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1.
Intra-deme molecular diversity in spatially expanding populations   总被引:23,自引:0,他引:23  
We report here a simulation study examining the effect of a recent spatial expansion on the pattern of molecular diversity within a deme. We first simulate a range expansion in a virtual world consisting in a two-dimensional array of demes exchanging a given proportion of migrants (m) with their neighbors. The recorded demographic and migration histories are then used under a coalescent approach to generate the genetic diversity in a sample of genes. We find that the shape of the gene genealogies and the overall pattern of diversity within demes depend not only on the age of the expansion but also on the level of gene flow between neighboring demes, as measured by the product Nm, where N is the size of a deme. For small Nm values (< approximately 20 migrants sent outwards per generation), a substantial proportion of coalescent events occur early in the genealogy, whereas with larger levels of gene flow, most coalescent events occur around the time of the onset of the spatial expansion. Gene genealogies are star shaped, and mismatch distributions are unimodal after a range expansion for large Nm values. In contrast, gene genealogies present a mixture of both very short and very long branch lengths, and mismatch distributions are multimodal for small Nm values. It follows that statistics used in tests of selective neutrality like Tajima's D statistic or Fu's F(S) statistic will show very significant negative values after a spatial expansion only in demes with high Nm values. In the context of human evolution, this difference could explain very simply the fact that analyses of samples of mitochondrial DNA sequences reveal multimodal mismatch distributions in hunter-gatherers and unimodal distributions in post-Neolithic populations. Indeed, the current simulations show that a recent increase in deme size (resulting in a larger Nm value) is sufficient to prevent recent coalescent events and thus lead to unimodal mismatch distributions, even if deme sizes (and therefore Nm values) were previously much smaller. The fact that molecular diversity within deme is so dependent on recent levels of gene flow suggests that it should be possible to estimate Nm values from samples drawn from a single deme.  相似文献   

2.
In cyclic populations, high genetic diversity is currently reported despite the periodic low numbers experienced by the populations during the low phases. Here, we report spatio-temporal monitoring at a very fine scale of cyclic populations of the fossorial water vole (Arvicola terrestris) during the increasing density phase. This phase marks the transition from a patchy structure (demes) during low density to a continuous population in high density. We found that the genetic diversity was effectively high but also that it displayed a local increase within demes over the increasing phase. The genetic diversity remained relatively constant when considering all demes together. The increase in vole abundance was also correlated with a decrease of genetic differentiation among demes. Such results suggest that at the end of the low phase, demes are affected by genetic drift as the result of being small and geographically isolated. This leads to a loss of local genetic diversity and a spatial differentiation among demes. This situation is counterbalanced during the increasing phase by the spatial expansion of demes and the increase of the effective migration among differentiated demes. We provide evidences that in cyclic populations of the fossorial water voles, the relative influence of drift operating during low density populations and migration occurring principally while population size increases interacts closely to maintain high genetic diversity.  相似文献   

3.
Wegmann D  Currat M  Excoffier L 《Genetics》2006,174(4):2009-2020
Recent range expansions have probably occurred in many species, as they often happen after speciation events, after ice ages, or after the introduction of invasive species. While it has been shown that range expansions lead to patterns of molecular diversity distinct from those of a pure demographic expansion, the fact that many species do live in heterogeneous environments has not been taken into account. We develop here a model of range expansion with a spatial heterogeneity of the environment, which is modeled as a gamma distribution of the carrying capacities of the demes. By allowing temporal variation of these carrying capacities, our model becomes a new metapopulation model linking ecological parameters to molecular diversity. We show by extensive simulations that environmental heterogeneity induces a loss of genetic diversity within demes and increases the degree of population differentiation. We find that metapopulations with low average densities are much more affected by environmental heterogeneity than metapopulations with high average densities, which are relatively insensitive to spatial and temporal variations of the environment. Spatial heterogeneity is shown to have a larger impact on genetic diversity than temporal heterogeneity. Overall, temporal heterogeneity and local extinctions are not found to leave any specific signature on molecular diversity that cannot be produced by spatial heterogeneity.  相似文献   

