysis was performed to examine the relationship between strains. Phylogenetic analysis was used to corroborate the findings of the cluster analysis with T. equinum strains serving as an out-group. In total, 47 distinct strain types were identified represented by seven clusters and one singleton. There appeared to be a moderate degree of clustering among isolates obtained from North America, Asia and Australia, although European isolates were uniformly distributed among the majority of clusters. The degree of genetic variation observed in this study coupled with the geographic localization would support the argument for allopatric divergence within this species.     

Population structure of the butternut canker fungus,Ophiognomonia clavigignenti‐juglandacearum,in North American forests

The occurrence of multiple introduction events, or sudden emergence from a host jump, of forest pathogens may be an important factor in successful establishment in a novel environment or on a new host; however, few studies have focused on the introduction and emergence of fungal pathogens in forest ecosystems. While Ophiognomonia clavigignenti‐juglandacearum (Oc‐j), the butternut canker fungus, has caused range‐wide mortality of butternut trees in North America since its first observation in 1967, the history of its emergence and spread across the United States and Canada remains unresolved. Using 17 single nucleotide polymorphic loci, we investigated the genetic population structure of 101 isolates of Oc‐j from across North America. Clustering analysis revealed that the Oc‐j population in North America is made up of three differentiated genetic clusters of isolates, and these genetic clusters were found to have a strong clonal structure. These results, in combination with the geographic distribution of the populations, suggest that Oc‐j was introduced or has emerged in North America on more than one occasion, and these clonal lineages have since proliferated across much of the range of butternut. No evidence of genetic recombination was observed in the linkage analysis, and conservation of the distinct genetic clusters in regions where isolates from two or more genetic clusters are present, would indicate a very minimal or non‐existent role of sexual recombination in populations of Oc‐j in North America.     

Patterns of genetic diversity in population complexes of pacific chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis> Walbaum,from Asia and America,inferred from allozyme polymorphism data

Based on the data of Russian and foreign researchers, a database, consisting of 100 allozyme-coding loci examined in 288 chum salmon populations from Asia and Northern America, was constructed. Using G-test, genetic heterogeneity of Asian population samples of chum salmon was evaluated. Correlations between the frequencies of major alleles and geographic latitude of the mouths of native rivers were estimated. Using the methods of Nei and Cavalli-Sforza and Edwards, for different local chum salmon stock groups the genetic distances at the number of polymorphic enzyme loci were determined. Analysis of these distances made it possible to evaluate the patterns of genetic diversity in regional population groups from the Russian Far East, Japan, and North America. The proportions of genetic variation at each hierarchical level, identified in accordance with the geographical positions of the populations, were estimated through partitioning of variation in Asian populations into within and between-population components. It was demonstrated that intraspecific genetic structure of chum salmon corresponded geographic subdivision into regional population groups.     

Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus

As the frequency of antifungal drug resistance continues to increase, understanding the genetic structure of fungal populations, where resistant isolates have emerged and spread, is of major importance. Aspergillus fumigatus is an ubiquitously distributed fungus and the primary causative agent of invasive aspergillosis (IA), a potentially lethal infection in immunocompromised individuals. In the last few years, an increasing number of A. fumigatus isolates has evolved resistance to triazoles, the primary drugs for treating IA infections. In most isolates, this multiple-triazole-resistance (MTR) phenotype is caused by mutations in the cyp51A gene, which encodes the protein targeted by the triazoles. We investigated the genetic differentiation and reproductive mode of A. fumigatus in the Netherlands, the country where the MTR phenotype probably originated, to determine their role in facilitating the emergence and distribution of resistance genotypes. Using 20 genome-wide neutral markers, we genotyped 255 Dutch isolates including 25 isolates with the MTR phenotype. In contrast to previous reports, our results show that Dutch A. fumigatus genotypes are genetically differentiated into five distinct populations. Four of the five populations show significant linkage disequilibrium, indicative of an asexual reproductive mode, whereas the fifth population is in linkage equilibrium, indicative of a sexual reproductive mode. Notably, the observed genetic differentiation among Dutch isolates does not correlate with geography, although all isolates with the MTR phenotype nest within a single, predominantly asexual, population. These results suggest that both reproductive mode and genetic differentiation contribute to the structure of Dutch A. fumigatus populations and are probably shaping the evolutionary dynamics of drug resistance in this potentially deadly pathogen.     

