Comparative analysis of genetic structure in natural populations of two <Emphasis Type="Italic">Arabidopsis</Emphasis> species with different degree of panmixia

Comparative analysis of genetic structure of northern natural populations of two Arabidopsis species with different degrees of panmixia was performed. The variability of 121 RAPD loci in seven populations of model plant A. thaliana possessing high degree of self fertility was studied together with 93 RAPD loci in population of cross-pollinating species A. lyrata ssp. petraea. The population of A. l. petraea demonstrated higher level of genetic variability (P _99% = 62.50%; H _exp = 0.169) than the populations of A. thaliana, which is obviously connected with biological features of reproduction of the species. A significant level of genetic variability (P _99% = 42.27%; H _exp = 0.126) was revealed in populations of A. thaliana, which is not typical for self-pollinating plant species. The high population polymorphism of A. thaliana in the northern part of its range may be connected with adverse environmental conditions. The genetic distances between populations of the species studied (average D _N = 0.494) confirm close relatedness between A. thaliana and A. l. petraea.     

猕猴桃自然居群SSR遗传变异的空间自相关分析

本研究采用空间自相关分析方法对同域分布的中华猕猴桃(Actinidiachinensis)和美味猕猴桃(A.deliciosa)自然居群SSR遗传变异的空间结构进行了研究,以探讨猕猴桃自然居群遗传变异的分布特征。选用的9对SSR引物在两物种中共扩增出104个等位基因。选择频率在20–80%的SSR等位基因,运用等样本对频率方法分别对同域分布的中华猕猴桃和美味猕猴桃各1个居群及其中华/美味猕猴桃复合居群进行了空间自相关系数Moran’sI值计算。结果表明:中华猕猴桃和美味猕猴桃的遗传变异在居群内均存在着一定程度的空间结构,尽管近半数或半数以上的等位基因在居群内表现为随机分布的空间模式,但也有相当比例(29.6–48.0%)的等位基因在种内居群中和复合居群中(河南西峡51.0%,陕西商南44.7%)呈现渐变、衰退、双向衰退或侵扰模式。而且其居群内遗传变异的空间分布规律,不论是在种内还是复合居群中都基本一致:相距在100m以内,特别是30m范围内的个体间的等位基因表现出显著性的正相关,但随着地理距离的增大逐渐显示出负相关,说明猕猴桃属植物的有效传粉距离可能在100m左右,种子散播主要集中在30m的近距离内。猕猴桃自然居群遗传变异的空间结构是其传粉和种子散播等生物学特性与生境共同作用的结果,其中种子近距离的散播、花粉传播的有限距离及人为干扰是最主要的因素。本研究结果揭示了这两个近缘物种居群遗传变异的空间分布特征及相互关系,有助于进一步探讨猕猴桃属植物的遗传变异、居群扩散及其地理系统发育进化等方面的规律,并为制定相应的保育策略和措施提供基础数据和科学依据。     

Comparative analysis of symbiont ratios and gene expression in natural populations of two Bathymodiolus mussel species

Bathymodiolus mussels associated with deep-sea hydrothermal vents and cold seeps harbor chemosynthetic endosymbiotic bacteria in bacteriocytes located in the gill epithelium. Two distinct morphotypes of γ-proteobacteria, sulfur- and methane-oxidizing, have been identified and form a dual symbiosis in B. azoricus mussels from the Mid-Atlantic Ridge and in B. aff. boomerang from cold seeps in the Gulf of Guinea. Thiotrophic bacteria (SOX) are capable of fixing CO2 in the presence of sulfide or thiosulfate and methanotrophic bacteria (MOX) use methane both as a carbon and an energy source. In this study we used quantitative real-time PCR to test whether symbiont abundance and gene expression varied between the two mussel species. Results showed that B. azoricus from two hydrothermal sites had similar ratios and gene expression pattern for both symbiont types. In B. aff. boomerang, SOX ratio and ATP sulfurylase gene expression show differences between specimens collected on the different sites. Analysis of symbiont ratios in both species indicated a clear dominance of MOX symbionts in B. aff. boomerang and SOX symbionts in B. azoricus. We also evidenced that the species from the deeper sites (B. aff. boomerang) and mussels collected from sulfur and methane rich habitats showed higher symbiont ratio suggesting that environmental parameters may have significant impacts on the symbiont ratios in Bathymodiolus mussels.     