4.
Currently many attempts are made to reconstruct the colonization history of plant species after the last ice age. A surprising finding is that during the colonization phase genetic diversity did not decrease as much as expected. In this paper we examine whether long distance seed dispersal events could play a role in the unexpected maintenance of genetic diversity during range expansion. This study is based on simulations carried out with a maternally inherited haploid locus using a cellular automaton. The simulations reveal a close relationship between the frequency of long distance seed dispersal events and the amount of genetic diversity preserved during colonization. In particular, when the colonized region is narrow, a complete loss of genetic diversity results from the occurrence of very rare long distance dispersal (LDD) events. We call this phenomenon the 'embolism effect'. However, slightly higher rates of LDD events reverse this effect, up to the point that diversity is better preserved than in a pure diffusion model. This phenomenon is linked to the reorganization of the genetic structure during colonization and is called the 'reshuffling effect'.  相似文献   

5.
Rapid range expansions can cause pervasive changes in the genetic diversity and structure of populations. The postglacial history of the Balsam Poplar, Populus balsamifera, involved the colonization of most of northern North America, an area largely covered by continental ice sheets during the last glacial maximum. To characterize how this expansion shaped genomic diversity within and among populations, we developed 412 SNP markers that we assayed for a range‐wide sample of 474 individuals sampled from 34 populations. We complemented the SNP data set with DNA sequence data from 11 nuclear loci from 94 individuals, and used coalescent analyses to estimate historical population size, demographic growth, and patterns of migration. Bayesian clustering identified three geographically separated demes found in the Northern, Central, and Eastern portions of the species’ range. These demes varied significantly in nucleotide diversity, the abundance of private polymorphisms, and population substructure. Most measures supported the Central deme as descended from the primary refuge of diversity. Both SNPs and sequence data suggested recent population growth, and coalescent analyses of historical migration suggested a massive expansion from the Centre to the North and East. Collectively, these data demonstrate the strong influence that range expansions exert on genomic diversity, both within local populations and across the range. Our results suggest that an in‐depth knowledge of nucleotide diversity following expansion requires sampling within multiple populations, and highlight the utility of combining insights from different data types in population genomic studies.  相似文献   

6.
Classical models of structured populations do not apply well to species leaving in semilinear habitats such as freshwater fishes, since these habitats are intermediate between one‐dimensional and two‐dimensional stepping‐stone models. In order to investigate the genetic diversity of such populations, we have developed a new simulation program called aquasplatche . It starts by dividing a user‐defined vectorized network into segments of arbitrary length, each segment hosting a single deme. The program then proceeds by simulating the colonization of the environment from an arbitrary source, recording the evolution of the deme densities and the migration events between adjacent demes over time. This demographic history is then used to generate genetic data of population samples located in various segments of the network, using a backward coalescent framework. Different versions of aquasplatche are freely available on http://cmpg.unibe.ch/software/aquasplatche .  相似文献   

7.
For a species rapidly expanding its geographic range, such as during biological invasion, most alleles in the introduced range will have their evolutionary origins in the native range. Yet, the way in which historical processes occurring over evolutionary time in the native range contribute to the diversity sampled during contemporary invasion is largely unknown. We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S. vulgaris. We examined how phylogenetic diversity was shaped by demographic growth and historical range expansions in the native European range, and how this history affected the diversity sampled during their recent invasion of North America. Genealogies from both species depart from neutrality, likely as a result of demographic expansion in the ancestral range, the timing of which corresponds to shortly after each species originated. However, the species differ in the spatial distribution of cpDNA lineages across the native range. Silene latifolia shows a highly significant phylogeographic structure that most likely reflects different avenues of the post-glacial expansion into northern Europe from Mediterranean refugia. By contrast, cpDNA lineages in S. vulgaris have been widely scattered across Europe during, or since, the most recent post-glacial expansion. These different evolutionary histories resulted in dramatic differences in how phylogenetic diversity was sampled during invasion of North America. In S. latifolia, relatively few, discrete invasion events from a structured native range resulted in a rather severe genetic bottleneck, but also opportunities for admixture among previously isolated lineages. In S. vulgaris, lack of genetic structure was accompanied by more representative sampling of phylogenetic diversity during invasion, and reduced potential for admixture. Our results provide clear insights into how historical processes may feed forward to influence the phylogenetic diversity of species invading new geographic ranges.  相似文献   

