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1.
Insights into the relative contributions of locus specific and genome-wide effects on population genetic diversity can be gained through separation of their resulting genetic signals. Here we explore patterns of adaptive and neutral genetic diversity in the disjunct natural populations of Pinus radiata (D. Don) from mainland California. A first-generation common garden of 447 individuals revealed significant differentiation of wood phenotypes among populations (P ST), possibly reflecting local adaptation in response to environment. We subsequently screened all trees for genetic diversity at 149 candidate gene single nucleotide polymorphism (SNP) loci for signatures of adaptation. Ten loci were identified as being possible targets of diversifying selection following F ST outlier tests. Multivariate canonical correlation performed on a data set of 444 individuals identified significant covariance between environment, adaptive phenotypes and outlier SNP diversity, lending support to the case for local adaptation suggested from F ST and P ST tests. Covariation among discrete sets of outlier SNPs and adaptive phenotypes (inferred from multivariate loadings) with environment are supported by existing studies of candidate gene function and genotype–phenotype association. Canonical analyses failed to detect significant correlations between environment and 139 non-outlier SNP loci, which were applied to estimate neutral patterns of genetic differentiation among populations (F ST 4.3 %). Using this data set, significant hierarchical structure was detected, indicating three populations on the mainland. The hierarchical relationships based on neutral SNP markers (and SSR) were in contrast with those inferred from putatively adaptive loci, potentially highlighting the independent action of selection and demography in shaping genetic structure in this species.  相似文献   

2.
In continuous populations, fine-scale genetic structure tends to be stronger in species with restricted pollen and seed dispersal. However, habitat fragmentation and disturbances can affect genetic diversity and spatial genetic structure due to disruption in ecological processes, such as plant reproduction and seed dispersal. In this study, we compared the genetic diversity and fine-scale spatial genetic structure (SGS) in two populations of Annona crassiflora (Annonaceae) in a pristine savanna Reserve (ESECAE) and in a fragmented disturbed savanna area (PABE), both in Cerrado biome in Central Brazil. The analyses were based on the polymorphism at 10 microsatellite loci. Our working hypothesis was that SGS is stronger and genetic diversity is lower in population at fragmented area (PABE) than at pristine area (ESECAE). Both populations presented high levels of polymorphism and genetic diversity and showed no sign of bottleneck for both Wilcoxon sign-rank test for heterozygosity excess (p > 0.05) and coalescent analyses (growth parameter g not different from zero), but population at fragmented area showed higher fixation index and stronger SGS. Besides, populations are significantly differentiated (F ST = 0.239, R ST = 0.483, p < 0.001 for both). Coalescent analyses showed high historical effective population sizes for both populations, high gene flow between ESECAE and PABE and recent time to most recent common ancestor (~37 k year BP). Our results suggest that despite the high genetic diversity, fragmentation and disturbance may have been affecting populations of this species increasing mating between closely related individuals leading to high fixation index and strong SGS.  相似文献   

3.
The genetic diversity of 116 barley accessions, representing five Chinese eco-geographic populations, was studied using simple sequence repeat (SSR) markers. The 21 SSR loci revealed 128 alleles with an average of 6.1 alleles per locus. The highest values of proportion of polymorphic loci (P) and gene diversity index (He) were obtained in the Northern (P = 1.00; He = 0.60) and the Yangtze River reaches and Southern populations (P = 1.00; He = 0.59). The lowest values were in the populations of the Yellow River reaches (P = 0.86; He = 0.44). The highest average number of alleles per locus (4.52) and number of unique alleles (7) were found in the Qinghai–Tibet plateau population. Cluster analysis revealed that together with the row type, strong eco-geographic variables influenced the classification. Associations of SSR and eco-geographic values were established for 11 SSR loci. Four to six markers were found to discriminate among geographic groups, which may serve as tools for diagnosis of the eco-geographic populations and provide evidence for the adaptive nature of SSR markers.  相似文献   