Comparative analysis of three species populations of Profundulus (Teleostei: Cyprinodontiformes) using two genetic markers

Background and aims: The fish Family Profundulidae is endemic in south-southeast Mexico, with five known species. The species-level analysis of the genus based on morphological characters is insufficient and complex due to increased phenotypic and intraspecific variation. This variation might be owed to the existence of yet undescribed forms. Materials and methods: In the present study, the genetic composition of three species of the State of Chiapas, Mexico, is compared by examining different populations of the species Profundulus candalarius, Profundulus labialis, and Profundulus punctatus. Results: We identified specimens from 16 localities and sequenced mitochondrial DNA representing partial regions of the cytochrome b and cox1 genes. Conclusion: The results suggest an extreme divergence of the populations of P. labialis from El Sabinal.     

Quantitative genetic analysis of natural populations

Quantitative genetic studies in natural populations have been rare because they require large breeding programmes or known pedigrees. The relatedness that has been estimated from molecular markers can now be used to substitute for breeding, allowing studies of previously inaccessible species. Many behavioural ecologists have a sufficient number of markers and study species with characteristics that are amenable to this approach. It is now time to combine studies of selection with studies of genetic variation for a more complete understanding of behavioural evolution.     

Subdivision and haplotype structure in natural populations of Arabidopsis lyrata

High levels of inbreeding are expected to cause a strong reduction in levels of genetic variability, effective recombination rates and in adaptation compared with related outcrossing populations. We examined patterns of DNA polymorphism at five nuclear loci and one chloroplast locus within and between four populations of the outcrossing plant Arabidopsis lyrata, a close relative of the highly self-fertilizing model species A. thaliana. The observed patterns are compared with species-wide polymorphism at orthologous loci, as well as within- and between-population patterns at other studied loci in A. thaliana. In addition to evidence for much higher average within-population diversity, species-wide levels of silent polymorphism are generally higher in A. lyrata than in A. thaliana, unlike the results from a previous study of the ADH locus. However, polymorphism is also low in the North American A. lyrata subspecies lyrata compared with the European subspecies petraea, suggesting either a population bottleneck in North American populations or recent admixture involving diverged European populations. Differentiation between the two subspecies is strong, although there are few fixed differences, suggesting that their isolation is recent. Estimates of intralocus recombination rates and analysis of haplotype structure in European A. lyrata populations indicate lower recombination than predicted based on the variability together with physical recombination rates estimated from A. thaliana. This may be due to strong population subdivision, or to recent departures from demographic equilibrium such as a bottleneck or population admixture. Alternatively, there may be consistently lower recombination rates in the outcrossing species. In contrast, estimates of recombination rates from species-wide samples of A. thaliana are close to the values expected assuming a high rate of self-fertilization. Complex population histories in both A. thaliana and A. lyrata complicate theoretical predictions and empirical tests of the effects of inbreeding on polymorphism and molecular evolution.     

Peripheral genetic structure of Helicoverpa zea indicates asymmetrical panmixia

Seasonal climatic shifts create peripheral habitats that alternate between habitable and uninhabitable for migratory species. Such dynamic peripheral habitats are potential sites where migratory species could evolve high genetic diversity resulting from convergence of immigrants from multiple regionally distant areas. Migrant populations of Helicoverpa zea (Boddie) captured during two different seasons were assessed for genetic structure using microsatellite markers and for host plant type using stable carbon isotope analysis. Individuals (N = 568) were genotyped and divided into 13 putative populations based on collection site and time. Fixation indices (F‐statistics), analysis of molecular variance (AMOVA), and discriminant analysis of principal components (DAPC) were used to examine within and among population genetic variation. Mean number of alleles per locus was 10.25 (± 3.2 SD), and allelic richness ranged from 2.38 to 5.13 (± 3.2 SD). The observed and expected heterozygosity ranged from 0.07 to 0.48 and 0.08 to 0.62, respectively. Low F_ST (0.01 to 0.02) and high F_IS (0.08 to 0.33) values suggest captured migrants originated from breeding populations with different allele frequencies. We postulate that high genetic diversity within migrant populations and low genetic differentiation among migrant populations of H. zea are the result of asymmetrical immigration due to the high dispersal and reproductive behavior of H. zea, which may hinder the adaptation and establishment of H. zea to peripheral habitat. These findings highlight the importance of assessing peripheral population structure in relation to ecological and evolutionary dynamics of this and other highly reproductive and dispersive species.     