Population dynamics of the endangered plant, Phaedranassa tunguraguae, from the Tropical Andean hotspot

The Tropical Andes is a diversity hotspot for plants, but there is a scant knowledge about patterns of genetic variation within its constituent species. Phaedranassa tunguraguae is an IUCN endangered plant species endemic to a single valley in the Ecuadorian Andes. We estimate the levels of genetic differentiation across the geographic distribution of P. tunguraguae using 12 microsatellite loci. We discuss factors that might influence the genetic structure of this species. Genetic distance was used to evaluate relationship among populations and geographic patterns. Bayesian methods were used to investigate population structure, migration, evidence of recent bottlenecks, and time of divergence. The 7 populations form 2 genetic clusters. These clusters show highly significant differentiation between them, along with isolation by distance. Allele richness decreases from the most diverse westernmost population to the least diverse easternmost population. The species overall shows an excess of homozygotes, with highest levels of inbreeding in the easternmost population. We found evidence of recent bottleneck events. Migration rates were in general low but were higher between populations within each of the clusters. Time of divergence between populations was related to historical volcanic activity in the area. Based on our results, we propose 2 management units for P. tunguraguae.     

Significant difference in pathogenicity between MAT1-1 and MAT1-2 isolates in the wheat pathogen Mycosphaerella graminicola

Five Mycosphaerella graminicola populations from four geographic regions (Australia, Israel, Switzerland, and the USA) were assayed for neutral RFLP markers and mating type idiomorphs. On average, 25-30 genetically distinct isolates were selected from each population and their pathogenicity was measured on two wheat cultivars in a common garden experiment conducted in a greenhouse. A significant difference in pathogenicity was found between MAT1-1 and MAT1-2 isolates. On average, MAT1-1 isolates had 14-22% greater pathogenicity than MAT1-2 isolates. The pattern of higher pathogenicity in MAT1-1 isolates was consistent across four geographical populations and on two wheat cultivars. A uniform and continuous variation in pathogenicity was found among isolates within each mating type, but no genetic differentiation in selectively neutral RFLP loci was found between mating types, consistent with the hypothesis that differences in pathogenicity were not due to the effects of specific pathogenicity genes or non-random genetic backgrounds.     

Effect of white pine blister rust (<Emphasis Type="Italic">Cronartium ribicola</Emphasis>) and rust-resistance breeding on genetic variation in western white pine (<Emphasis Type="Italic">Pinus monticola</Emphasis>)

Western white pine (Pinus monticola) is an economically and ecologically important species from western North America that has declined over the past several decades mainly due to the introduction of blister rust (Cronartium ribicola) and reduced opportunities for regeneration. Amplified fragment length polymorphism (AFLP) was used to assess the genetic variation in northern Idaho populations of western white pine (including rust-resistant breeding stock) in relation to blister rust. A total of 176 individuals from four populations was analyzed using 163 AFLP loci. Within populations, an average 31.3% of the loci were polymorphic (P), and expected heterozygosity (H(e)) was 0.123. Genetic differentiation values (G(st)) showed that 9.4% of detected genetic variation was explained by differences among populations. The comparison between the rust-resistant breeding stock and a corresponding sample derived from multiple natural populations produced similar values of P (35% vs. 34.4%) and H(e) (0.134 vs. 0.131). No apparent signs of a genetic bottleneck caused by rust-resistance breeding were found. However, a comparison of two natural populations from local geographic areas showed that the population with low pressure from blister rust had higher polymorphism and heterozygosity than the population that had experienced high mortality due to blister rust: P (30.7% vs. 25.1%) and H(e) (0.125 vs. 0.100), respectively. In addition, the population from low blister-rust pressure had twice as many unique alleles as the blister rust-selected population. The genetic distance and Dice's similarity coefficients among the four populations indicated that the local population that survived high blister-rust pressure was genetically similar to the rust-resistant breeding stock.     