4.
Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.  相似文献   

5.
Populations with spatially restricted gene flow are characterized by genetic differentiation that may be positively correlated with the geographic distance separating populations, a pattern known as isolation by distance (IBD). Here we examined the fine-scale genetic structure of 66 chum salmon (Oncorhynchus keta) populations spawning in Alaska waterways and explored patterns of IBD using 90 nuclear and 3 mitochondrial single nucleotide polymorphisms. Estimating population structure of chum salmon in Alaska is of increasing concern because of fluctuating census sizes and the uncertain effects of harvest on specific populations. We hypothesized that IBD would be present because chum salmon spawn in coastal rivers that are distributed along a linear array and gene flow is spatially restricted due to homing. Evidence of very weak IBD was found throughout the region (R2 = 0.06, p < 0.0001) but the strength of the IBD relationship varied greatly over different spatial scales and geographic regions. Decomposed pairwise regression analyses identified nine outlier populations to regional IBD patterns, suggesting that geographic distance is not the only factor influencing genetic differentiation in the region. Instead, population structure appears to be heavily influenced by glacial history of the region and the presence of a glacial refugium on Kodiak Island.  相似文献   

6.
Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population percentage of polymorphic band (PPB = 75.92%, H S = 0.204, H pop = 0.319) and at species level (PPB = 96.95%, H T = 0.242, H sp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and Bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability.  相似文献   

7.
Understanding patterns of genetic diversity and population structure for rare, narrowly endemic plant species, such as Pinguicula ionantha (Godfrey’s butterwort; Lentibulariaceae), informs conservation goals and can directly affect management decisions. Pinguicula ionantha is a federally listed species endemic to the Florida Panhandle in the southeastern USA. The main goal of our study was to assess patterns of genetic diversity and structure in 17 P. ionantha populations, and to determine if diversity is associated with geographic location or population characteristics. We scored 240 individuals at a total of 899 AFLP markers (893 polymorphic markers). We found no relationship between the estimated population size with either of two measures of diversity (proportion of loci polymorphic, P = 0.37; Nei’s gene diversity, P = 0.50). We also found low levels of population genetic structure; there was no clear relationship of genetic isolation by distance (P = 0.23) and only a small (but significant) proportion of genetic variation was partitioned amongst regions (2.4 %, P = 0.02) or populations (20.8 %, P < 0.001). STRUCTURE analysis found that the model with two inferred clusters (K = 2) best described the AFLP data; the dominant cluster at each site corresponded to the results from PCoA and Nei’s genetic distance analyses. The observed patterns of genetic diversity suggest that although P. ionantha populations are isolated spatially by distance and both natural and anthropogenic barriers, some gene flow occurs among them or isolation has been too recent to leave a genetic signature. The relatively low level of genetic diversity associated with this species is a concern as it may impair fitness and evolutionary capability in a changing environment. The results of this study provide the foundation for the development of management practices that will assist in the protection of this rare carnivorous plant.  相似文献   

8.
A decreasing population size is often causing species extinction, however, relict species persisting in small-sized populations counter this. We analysed spatial genetic variation and past changes in population size at the maternally-inherited mitochondrial DNA level to clarify the origin of all recently known isolated populations of Pholidoptera frivaldskyi occurring in the range of Carpathian Mountains. Along with that we analysed also morphological variation as some phenotypic traits can retain useful information on population genetic structure. We found a relatively low genetic diversity within isolated populations as 778 bp COI gene sequences revealed only 13 unique haplotypes (n = 173 individuals from 10 populations). The spatial analysis of molecular variance identified three geographically homogenous genetic clusters (one in Slovakia and two in Romania) with a high level of differentiation among them, suggesting restricted gene flow, whilst Bayesian skyline simulation reconstructed a negative demographic change through evolutionary time. Inferred genetic pattern clearly coincides with differences in males’ colour phenotype as the extent of pigmentation on the lateral pronotum varied significantly among genetic lineages. We suggest that geographical variation in the species populations has relict-like character and their isolated occurrence is not a result of recent introduction events. Identification of ‘evolutionary units’ may help in the conservation and management of this rare insect species.  相似文献   