8.
The reduced immigration and emigration rates resulting from the lack of landscape connectivity of patches and the hospitality of the intervening matrix could favor the loss of alleles through genetic drift and an increased chance of inbreeding. In order for isolated populations to maintain sufficient levels of genetic diversity and adapt to environmental changes, one important conservation goal must be to preserve or reestablish connectivity among patches in a fragmented landscape. We studied the last known population of Ambystoma leorae, an endemic and critically threatened species. The aims of this study were: (1) to assess the demographic parameters of A. leorae and to distinguish and characterize the microhabitats in the river, (2) to determine the number of existing genetic groups or demes of A. leorae and to describe possible relationships between microhabitats types and demes, (3) to determine gene flow between demes, and (4) to search for geographic locations of genetic discontinuities that limit gene flow between demes. We found three types of microhabitats and three genetically differentiated subpopulations with a significant level of genetic structure. In addition, we found slight genetic barriers. Our results suggest that mole salamander’s species are very sensitive to microhabitat features and relatively narrow obstacles in their path. The estimates of bidirectional gene flow are consistent with the pattern of a stepping stone model between demes, where migration occurs between adjacent demes, but there is low gene flow between distant demes. We can also conclude that there is a positive correlation between microhabitats and genetic structure in this population.  相似文献   

9.
Lichens associated with old forest are commonly assumed to be negatively affected by tree logging or natural disturbances. However, in this study performed in a spruce-dominated sylvopastoral landscape in the Swiss Jura Mountains, we found that genetic diversity of the epiphytic old-forest lichen Lobaria pulmonaria depends on the type of disturbance. We collected 923 thalli from 41 sampling plots of 1 ha corresponding to the categories stand-replacing disturbance (burnt), intensive logging (logged) and uneven-aged forestry (uneven-aged), and analysed the thalli at six mycobiont-specific microsatellite loci. We found evidence for multiple independent immigrations into demes located in burnt and logged areas. Using spatial autocorrelation methods, the spatial scale of the genetic structure caused by the clonal and recombinant component of genetic variation was determined. Spatial autocorrelation of genotype diversity was strong at short distances up to 50 m in logged demes, up to 100 m in uneven-aged demes, with the strongest autocorrelation up to 150 m for burnt demes. The spatial autocorrelation was predominantly attributed to clonal dispersal of vegetative propagules. After accounting for the clonal component, we did not find significant spatial autocorrelation in gene diversity. This pattern may indicate low dispersal ranges of clonal propagules, but random dispersal of sexual ascospores. Genetic diversity was highest in logged demes, and lowest in burnt demes. Our results suggest that genetic diversity of epiphytic lichen demes may not necessarily be impacted by stand-level disturbances for extended time periods.  相似文献   

10.
In a metapopulation, the process of recurrent local extinction and recolonization gives rise to an age structure among demes. Recently established demes will tend to differ from older demes in terms of the levels of genetic diversity found within them and the way this diversity is distributed among demes in the same and different ages. The effects of population turnover on average levels of genetic diversity among demes in a metapopulation have been the focus of much attention, both for neutral and nonneutral loci, but much less is known about the distribution of nonneutral genetic diversity among demes of different ages. In this paper, we used computer simulations to study the distribution of genetic load, inbreeding depression and heterosis in an age‐structured metapopulation. We found that, for mildly deleterious mutations, within‐deme inbreeding depression increased, whereas heterosis and genetic load decreased with deme age following severe colonization bottlenecks. In contrast, recessive lethal alleles tended to be purged during colonization, with older populations showing higher genetic load and higher within‐deme inbreeding depression. Heterosis caused by recessive lethal alleles and resulting from gene flow among different demes tended to be greatest for young demes, because the mutations responsible tended to be purged in the first few generations after colonization, but its effects increased again as populations grow older as a result of immigration. Our results point to a need for estimates of genetic diversity, genetic load, within‐deme inbreeding depression and heterosis in demes of different age classes separately.  相似文献   

11.
The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species’ dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large ‘central’ population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations.  相似文献   

12.
For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion, while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to postglacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial data set encompassing 23 previously identified lineages from all seven marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian model averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.  相似文献   