Population genetic consequences of geographic disjunction: a prairie plant isolated on Great Lakes alvars

Species may often exhibit geographic variation in population genetic structure due to contemporary and historical variation in population size and gene flow. Here, we test the predictions that populations on the margins of a species' distribution contain less genetic variation and are more differentiated than populations towards the core of the range by comparing patterns of genetic variation at five microsatellite loci between disjunct and core populations of the perennial, allohexaploid herb Geum triflorum. We sampled nine populations isolated on alvar habitat within the eastern Great Lakes region in North America, habitats that include disjunct populations of several plant species, and compared these to 16 populations sampled from prairie habitat throughout the core of the species' distribution in midwestern Canada and the USA. Alvar populations exhibited much lower within-population diversity and contained only a subset of alleles found in prairie populations. We detected isolation by distance across the species' range and within alvar and prairie regions separately. As predicted, genetic differentiation was higher among alvar populations than among prairie populations, even after controlling for the geographic distance between sampled populations. Low diversity and high differentiation can be accounted for by the greater contemporary spatial isolation of alvar populations. However, the genetic structure of alvar populations may also have been influenced by postglacial range expansion and contraction. Our results are consistent with alvar populations being founded during an expansion of prairie habitat during the warmer, hypsithermal period approximately 5000 bp and subsequently becoming stranded on isolated alvar habitat as the climate grew cooler and wetter.     

Genetic differentiation in Hippocrepis emerus (Leguminosae): allozyme and DNA fingerprint variation in disjunct Scandinavian populations

The structure of genetic variation in disjunct Scandinavian populations of Hippocrepis emerus was studied using allozymes and DNA fingerprinting. Variation in the three native regional populations in Scandinavia was compared with that in a recently introduced population in Sweden. In contrast to the recently introduced population, the native Scandinavian isolates of H. emerus showed high levels of allozyme fixation and low levels of DNA diversity. Variation in allozymes and at DNA fingerprint loci showed closely congruent patterns of geographic variation, with pronounced differentiation between the native Norwegian and Swedish isolates of the species. The structure of genetic variation in native Scandinavian H. emerus is interpreted in terms of historical population bottlenecks and founder events during the species' postglacial immigration into Scandinavia.     

Population structure and conservation genetic assessment of the endangered Pugnose Shiner,Notropis anogenus

The Pugnose Shiner is a small minnow with a fragmented distribution across the Great Lakes and Upper Mississippi River in North America. The species is listed federally as endangered in Canada, and in the United States its status varies by state, from Special Concern to Endangered (as well as Extirpated). We conducted a thorough genetic assessment of the Pugnose Shiner using both microsatellite loci and mitochondrial DNA collected for samples across the species range. Our results indicate high levels of population differentiation suggesting restricted dispersal, in some cases at very small geographical scales. We also found strong evidence of small effective population sizes and one case of a genetic bottleneck. Although significant range-wide genetic variation was observed in both microsatellite loci and mitochondrial DNA, the species is best characterized as a single evolutionarily significant unit for conservation purposes.     

欧洲中部刺槐种源群体等位酶变异研究

从欧洲中部及美国收集了18个刺槐种源种子,以2年生苗木为材料,采用水平切片淀粉凝胶电泳和聚丙烯酰胺凝胶电泳对11个酶系统进行了检测,共发现20个酶位点,其中14个为多态位点,多态性位点百分数为70％。在参加计算的7个酶系统的12个多态性位点中,平均每个位点的等位基因数(A)和平均每位点等位基因有效数(Ae)为2.733和1．794,平均每个位点的实际杂合度(Ho)和预期杂合度(He)为0．368和0．400,固定指数(F)为0．080,绝大多数位点固定指数为正值。各基因位点遗传参数与12个位点平均值进行相关分析表明,Fe-6和Lap-a的大部分群体遗传参数(A、Ae、Ho、He等)与平均值存在紧密的相关关系,其他位点各项遗传参数和总平均值相关不明显,这些位点的重要性可能比相关性较好的位点更大。德国8个种源群体间遗传距离变化在0．09-0．26之间,来自匈牙利的6个种源之间遗传距离很小,绝大部分均在0．11以下;德国的8个种源与匈牙利和斯洛伐克的8个种源之间的遗传距离变化在0．09-0．24之间;来自美国的2个种源,与欧洲的种源间的遗传距离在0．09-0．23之间,这一距离没有超出欧洲种源之间的差异。匈牙利和斯洛伐克的8个种源群体的各项遗传参数均高于德国种源,表明这两个国家的遗传多样性水平较高。同时来自这两个国家的种源群体间变异系数变化在2．92％-9．97％,说明群体之间的遗传差别很小。德国的8个种源群体各项遗传参数相对较低,但群体间变异系数较高,群体间遗传差别较大。以各个国家为群体单位,4个群体间各项遗传参数的变异均较小,变异系数变化在3．861％-5．139％,表明刺槐种源间地理变异模式不明显。