9.
The genetic diversity of seven wild populations of the grass Brachypodium distachyon (2n = 10), 4 of B. stacei (2n = 20) and 13 of B. hybridum (2n = 30) from the Mediterranean and southern areas of the Iberian Peninsula was studied via the analysis of microsatellite (SSR) and inter-microsatellite (ISSR) markers. The 11 SSR markers analysed provided a total of 156 polymorphic fragments. The B. hybridum populations returned more fragments (98) than the B. stacei populations (87), and more than twice the number recorded for the B. distachyon populations (44). Some fragments were specific to the B. distachyon (3.85 %), B. stacei (27.56 %) or B. hybridum populations (18.58 %). The analysis of 16 ISSR markers returned similar results: the B. hybridum populations returned more polymorphic fragments than the B. distachyon or B. stacei populations. The analysis of molecular variance, with distances between individuals, populations and species estimated on the basis of the presence/absence of the SSR and ISSR fragments, showed most of the variation (67 %) to occur among populations. This was followed by differences among individuals within populations (24 %), and finally among species (9 %). Grouping based on UPGMA and principal coordinate analysis showed a clear separation of three groups corresponding to the populations of the same species. Principal component analysis, involving chromosome number, low-molecular weight-glutenin subunits and the most influential climatic and geographic factors, was also performed. This revealed an obvious separation among the populations of B. distachyon and B. hybridum. The index of Mediterraneity and altitude explained 70.56 % of the total variation associated with the first axis. A trend was seen towards a greater presence of B. distachyon forms in areas of the Peninsular interior and higher altitude, with the B. hybridum forms more common in regions of greater summer rainfall and a lower index of Mediterraneity.  相似文献   

10.
We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area.  相似文献   

11.
Jian-Li Zhao  Tianhua He  Qiao-Ming Li 《Genetica》2010,138(9-10):939-944
Trees of the Magnoliaceae family are of scientific, cultural and socio-economic importance. Kmeria septentrionalis Dandy (Magnoliaceae) is a dioecious tree, found in small, isolated, relic populations in Southern China, and is subject to extensive protection due to its rarity and high economic values. To improve conservation outcomes and in particular, germplasm collection guidelines, information on spatial genetic structure of the species is required. In this study, we investigated the spatial genetic structure and genetic diversity of 161 individuals of K. septentrionalis collected from five natural populations using AFLP molecular markers. Within-population genetic variation was measured, with percentage of polymorphic bands (PPB) ranged from 63% to 87%, while H S (genetic diversity within population) varied from 0.185 to 0.244 with a mean of 0.215 ± 0.025. Significant genetic differentiations were revealed between pairwise populations, indicating each population existing as an independent evolutionarily significant unit. Mantel test results showed no pattern of isolation-by-distance among populations separated by large distance. Fine scale spatial patterns of genetic variation suggested significant effects of isolation-by-distance within population at distances of 22 m. The results of contrasting genetic structure at coarse and fine scale in K. septentrionalis may indicate restricted pollen flow and seed dispersal at fine scales, and separated evolution in isolated populations over long period of time at coarser scales. Finally, we make several suggestions for improved management practices that may assist in the conservation of this species.  相似文献   

12.
We studied the population genetic and clonal structure of the endangered long-lived perennial plant Narcissus pseudonarcissus using random amplified polymorphic markers. Estimates for mean gene diversity within 15 populations of N. pseudonarcissus of three neighbouring geographical regions were high in comparison to other long-lived perennials (H eN = 0.33). The genetic diversity of the two smallest populations (<200 plants) was significantly reduced, indicating loss of genetic variability due to drift. The analysis of the population genetic structure revealed a significant genetic differentiation both between regions (ΦST = 0.06) and between populations within regions (ΦST = 0.20). However, there was incomplete correspondence between geographical regions and the population genetic structure. In order to preserve the overall genetic variation in wild populations of N. pseudonarcissus, management measures should thus aim to protect many populations in each region. The spatial genetic structure within populations of N. pseudonarcissus was in agreement with an isolation by distance model indicating limited gene flow due to pollinator behaviour and restricted seed dispersal. The very restricted spatial extent of clonal growth (<5 cm) and the high level of clonal diversity indicate that clonal growth in N. pseudonarcissus is not an important mode of propagation and that management measures should favour sexual reproduction in order to avoid further reductions in the size and number of populations.  相似文献   