13.
Human dispersal of organisms is an important process modifying natural patterns of biodiversity. Such dispersal generates new patterns of genetic diversity that overlie natural phylogeographical signatures, allowing discrimination between alternative dispersal mechanisms. Here we use allele frequency and DNA sequence data to distinguish between alternative scenarios (unassisted range expansion and long range introduction) for the colonization of northern Europe by an oak-feeding gallwasp, Andricus kollari. Native to Mediterranean latitudes from Portugal to Iran, this species became established in northern Europe following human introduction of a host plant, the Turkey oak Quercus cerris. Colonization of northern Europe is possible through three alternative routes: (i) unassisted range expansion from natural populations in the Iberian Peninsula; (ii) unassisted range expansion from natural populations in Italy and Hungary; or (iii) descent from populations imported to the UK as trade goods from the eastern Mediterranean in the 1830s. We show that while populations in France were colonized from sources in Italy and Hungary, populations in the UK and neighbouring parts of coastal northern Europe encompass allozyme and sequence variation absent from the known native range. Further, these populations show demographic signatures expected for large stable populations, rather than signatures of rapid population growth from small numbers of founders. The extent and spatial distribution of genetic diversity in the UK suggests that these A. kollari populations are derived from introductions of large numbers of individuals from each of two genetically divergent centres of diversity in the eastern Mediterranean. The strong spatial patterning in genetic diversity observed between different regions of northern Europe, and between sites in the UK, is compatible with leptokurtic models of population establishment.  相似文献   

14.
There is an increasing recognition that long distance dispersal (LDD) plays a key role in establishing spatial genetic structure during colonization. Recent works, focused on short distance dispersal, demonstrated that a neutral mutation arising at the colonization front can either ‘surf’ with the wave front and reach high frequencies or stay near its place of origin at low frequencies. Here, we examine how LDD, and more generally the shape of the dispersal kernel, modifies this phenomenon and how the width of the colonization corridor affects the fate of the mutation. We demonstrate that when LDD events are more frequent, the ‘surfing phenomenon’ is less frequent, probably because any alleles can get far ahead from the colonization front and preclude the invasion by others alleles, thus leading to an attenuation of the diversity loss. We also demonstrate that the width of the colonization corridor influences the fate of the mutation, wide spaces decreasing the probability of invasion. Overall, the genetic structure of diversity resulted not only from LDD but also particularly from the shape of the dispersal kernel.  相似文献   

15.
Climate is an important factor limiting species distributions. Historic climate‐change related range movements have modified the genetic diversity of species by the merging and splitting of gene pools and by the effects associated with recurrent founder events. These effects are often inferred, either from retrospective analyses of current genetic patterns or from simulations. Rarely has it been possible for the population genetic effects of range expansion to be examined with contemporaneous demographic data. We characterized the genetic signature of rapid range expansion by southern flying squirrels (Glaucomys volans) and compared these results to a stationary population of the closely related northern flying squirrel (Glaucomys sabrinus) in Ontario, Canada. Samples were taken during an approximately 200 km range expansion by G. volans (1994–2003) and genotyped at 6 (G. sabrinus) and 8 (G. volans) microsatellite loci. For G. volans, but not G. sabrinus, we found evidence of a latitudinal gradient in allele frequencies and a decrease in allelic richness along the axis of expansion. We found no evidence of isolation‐by‐distance in either species or of genetic bottlenecks in the area of G. volans expansion. These results suggest that serial founder events can cause an immediate reduction in genetic diversity following rapid range expansion with high levels of gene flow giving rise to heterogeneity within what would classically be termed panmixia. Given the pace of anthropogenic climate change, and the increasing incidence of range movements in response, this may be an important, immediate consequence of climate change.  相似文献   

