Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (Picea abies K.).

Three chloroplast microsatellites (cpSSRs), previously sequence characterized and for which paternal inheritance was tested and confirmed, were used to assess their usefulness as informative markers for phylogeographic studies in Norway spruce (Picea abies K.) and to detect spatial genetic differentiation related to the possible recolonization processes in the postglacial period. Ninety-seven populations were included in the survey. Some 8, 7, and 6 different size variants for the three cpSSRs, respectively, were scored by analysing 1105 individuals. The above 21 variants combined into 41 different haplotypes. The distribution of some haplotypes showed a clear geographic structure and seems to be related to the existence of different refugia during the last glacial period. The analysis of chloroplast SSR variation detected the presence of two main gene pools (Sarmathic-Baltic and Alpine--Centre European) and a relatively low degree of differentiation (RST of about 10%), characteristic of tree species with large distribution and probably influenced by an intensive human impact on this species. Based on our data, we were not able to detect any evidence concerning the existence of additional gene pools (e.g., from Balkan and Carpathian glacial refugia), though we cannot exclude the existence of genetic discontinuity within the species' European range. A large proportion of population-specific haplotypes were scored in this species, thus indicating a possible usefulness of these markers for the identification of provenances, seed-lots, and autochthonous stands.     

Population history and gene dispersal inferred from spatial genetic structure of a Central African timber tree,Distemonanthus benthamianus (Caesalpinioideae)

African rainforests have undergone major distribution range shifts during the Quaternary, but few studies have investigated their impact on the genetic diversity of plant species and we lack knowledge on the extent of gene flow to predict how plant species can cope with such environmental changes. Analysis of the spatial genetic structure (SGS) of a species is an effective method to determine major directions of the demographic history of its populations and to estimate the extent of gene dispersal. This study characterises the SGS of an African tropical timber tree species, Distemonanthus benthamianus, at various spatial scales in Cameroon and Gabon. Displaying a large continuous distribution in the Lower Guinea domain, this is a model species to detect signs of past population fragmentation and recolonization, and to estimate the extent of gene dispersal. Ten microsatellite loci were used to genotype 295 adult trees sampled from eight populations. Three clearly differentiated gene pools were resolved at this regional scale and could be linked to the biogeographical history of the region, rather than to physical barriers to gene flow. A comparison with the distribution of gene pools observed for two other tree species living in the same region invalidates the basic assumption that all species share the same Quaternary refuges and recolonization pathways. In four populations, significant and similar patterns of SGS were detected. Indirect estimates of gene dispersal distances (sigma) obtained for three populations ranged from 400 to 1200 m, whereas neighbourhood size estimates ranged from 50 to 110.     

Efficient long-distance gene flow into an isolated relict oak stand

Geographically isolated and small populations outside a species' central distribution range are likely to be of major importance to a species' ability to quickly adjust its distribution range to global change dynamics. Gene flow from the outside plays a pivotal role in the fate of these marginal populations. It has been proposed that spatial fragmentation and perceived geographic isolation do not necessarily reflect a loss of genetic connectivity in tree species. However, the spatial limits of long-distance gene flow, as well as its magnitude and impact, are still generally unknown. In the present study, we analyzed long-distance pollen-mediated gene flow into an isolated relict stand consisting of 7 individuals of Quercus robur L. based on a total sample of 177 trees and 9 microsatellite loci. We show that pollen-mediated gene flow across more than 80 km in this wind-pollinated tree species contributed at least 35% of all successful pollinations in the investigated isolated and small oak stand at the eastern limit of the species' distribution. The observed pollen immigration shaped the genetic diversity of acorn progenies in the stand and might explain the comparably high genetic diversity in the persisting adult population.     

Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus)

Geographic distributions of most temperate marine fishes are affected by postglacial recolonisation events, which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species' distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed significant isolation by distance and a complex population structure across the species' distribution (overall θ(ST)=0.038, P<0.01). Across transition zones markers indicated larger effects of genetic drift over mutations in the northern distribution of sprat contrasting a stronger relative impact of mutation in the species' southern distribution in the Mediterranean region. These results were interpreted to reflect more recent divergence times between northern populations in accordance with previous findings. This study demonstrates the usefulness of comparing inference from different markers and estimators of divergence for phylogeographic and population genetic studies in species with weak genetic structure, as is the case in many marine species.     