13.
Tricyrtis ishiiana is a relic endemic plant taxon of the Convallariaceae that inhabits two nearby gorges in Kanagawa Prefecture, Japan. The distribution range and number of populations are thought to have been reduced to the present refugial populations during the Quaternary climatic oscillations. Because of its showy flowers, this plant has faced illegal removal from its natural habitats for horticultural use and has been designated a critically endangered species (class IA). In this study, we analyzed the genetic structure of the relict populations of T. ishiiana in order to contribute to the conservation strategies of the prefectural government. Our analyses of nine nuclear microsatellite loci detected high genetic diversity (H E = 0.704 and H O = 0.541) for the two populations. The two populations were slightly differentiated (R ST = 0.032), accompanied by faint substructure across the populations (K = 3). In addition, each population exhibited spatial genetic structuring. The relatively low inbreeding coefficient for both populations together (F IS = 0.233) and each population separately (F IS = 0.217?C0.246) may be attributable to crossing among descendants within a population along with occasional gene flow between the populations. These results suggested that the extant populations have not experienced a severe bottleneck. The two extant populations were genetically differentiated at a very low level, accompanied by occasional pollen flow via pollinators and/or seed dispersal by gravity in the mountainous environment. Occasional gene exchange between the populations has allowed T. ishiiana to harbor high genetic diversity despite being a relic plant confined to two small refugial populations.  相似文献   

14.
The shrub Rosa rugosa (Japanese Rose), native to East Asia, is considered one of the most troublesome invasive plant species in natural or semi-natural habitats of northern Europe and has proven very difficult to control. We aimed at disentangling the species’ invasion history in Europe, including determining the number of introductions and their geographic origin, and at investigating whether populations in the introduced and native ranges differ in genetic diversity, structure and degree of differentiation. We found that introduced (n = 16) and native (n = 16) populations had similar levels of genetic diversity at seven nuclear SSR (microsatellite) loci. European populations lack isolation by distance and are less genetically differentiated than are populations in East Asia. Multiple and at least three independent colonization events, one of which was particularly successful, gave rise to current R. rugosa populations in Europe. The geographic distribution patterns of these three genetic clusters could not be explained by natural dispersal alone, indicating that human mediated secondary dispersal is driving the expansion in Europe. One cluster representing three of the European populations was most likely derived from NW Japan, whereas the origin of the remaining thirteen populations could not clearly be resolved. The introduction and expansion in Europe occurred with no significant loss of genetic diversity. We conclude that high propagule pressure at the primary establishment phase is the most parsimonious explanation for this pattern. A potential for long distance seed dispersal, coastal habitat connectivity and an outcrossing breeding system are factors likely to have enabled populations of R. rugosa to avoid detrimental effects of genetic bottlenecks and will further increase the species’ range size and abundance in Europe. We recommend that human-mediated dispersal should be prevented in order to halt the continued expansion.  相似文献   

15.
The lark sparrow (Chondestes grammacus) is a ground-nesting passerine that breeds across much of the central North American steppe and sand barrens. Through genotyping and sequencing of avian malaria parasites we examined levels of malaria prevalence and determined the distribution of Haemoproteus and Plasmodium lineages across the breeding range of the lark sparrow. Analysis of 365 birds collected from five breeding locations revealed relatively high levels of malaria prevalence in adults (80 %) and juveniles (46 %), with infections being primarily of Haemoproteus (91 % of sequenced samples). Levels of genetic diversity and genetic structure of malaria parasites with respect to the avian host populations revealed distinct patterns for Haemoproteus and Plasmodium, most likely as a result of their distinct life histories, host specificity, and transmission vectors. With the exception of one common Haemoproteus haplotype detected in all populations, all other haplotypes were either population-specific or shared by two to three populations. A hierarchical analysis of molecular variance of Haemoproteus sequences revealed that 15–18 % of the genetic variation can be explained by differences among host populations/locations (p < 0.001). In contrast to the regional patterns of genetic differentiation detected for the lark sparrow populations, Haemoproteus parasites showed high levels of population-specific variation and no significant differences among regions, which suggests that the population dynamics of the parasites may be driven by evolutionary processes operating at small spatial scales (e.g., at the level of host populations). These results highlight the potential effects of host population structure on the demographic and evolutionary dynamics of parasites.  相似文献   

16.
The bare-faced curassow (Crax fasciolata) is a large Neotropical bird that suffers anthropogenic pressure across much of its range. A captive population is maintained for conservation management, although there has been no genetic screening of stocks. Based on the six microsatellite markers developed for Crax globulosa, the genetic variability of C. fasciolata and possible differences between a wild and a captive population were investigated. Only three loci were polymorphic, with a total of 27 alleles. More than half of these alleles were private to the wild (n = 8) or captive (n = 7) populations. Significant deviations from Hardy–Weinberg equilibrium were restricted to the captive population. Despite the number of private alleles, genetic drift has probably promoted differentiation between populations. Our results indicate that wild C. fasciolata populations are genetically impoverished and structured, but species-specific microsatellite markers will be necessary for a more reliable assessment of the species’ genetic diversity.  相似文献   