16.
Recovery of natural populations occurs often with simultaneous or subsequent range expansions. According to population genetic theory, genetic structuring emerges at the expansion front together with decreasing genetic diversity, owing to multiple founder events. Thereupon, as the expansion proceeds and connectivity among populations is established, homogenization and a resurgence of genetic diversity are to be expected. Few studies have used a fine temporal scale combined with genetic sampling to track range expansions as they proceed in wild animal populations. As a natural experiment, the historical eradication of large terrestrial carnivores followed by their recovery and recolonization may facilitate empirical tests of these ideas. Here, using brown bear (Ursus arctos) as model species, we tested predictions from genetic theory of range expansion. Individuals from all over Finland were genotyped for every year between 1996 and 2010 using 12 validated autosomal microsatellite markers. A latitudinal shift of about 110 km was observed in the distribution and delineation of genetic clusters during this period. As the range expansion proceeded, we found, as theory predicts, that the degree of genetic structure decreased, and that both genetic variation and admixture increased. The genetic consequences of range expansions may first be detected after multiple generations, but we found major changes in genetic composition after just 1.5 generations, accompanied by population growth and increased migration. These rapid genetic changes suggest an ongoing concerted action of geographical and demographic expansion combined with substantial immigration of bears from Russia during the recovery of brown bears within the large ecosystem of northern Europe.  相似文献   

17.
Schug MD  Smith SG  Tozier-Pearce A  McEvey SF 《Genetics》2007,175(3):1429-1440
Information about genetic structure and historical demography of natural populations is central to understanding how natural selection changes genomes. Drosophila ananassae is a widespread species occurring in geographically isolated or partially isolated populations and provides a unique opportunity to investigate population structure and molecular variation. We assayed microsatellite repeat-length variation among 13 populations of D. ananassae to assess the level of structure among the populations and to make inferences about their ancestry and historic biogeography. High levels of genetic structure are apparent among all populations, particularly in Australasia and the South Pacific, and patterns are consistent with the hypothesis that the ancestral populations are from Southeast Asia. Analysis of population structure and use of F-statistics and Bayesian analysis suggest that the range expansion of the species into the Pacific is complex, with multiple colonization events evident in some populations represented by lineages that show no evidence of recent admixture. The demographic patterns show isolation by distance among populations and population expansion within all populations. A morphologically distinct sister species, D. pallidosa, collected in Malololelei, Samoa, appears to be more closely related to some of the D. ananassae populations than many of the D. ananassae populations are to one another. The patterns of genotypic diversity suggest that many of the individuals that we sampled may be morphologically indistinguishable nascent species.  相似文献   

18.
Species invading new ranges are subject to a series of demographic events that can strongly shape genetic diversity. Describing this demographic history is important for understanding where invasive species come from and how they spread, and is critical to testing hypotheses of postinvasion adaptation. Here, we analyse nuclear and chloroplast genetic diversity to study the invasion history of the widespread colonizing weed, Silene latifolia (Caryophyllaceae). Bayesian clustering and PCA revealed strong population structure in the native range of Europe, and although genotypes from multiple native sources were present in the introduced range of North America, the spatial distribution of genetic variance was dramatically reorganized. Using approximate Bayesian computation (ABC), we compared support for different invasion scenarios, including the number and size of independent introduction events and the amount of admixture occurring between sources of introduced genotypes. Our results supported independent introductions into eastern and western North America, with the latter forming a bridgehead for a secondary invasion into the Great Lakes region of central North America. Despite small estimated founder population sizes, the duration of the demographic bottleneck after the initial introduction appeared extremely short‐lived. This pattern of repeated colonization and rapid expansion has effectively eroded the strong population structure and cytonuclear associations present in Europe, but has retained overall high genetic diversity since invasion. Our results highlight the flexibility of the ABC approach for constructing a narrative of the demographic history of species invasions and provide baseline for future studies of evolutionary changes in introduced S. latifolia populations.  相似文献   

19.
Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase F ST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. F ST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.  相似文献   

20.
Climatic and oceanographic events occurring during the last glacial cycle in the Humboldt Current System (HCS) have left genetic footprints in marine invertebrate populations. The objective of this study was to evaluate the effect of the glacial period on Octopus mimus populations found throughout the HCS. This species lays a large number of small eggs which hatch into planktonic paralarvae with the potential to undergo wide dispersal. We sequenced the COIII gene to perform phylogeographic analyses of 197 octopuses sampled from seven localities. The genetic diversity of Octopus mimus was low and decreased towards the southern end of the distribution range, which comprises a single population. The haplotype genealogy and Bayesian Skyride plot suggest that O. mimus underwent a demographic expansion after the last glacial maximum (LGM). This would imply a contraction of the range of this organism toward northern latitudes during the LGM followed by southward expansion and recolonization once the contemporary interglacial period began.  相似文献   

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