Similarity in G matrix structure among natural populations of Arabidopsis lyrata

Understanding the stability of the G matrix in natural populations is fundamental for predicting evolutionary trajectories; yet, the extent of its spatial variation and how this impacts responses to selection remain open questions. With a nested paternal half‐sib crossing design and plants grown in a field experiment, we examined differences in the genetic architecture of flowering time, floral display, and plant size among four Scandinavian populations of Arabidopsis lyrata. Using a multivariate Bayesian framework, we compared the size, shape, and orientation of G matrices and assessed their potential to facilitate or constrain trait evolution. Flowering time, floral display and rosette size varied among populations and significant additive genetic variation within populations indicated potential to evolve in response to selection. Yet, some characters, including flowering start and number of flowers, may not evolve independently because of genetic correlations. Using a multivariate framework, we found few differences in the genetic architecture of traits among populations. G matrices varied mostly in size rather than shape or orientation. Differences in multivariate responses to selection predicted from differences in G were small, suggesting overall matrix similarity and shared constraints to trait evolution among populations.     

白皮松天然群体遗传结构的地理变异分析

为探讨白皮松天然群体遗传结构在地理分布上的差异,利用7对SSR引物对5个白皮松分布区域的遗传结构进行了分析。结果表明：7对SSR引物在5个区域内476个单株中共检测到14个多态性位点。各区域间观测等位基因数（Na）、有效等位基因数（Ne）、Shannon’s 信息指数（I）、观测杂合度（Ho）、期望杂合度（He）、Nei’s期望杂合度（Nei’s）分别介于1.7143~2.1429、1.1942~1.571、0.1948~0.4954、0.1726~0.3116、0.1178~0.3325、0.1172~0.3307之间。白皮松遗传多样性水平总体较低,区域间差异较大;遗传多样性水平最高的区域为秦岭西侧群体,其次为大巴山区群体;太行山与吕梁山群体多样性水平相对较低。区域间的遗传分化系数Fst介于0.0138~0.2242之间,基因流Nm介于0.865~17.8646之间。遗传分化较大、基因流水平较低的区域均发生在秦岭西侧及其与其他区域之间。各区域间遗传相似系数在0.8416~0.9964之间,遗传相似度最高的群体为太行山与吕梁山区域,遗传距离最大的为太行山与秦岭西侧区域。白皮松多样性分布的中心主要存在于秦岭西侧和大巴山区域,因此应对该区域进行重点保护。     

Lowland panmixia versus highland disjunction: genetic and bioacoustic differentiation in two species of East African White-eye birds

East-African mountain forest species often occur in small and isolated populations, whereas species inhabiting the dry lowland savannahs exist in large and interconnected population networks. Taxa with closely related highland and lowland species, such as the East-African White-eye birds, allow testing for the potential effects of the two contrasting distribution patterns, mountain disjunction versus lowland panmixia. In this study, we compare the population genetic and bioacoustic differentiation of two representatives of the genus Zosterops: Zosterops poliogaster is exclusively found in forests at higher elevations; in comparison, Zosterops abyssinicus, only occurs in the dry and warm lowland savannahs. Both species were analysed across a similar geographical scale. Population genetic differentiation was inferred using the same set of 15 polymorphic microsatellite loci for both species. In addition, we quantitatively analyzed bioacoustic traits. Both data sets indicate a strong population differentiation among populations of the highland species, but an absence of differentiation in the lowland species. In addition, the lowland Z. abyssinicus was characterised by a twofold higher genetic diversity than detected for the highland Z. poliogaster. These two contrasting intraspecific population structures may reflect the opposite ecology and distribution of these species: the strong population isolation of Z. poliogaster resulting from long-term restriction to the cool and moist mountain forests at higher elevations has led to strong differentiation among local populations and resulted in a comparatively low level of intraspecific variability. In contrast, population panmixia in the lowland Z. abyssinicus provides a high level of gene flow allowing the maintenance of high genetic diversity and avoiding strong population structuring. These findings need to be considered when planning conservation actions.     

Effect of chronic irradiation on the genetic structure of natural populations of Arabidopsis thaliana (L.) Heynh

The genetic structure of Arabidopsis thaliana populations from in the Chernobyl zone of radioactive contamination was studied. The dynamics of genotypic and allele frequencies of eight polymorphic loci were described. Analysis of the results obtained and earlier data revealed selection for loci Per1 and Acp2. Sharp fluctuations of allele frequencies were observed in consecutive generations of chronically irradiated A. thaliana populations. These fluctuations led to replacement of the most frequent alleles, including those close to fixation.     