17.
With increasing temperature and anthropogenic activity, endangered alpine species in the high altitudes of the Qinghai-Tibet Plateau face high risk of extinction; however, they have received little attention in the past. In this study, we used 12 nuclear and nine chloroplast microsatellites (simple sequence repeats, SSR) to assess genetic diversity within and among the only two populations of the highly endangered alpine species Sinadoxa corydalifolia (Adoxaceae). We identified only one individual exhibiting clonal reproduction across all 160 extant plants. The levels of genetic variability were estimated to be very low, with the allele number Na = 3.2 and the expected heterozygosity He = 0.368. The genetic differentiation is extremely high between the two regional populations (FST = 0.214), with a limited rate of gene flow in the recent past. In addition, numerous endemic alleles were found for each subpopulation within each population. Our analyses suggest that it is critical not only to conserve all surviving individuals of the two populations in situ but also to mediate gene flow artificially between subpopulations within each population in this endangered species.  相似文献   

18.
Effects of pond size and isolation on total vascular plant species richness and number of obligate wetland species were compared. Subsequently, the potential for the presence of spatial patterns in wetland species distribution among ponds in an agricultural landscape was explored. Relationships between species richness and two main biogeographic parameters were analysed using simple and multiple linearised regression models. Spatial patterns were looked for by means of analyses carried out with the R CRAN software (join-count statistics). Simple regression analyses performed on the regional scale (n = 50) revealed the significance of the effect of pond size only (r = 0.46 for total plant species richness and r = 0.28 for wetland species richness vs. pond area). Further analyses conducted on the local scale identified the best multiple regression models in the largest pond cluster (n = 20); the models showed statistical significance of relationships between the species richness and both independent variables (r = 0.80 for total plant species richness and r = 0.70 for wetland species richness vs. pond area and isolation, including mean distance to the nearest ten ponds). Spatial analyses were performed for 26 obligate wetland species selected from 149 species recorded in all the 50 ponds. Exploratory spatial data analysis revealed the presence of significant positive spatial autocorrelation in the distribution of 8 species. In such cases, it is possible to reject the random distribution hypothesis, which justifies exploration of spatial regimes. In practice, correct spatial model specifications may have implications for predicting species occurrences under changing environmental conditions, e.g. changes in the number of ponds.  相似文献   

19.
20.
When habitat becomes fragmented, populations of species may become increasingly isolated. In the absence of habitat corridors, genetic structure may develop and populations risk reductions in genetic diversity from increased genetic drift and inbreeding. Deforestation of the Cerrado biome of Brazil, particularly of the dry forests within the Paranã River Basin, has incrementally occurred since the 1970s and increased forest fragmentation within the region. We performed landscape genetic analyses of Pfrimer’s parakeet (Pyrrhura pfrimeri), a globally endangered endemic to the region, to determine if forest fragmentation patterns were associated with genetic structuring in this species. We used previously generated satellite imagery that identified the locations of Paranã River Basin forest fragments in 1977, 1993/94, and 2008. Behavioral data quantifying the affinity of Pfrimer’s parakeet for forest habitat was used to parameterize empirically derived landscape conductance surfaces. Though genetic structure was observed among Pfrimer’s parakeet populations, no association between genetic and geographic distance was detected. Likewise, least cost path lengths, circuit theory-based resistance distances, and a new measure of least cost path length complexity could not be conclusively associated with genetic structure patterns. Instead, a new quantity that encapsulated connection redundancy from the 1977 forest fragmentation data provided the clearest associations with pairwise genetic differentiation patterns (Jost’s D: r = 0.72, P = 0.006; FST: r = 0.741, P = 0.001). Our analyses suggest a 35-year or more lag between deforestation and its effect on genetic structure. Because 66 % of the Paranã River Basin has been deforested since 1977, we expect that genetic structure will increase substantially among Pfrimer’s Parakeet populations in the future, especially if fragmentation continues at its current pace.  相似文献   

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