Climate‐driven range shifts explain the distribution of extant gene pools and predict future loss of unique lineages in a marine brown alga

The climate‐driven dynamics of species ranges is a critical research question in evolutionary ecology. We ask whether present intraspecific diversity is determined by the imprint of past climate. This is an ongoing debate requiring interdisciplinary examination of population genetic pools and persistence patterns across global ranges. Previously, contrasting inferences and predictions have resulted from distinct genomic coverage and/or geographical information. We aim to describe and explain the causes of geographical contrasts in genetic diversity and their consequences for the future baseline of the global genetic pool, by comparing present geographical distribution of genetic diversity and differentiation with predictive species distribution modelling (SDM) during past extremes, present time and future climate scenarios for a brown alga, Fucus vesiculosus. SDM showed that both atmospheric and oceanic variables shape the global distribution of intertidal species, revealing regions of persistence, extinction and expansion during glacial and postglacial periods. These explained the distribution and structure of present genetic diversity, consisting of differentiated genetic pools with maximal diversity in areas of long‐term persistence. Most of the present species range comprises postglacial expansion zones and, in contrast to highly dispersive marine organisms, expansions involved only local fronts, leaving distinct genetic pools at rear edges. Besides unravelling a complex phylogeographical history and showing congruence between genetic diversity and persistent distribution zones, supporting the hypothesis of niche conservatism, range shifts and loss of unique genetic diversity at the rear edge were predicted for future climate scenarios, impoverishing the global gene pool.     

Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia's arid zone, the golden perch (Macquaria ambigua)

Rivers provide an excellent system to study interactions between patterns of biodiversity structure and ecological processes. In these environments, gene flow is restricted by the spatial hierarchy and temporal variation of connectivity within the drainage network. In the Australian arid zone, this variability is high and rivers often exist as isolated waterholes connected during unpredictable floods. These conditions cause boom/bust cycles in the population dynamics of taxa, but their influence on spatial genetic diversity is largely unknown. We used a landscape genetics approach to assess the effect of hydrological variability on gene flow, spatial population structure and genetic diversity in an Australian freshwater fish, Macquaria ambigua. Our analysis is based on microsatellite data of 590 samples from 26 locations across the species range. Despite temporal isolation of populations, the species showed surprisingly high rates of dispersal, with population genetic structure only evident among major drainage basins. Within drainages, hydrological variability was a strong predictor of genetic diversity, being positively correlated with spring-time flow volume. We propose that increases in flow volume during spring stimulate recruitment booms and dispersal, boosting population size and genetic diversity. Although it is uncertain how the hydrological regime in arid Australia may change under future climate scenarios, management strategies for arid-zone fishes should mitigate barriers to dispersal and alterations to the natural flow regime to maintain connectivity and the species' evolutionary potential. This study contributes to our understanding of the influence of spatial and temporal heterogeneity on population and landscape processes.     

The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym)

A primary goal of molecular ecology is to understand the influence of abiotic factors on the spatial distribution of genetic variation. Features including altitudinal clines, topography and landscape characteristics affect the proportion of suitable habitat, influence dispersal patterns, and ultimately structure genetic differentiation among populations. We studied the effects of altitude and topography on genetic variation of long-toed salamanders (Ambystoma macrodactylum), a geographically widespread amphibian species throughout northwestern North America. We focused on 10 low altitude sites (< 1200 m) and 11 high-altitude sites in northwestern Montana and determined multilocus genotypes for 549 individuals using seven microsatellite loci. We tested four hypotheses: (1) gene flow is limited between high- and low-altitude sites; and, (2) gene flow is limited among high-altitude sites due to harsh habitat and extreme topographical relief between sites; (3) low-altitude sites exhibit higher among-site gene flow due to frequent flooding events and low altitudinal relief; and (4) there is a negative correlation between altitude and genetic variation. Overall F(ST) values were moderate (0.08611; P < 0.001). Pairwise F(ST) estimates between high and low populations and a population graphing method supported the hypothesis that low-altitude and high-altitude sites, taken together, are genetically differentiated from each other. Also as predicted, gene flow is more prominent among low-altitude sites than high-altitude sites; low-altitude sites had a significantly lower F(ST) (0.03995; P < 0.001) than high altitude sites (F(ST) = 0.10271; P < 0.001). Use of Bayesian analysis of population structure (BAPS) resulted in delineation of 10 genetic groups, two among low-altitude populations and eight among high-altitude populations. In addition, within high altitude populations, basin-level genetic structuring was apparent. A nonequilibrium algorithm for detecting current migration rates supported these population distinctions. Finally, we also found a significant negative correlation between genetic diversity and altitude. These results are consistent with the hypothesis that topography and altitudinal gradients shape the spatial distribution of genetic variation in a species with a broad geographical range and diverse life history. Our study sheds light on which key factors limit dispersal and ultimately species' distributions.     

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.     