准噶尔无叶豆5个自然居群ISSR遗传变异的空间自相关分析

采用空间自相关分析方法对准噶尔无叶豆(Eremosparton songoricum)5个居群遗传变异的空间结构进行了研究。根据8对ISSR引物扩增的多态性位点,选择了基因频率在30–70%的ISSR位点,运用GenAlEx6和SAAP4.3软件以及地理距离间隔方法分别计算了5个居群的空间自相关系数。结果表明:准噶尔无叶豆居群具有明显的空间遗传结构,绝大多数ISSR位点变异呈非随机分布。位于沙漠腹地的B、D居群和位于沙漠东缘的F居群的遗传变异呈现渐变模式,分别在7m,7m及9m范围内个体呈现显著正相关,推测与克隆繁殖占绝对优势、有性更新罕见发生有关,而克隆大小的差别则主要由微生境差异所引起。位于沙漠北缘的G居群的遗传变异呈现双向渐变模式,在3m内个体呈现显著正相关,这与该居群实生幼苗增补密切相关,但花粉和种子的有限散布所导致的距离隔离对该居群空间遗传结构产生了重要影响。而沙漠腹地的A居群呈现衰退模式,是因为小居群增加了近交的几率,并引起了遗传漂变。     

Landscape genetic structure of natural populations of Acacia caven in Argentina

Acacia caven is a South American species which shows remarkable climate tolerance and ecological adaptability; as such, this species is suitable for colonizing anthropogenically degraded sites. This species is widely distributed, and six varieties have been described based on both morphological traits and molecular markers. Moreover, Aronson (1992) suggests that, for this species, geographical separation could be associated with ecological differentiation. In this study, amplified fragment length polymorphisms were used to study genetic variation within and among 15 populations of A. caven from five eco-regions of Argentina and to investigate (1) whether the varieties are genetically coherent, (2) whether the varieties correspond consistently to a single eco-region, (3) the proportion of the species diversity explained within and among varieties and eco-regions. Eight of the 225 bands appear to be under positive selection. The remaining 217 neutral loci showed a high percentage of polymorphism (99.1%). The estimates of genetic diversity H _j were generally high. The F _ST (0.315) was highly significant, providing evidence for genetic structure among populations. Hierarchical analysis of molecular variance indicated that variation among eco-regions was 8.2% and highly significant. The higher component of variance was found within populations (67.5%). STRUCTURE analysis suggested that the optimal number of K?=?11. The results showed that, in most cases, geographic separation is associated with ecological differentiation. Since differentiation of A. caven populations studied here in eco-regions was highly significant, sampling should include a large number of trees within populations as well as covering the wide ecological diversity of the species.     

Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata

We describe analyses of almost full-length sequences (including both the kinase domain and the S-domain) of the putative SRK incompatibility gene of the self-incompatible plant Arabidopsis lyrata. In A. lyrata, the SRK S-domain controls the pistil recognition specificity, as in self-incompatible Brassica species. In alleles from plants derived from natural A. lyrata populations, nonsynonymous and synonymous site diversity values are very high in both domains; even in exons 3 to 7 of the kinase domain, which probably have no recognition functions, 39% of the amino acids are polymorphic. Within populations, diversity between alleles is high, as expected for an incompatibility locus, which should be under frequency-dependent selection within populations, whereas within the different putative allelic classes polymorphism is very low, as predicted from theoretical models when recombination is rare. Nonsynonymous site variability declines in the kinase domain with increasing distance from the S-domain border, although synonymous diversity remains high, and the introns are unalignable. A decline in nonsynonymous diversity is expected due to selective constraints in the kinase domain, in combination with recombination (allowing diversity to decrease at sites distant from those under balancing selection). However, it is unclear whether recombination occurs in the SRK locus, and interpretation of the observed diversity pattern is complicated by apparent gene conversion with a paralogous gene (or genes). Patterns of linkage disequilibrium in our SRK sequences do not support the conclusion that recombination occurs, which was suggested from previous analyses based on Brassica SLG sequences.     

Comparative analysis of fungal communities in colonies of two leaf-cutting ant species with different substratum preferences

Fungus gardens of leaf-cutting ants harbor diverse alien fungi in addition to their fungal cultivar. Previous work suggested that alien microorganisms are likely derived from the substrata foraged by ant workers and incorporated into the fungus gardens. To test this hypothesis, we sampled 1014 garden fragments from 16 field colonies of Atta sexdens rubropilosa (a dicot-cutting ant) and Atta capiguara (a grass-cutting ant) in Brazil. From a total of 615 fungal isolates recovered, we observed similar diversity of fungi between colonies of both ant species. However, fungal communities differed in composition of taxa between ant colonies. Trichoderma spirale, Trichosporon chiarellii and Penicillium citrinum were prevalent accounting for 18.5%, 12.2% and 11.7% of the total isolates, respectively. As expected, fungal communities clustered in two major groups supporting the hypothesis that plant substratum has an impact on the composition of the alien fungi found in leaf-cutting ant gardens.     