Effects of seed dispersal on spatial genetic structure in populations of Rutidosis leptorrhychoides with different levels of correlated paternity

Rutidosis leptorrynchoides is a perennial forb endemic to grasslands and grassy woodlands in southeastern Australia. Studies of seed dispersal, spatial genetic structure and clonality were carried out in four populations around the Canberra region that varied in levels of correlated paternity to examine: (1) whether R. leptorrhynchoides populations exhibit fine-scale spatial genetic structure and whether this varies between populations as a function of correlated paternity; (2) whether there is a correlation between seed dispersal distance and genetic relatedness within populations; and (3) whether clonal reproduction occurs in this species and to what degree this could account for the observed spatial genetic structure. The results show that there is variation in the magnitude and extent of spatial genetic structure between R. leptorrhynchoides populations. The three larger populations, with low to moderate full-sib proportions, showed significant patterns of coancestry between plants over scales of up to one metre, whereas the smallest population, with a high full-sib proportion, had erratically high but non-significant coancestry values. The observed patterns of genetic clumping could be explained by a combination of limited seed dispersal and correlated mating owing to limited mate availability resulting from the species' sporophytic self-incompatibility system. Clonality does not appear to be an important factor contributing to genetic structure in this species.     

Projected climate changes threaten ancient refugia of kelp forests in the North Atlantic

Intraspecific genetic variability is critical for species adaptation and evolution and yet it is generally overlooked in projections of the biological consequences of climate change. We ask whether ongoing climate changes can cause the loss of important gene pools from North Atlantic relict kelp forests that persisted over glacial–interglacial cycles. We use ecological niche modelling to predict genetic diversity hotspots for eight species of large brown algae with different thermal tolerances (Arctic to warm temperate), estimated as regions of persistence throughout the Last Glacial Maximum (20,000 YBP), the warmer Mid‐Holocene (6,000 YBP), and the present. Changes in the genetic diversity within ancient refugia were projected for the future (year 2100) under two contrasting climate change scenarios (RCP2.6 and RCP8.5). Models predicted distributions that matched empirical distributions in cross‐validation, and identified distinct refugia at the low latitude ranges, which largely coincide among species with similar ecological niches. Transferred models into the future projected polewards expansions and substantial range losses in lower latitudes, where richer gene pools are expected (in Nova Scotia and Iberia for cold affinity species and Gibraltar, Alboran, and Morocco for warm‐temperate species). These effects were projected for both scenarios but were intensified under the extreme RCP8.5 scenario, with the complete borealization (circum‐Arctic colonization) of kelp forests, the redistribution of the biogeographical transitional zones of the North Atlantic, and the erosion of global gene pools across all species. As the geographic distribution of genetic variability is unknown for most marine species, our results represent a baseline for identification of locations potentially rich in unique phylogeographic lineages that are also climatic relics in threat of disappearing.     

Gene flow, historical population dynamics and genetic diversity within French Guianan populations of a rainforest tree species, Vouacapoua americana

Both gene flow and historical events influence the genetic diversity of natural populations. One way to understand their respective impact is to analyze population genetic structure at large spatial scales. We studied the distribution of genetic diversity of 17 populations of Vouacapoua americana (Caesalpiniaceae) in French Guiana, using nine microsatellite loci. Low genetic diversity was observed within populations, with a mean allelic richness and gene diversity of 4.1 and 0.506, respectively, which could be due to low effective population size and/or past bottlenecks. Using the regression between Fst/(1-Fst), estimated between pairs of populations, and the logarithm of the geographical distance, the spatial genetic structure can partly be explained by isolation-by-distance and limited gene flow among populations. This result is in agreement with the species' biology, including seed and pollen dispersal by rodents and insects, respectively. In contrast, no clear genetic signal of historical events was found when examining genetic differentiation among populations in relation to biogeographical hypotheses or by testing for bottlenecks within populations. Our conclusion is that nuclear spatial genetic structure of V. americana, at the geographic scale of French Guiana, is better explained by gene flow rather than by historical events.     

Drought survival strategies,dispersal potential and persistence of invertebrate species in an intermittent stream landscape

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Population differentiation in the open sea: insights from the pelagic copepod Pleuromamma xiphias

Although a number of recent studies of marine holoplankton have reported significant genetic structure among populations, little is currently known about the biological and oceanographic processes that influence population connectivity in oceanic plankton. In order to examine how depth preferences influence dispersal in oceanic plankton, I characterized the genetic structure of a copepod with diel vertical migration (DVM) (Pleuromamma xiphias), throughout its global distribution, and compared these results to those expected given the interaction of this species' habitat depth with ocean circulation and bathymetry. Mitochondrial COI sequences from 651 individuals from 28 sites in the Indian, Pacific, and Atlantic Oceans revealed highly significant genetic differentiation both within and among ocean basins. Limited dispersal among distinct pelagic provinces seems to have played a major role in population differentiation in this species, with strong genetic breaks observed across known oceanographic fronts or current systems in all three ocean basins. The Indo-West Pacific (IWP) holds a highly distinct genetic population of this species that was sampled in both the western Pacific and eastern Indian Oceans. This suggests that the IWP does not act as a strong barrier to gene flow between basins, as expected, despite the relatively shallow water depth (<200 m) and vertically extensive (>400 m) diel migration of this species. A pattern of isolation by distance was observed in the Indian Ocean with genetic differentiation among samples down to spatial scales of ～800 km, indicating that realized dispersal in P. xiphias occurs over much smaller spatial scales than in previously reported oceanic holoplankton. Given its highly regionalized population genetic structure, P. xiphias may have some capacity to adapt to local oceanographic conditions, and it should not be assumed that populations of this species in distinct pelagic biomes will respond in the same way to shared physical or climatic forcing.     