Spatial structure and genetic diversity of three tropical tree species with different habitat preferences within a natural forest

Analyses of the spatial distribution pattern, spatial genetic structure and genetic diversity were carried out using a 33-ha plot in a hill dipterocarp forest for three dipterocarps with different habitat preferences, i.e. Shorea curtisii on the ridges, Shorea leprosula in the valleys and Shorea macroptera both on the ridges and in the valleys. The significant spatial aggregation in small-diameter trees of all the three species was explained by limited seed dispersal. At the large-diameter trees, only S. macroptera showed random distribution and this might further prove that S. macroptera is habitat generalist, whilst S. curtisii and S. leprosula are habitat specific. The levels of genetic diversity estimated based on five microsatellite loci were high and comparable in all the three studied species. As the three studied species reproduced mainly through outcrossing, the observed high levels of genetic diversity might support the fact that the plant mating system can be used as guideline to infer the levels of genetic diversity, regardless of whether the species is habitat specific or habitat generalist. The lack of spatial genetic structure but significant aggregation in the small-diameter trees of all the three species might indicate limited seed dispersal but extensive pollen flow. Hence, if seed dispersal is restricted but pollen flow is extensive, significant spatial aggregation but no spatial genetic structure will be observed at the small-diameter trees, regardless of whether the species is habitat specific or habitat generalist. The inferred extensive pollen flow might indicate that energetic pollinators are involved in the pollination of Shorea species in the hill dipterocarp forests.     

Genetic diversity and genetic structure of different populations of the endangered species Davidia involucrata in China detected by inter-simple sequence repeat analysis

Dove tree (Davidia involucrate) is a Tertiary relic species endemic to China and is reputed to be a ‘living fossil’ in the plant kingdom. Genetic diversity and genetic structure of this species were analyzed for its conservation and management, using inter-simple sequence repeat (ISSR) data obtained from eight populations distributed throughout seven provinces of China. A relatively high level of genetic diversity, at both population and species levels, was detected using the POPGENE software. Analysis of molecular variance (AMOVA) revealed a moderate level of among-population variation (i.e., 33.21%). The genetic structure of dove tree was closely consistent with their isolated topographical distribution region based on the results of the STRUCTURE, POPGENE-UPGMA and PCA analysis. It is postulated that the relatively high level of genetic diversity has been maintained because of: (a) the original wild geographical distribution, (b) propagation through outcrossing seeds or root suckers, (c) the longevity of individuals and (d) the relatively little human disturbance. Genetic drift and restricted gene are important factors affecting genetic differentiation. There was no significant correlation between geographical distances and a pairwise comparison with genetic distances, as analyzed by the Mantel test, but the clustering result of genetic diversity was consistent with their isolated topographical distribution regions. Thus, maintaining the stable special habitats associated with this species is recommended for the in situ conservation. Furthermore, it is important to develop an effective seed germination system for the maintenance of an ex situ conservation pool of the germplasm resources.     

The genetic structure of roach populations in two contrasted large rivers

Overall heterozygosity was high in all roach populations, and so was gene flow between them. However, genetic diversity was greater in the fast-flowing and more diverse French Upper Rhone than in the uniformly lentic River Saone. Rhone backwaters may be considered as ecotones and reservoirs of genetic diversity, but such is not the case in the Saone owing to the uniformity of the environment.(U.R.A. 1451 Ecologie des Eaux Douces et des Grands Fleuves)     

Comparative genomic analysis of two Burkholderia glumae strains from different geographic origins reveals a high degree of plasticity in genome structure associated with genomic islands

Burkholderia glumae is the major causal agent of bacterial panicle blight of rice, a growing disease problem in global rice production. To better understand its genome-scale characteristics, the genome of the highly virulent B. glumae strain 336gr-1 isolated from Louisiana, USA was sequenced using the Illumina Genome Analyser II system. De novo assembled 336gr-1 contigs were aligned and compared with the previously sequenced genome of B. glumae strain BGR1, which was isolated from an infected rice plant in South Korea. Comparative analysis of the whole genomes of B. glumae 336gr-1 and B. glumae BGR1 revealed numerous unique genomic regions present only in one of the two strains. These unique regions contained accessory genes including mobile elements and phage-related genes, and some of the unique regions in B. glumae BGR1 corresponded to predicted genomic islands. In contrast, little variation was observed in known and potential virulence genes between the two genomes. The considerable amount of plasticity largely based on accessory genes and genome islands observed from the comparison of the genomes of these two strains of B. glumae may explain the versatility of this bacterial species in various environmental conditions and geographic locations.