中国扁桃亚属四种野生扁桃的系统发育与物种分化

基于核基因ITS序列研究中国4种野生扁桃: 新疆野扁桃(Amygdalus ledebouriana)、蒙古扁桃(A. mongolica)、长柄扁桃(A. pedunculata)和西康扁桃(A. tangutica)的系统发育关系和物种分化, 为4种植物的遗传与演化研究提供数据支撑。利用单倍型网络和主坐标分析揭示单倍型的聚类关系; 利用最大似然树和贝叶斯系统树分析单倍型的系统发育关系; 利用R语言“ecospat”包分析4种扁桃的生态位分化及其环境驱动因子。4种扁桃ITS1-ITS4片段总长为634 bp, 鉴别出27个核苷酸变异位点, 共定义了28个单倍型。4种扁桃种间最小遗传距离均大于种内最大遗传距离, 种间存在显著的遗传分化。4种扁桃的单倍型聚为两支: 新疆野扁桃、蒙古扁桃和西康扁桃聚为一支, 长柄扁桃为另一支; 单倍型网络和主坐标分析揭示的单倍型聚类关系与系统树一致。西康扁桃与蒙古扁桃、与长柄扁桃之间均表现出了显著的生态位分化, 最暖月最高气温、年平均气温、最冷月最低气温和最暖季降水量是驱动物种生态位分化的关键因子。     

Plant dispersal in the sub-Antarctic inferred from anisotropic genetic structure

Climatic conditions and landscape features often strongly affect species' local distribution patterns, dispersal, reproduction and survival and may therefore have considerable impacts on species' fine-scale spatial genetic structure (SGS). In this study, we demonstrate the efficacy of combining fine-scale SGS analyses with isotropic and anisotropic spatial autocorrelation techniques to infer the impact of wind patterns on plant dispersal processes. We genotyped 1304 Azorella selago (Apiaceae) specimens, a wind-pollinated and wind-dispersed plant, from four populations distributed across sub-Antarctic Marion Island. SGS was variable with Sp values ranging from 0.001 to 0.014, suggesting notable variability in dispersal distance and wind velocities between sites. Nonetheless, the data supported previous hypotheses of a strong NW-SE gradient in wind strength across the island. Anisotropic autocorrelation analyses further suggested that dispersal is strongly directional, but varying between sites depending on the local prevailing winds. Despite the high frequency of gale-force winds on Marion Island, gene dispersal distance estimates (σ) were surprisingly low (<10 m), most probably because of a low pollen dispersal efficiency. An SGS approach in association with isotropic and anisotropic analyses provides a powerful means to assess the relative influence of abiotic factors on dispersal and allow inferences that would not be possible without this combined approach.     

Population structure in the endangered cyprinid fish Pararasbora moltrechti in Taiwan, based on mitochondrial and microsatellite DNAs

The genetic structure of four populations of Pararasbora moltrechti, an endemic species of the Cyprinidae in Taiwan, was investigated based on the genetic variation of mtDNA Cyt b gene and five microsatellite loci. High haplotype diversity (h = 0.92) but low nucleotide diversity (0.004) in mtDNA was detected in this endangered species. In total, 33 haplotypes and four clusters were identified in its mtDNA. Nevertheless, low correspondence was found between geographical division and mtDNA clusters. In contrast, Bayesian cluster analysis of the microsatellite data identified four genetic groups and revealed highly structured populations. Significantly negative Tajima's D statistics and mismatch distribution analyses suggest that P. moltrechti populations may have experienced a demographic expansion. In light of the results of a nested clade analysis of mtDNA haplotypes, we conclude that recent population fluctuations and restricted gene flow played major roles in shaping the spatial genetic structure of P. moltrechti populations.     

New interpretations of fine-scale spatial genetic structure

Recent methodological advances permit refined inferences of evolutionary processes from the fine-scale spatial genetic structure of plant populations. In this issue of Molecular Ecology, Born et al. (2008) exploit the full power of these methods by examining effects of ancient and recent landscape histories in an African rainforest tree species. The authors first detected admixture of distinct gene pools that may have formed in Pleistocene forest refuges. Then, comparing across six study populations in Gabon, the authors found similar patterns of fine-scale spatial genetic structure despite natural and anthropogenic variation in population density. The latter results suggest that enhanced gene dispersal may compensate for low population densities in fragmented landscapes.