A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants

Abstract.— Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable out crossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration.     

Does population size affect genetic diversity? A test with sympatric lizard species

Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations.     

Moisture variables, and not temperature, are responsible for climate filtering and genetic bottlenecks in the South African endemic terrestrial mollusc Prestonella (Orthalicoidea)

Non-vagile taxa such as terrestrial molluscs are susceptible to stochastic environmental events that can cause local extinctions or population declines, and extinctions of terrestrial mollusc species are among the highest documented. Many terrestrial snails are habitat specialists, and genetic studies using both allozyme and DNA sequence data have indicated that many species contain substantial and geographically structured genetic variation. In this study, we assess the genetic variation within two species of the rare terrestrial snail genus Prestonella, an inhabitant of rocky areas along water courses in the southern Great Escarpment of South Africa, and correlate genetic diversity to climatic variables. DNA sequence data from mitochondrial 16S rDNA and partial cytochrome oxidase I genes indicate that neither species is monophyletic, and that populations are deeply divergent, even over distances of a few hundred metres. Principal components anaylsis of climatic variables derived from two databases indicates that genetic diversity of the populations is correlated to moisture-related climatic variables. Populations with little or no diversity occur in more arid regions, and are thus most at risk from any future climatic changes that would increase aridification. These moisture variables are thus potent drivers of genetic bottlenecks and may have resulted in historical climate filtering or limitation of the distribution of these species. Temperature appears to be a less important variable, a finding supported by physiological data based on heart rates that show that death occurs only at temperatures far higher than found in their environment.     

Global analysis of regional differences in craniometric diversity and population substructure.

Estimates of genetic diversity in major geographic regions are frequently made by pooling all individuals into regional aggregates. This method can potentially bias results if there are differences in population substructure within regions, since increased variation among local populations could inflate regional diversity. A preferred method of estimating regional diversity is to compute the mean diversity within local populations. Both methods are applied to a global sample of craniometric data consisting of 57 measurements taken on 1734 crania from 18 local populations in six geographic regions: sub-Saharan Africa, Europe, East Asia, Australasia, Polynesia, and the Americas. Each region is represented by three local populations. Both methods for estimating regional diversity show sub-Saharan Africa to have the highest levels of phenotypic variation, consistent with many genetic studies. Polynesia and the Americas both show high levels of regional diversity when regional aggregates are used, but the lowest mean local population diversity. Regional estimates of F(ST) made using quantitative genetic methods show that both Polynesia and the Americas also have the highest levels of differentiation among local populations, which inflates regional diversity. Regional differences in F(ST) are directly related to the geographic dispersion of samples within each region; higher F(ST) values occur when the local populations are geographically dispersed. These results show that geographic sampling can affect results, and suggest caution in making inferences regarding regional diversity when population substructure is ignored.     

Ancient,but not recent,population declines have had a genetic impact on alpine yellow-bellied toad populations,suggesting potential for complete recovery

Reduction in population size and local extinctions have been reported for the yellow-bellied toad, Bombina variegata, but the genetic impact of this is not yet known. In this study, we genotyped 200 individuals, using mtDNA cytochrome b and 11 nuclear microsatellites. We investigated fine-scale population structure and tested for genetic signatures of historical and recent population decline, using several statistical approaches, including likelihood methods and approximate Bayesian computation. Five major genetically divergent groups were found, largely corresponding to geography but with a clear exception of high genetic isolation in a highly touristic area. The effective sizes in the last few generations, as estimated from the random association among markers, never exceeded a few dozen of individuals. Our most important result is that several analyses converge in suggesting that genetic variation was shaped in all groups by a 7- to 45-fold demographic decline, which occurred between a few hundred and a few 1000 years ago. Remarkably, only weak evidence supports recent genetic impact related to human activities. We believe that the alpine B. variegata populations should be monitored and protected to stop their recent decline and to prevent local extinctions, with highest priority given to genetically isolated populations. Nonetheless, current genetic variation pattern, being mostly shaped in earlier times, suggests that complete recovery can be achieved. In general, our study is an example of how the potential for recovery should be inferred even under the co-occurrence of population decline, low genetic variation, and genetic bottleneck signals.     

Temporal genetic dynamics among mosquitofish (<Emphasis Type="Italic">Gambusia holbrooki</Emphasis>) populations in invaded watersheds

The temporal components of genetic diversity and geographical structure of invasive mosquitofish populations are poorly known. Through the genetic monitoring of four consecutive cohorts of Gambusia holbrooki from three different river basins we aimed to determine temporal patterns of regional genetic variation and dispersal rates within invasive populations. Despite showing evidence of strong population size fluctuations, genetic diversity levels were maintained among local cohorts. We only detected temporal allele frequency changes associated with seasonal flooding that did not modify major trends on population structure among cohorts. Downstream gene flow coupled with increased connectivity at lowland locations to increase genetic diversity levels in these areas. A large proportion of local fish (up to 50 %) were dispersers, often originated from locations within the same river basin. High dispersal capability, ecological tolerance, and reproductive traits likely promote river colonization. Finally, our results also confirmed that human-assisted translocations promote within and among basin gene flow and maintained levels of genetic diversity, particularly in upstream locations.     

Diversity of parental environments increases phenotypic variation in Arabidopsis populations more than genetic diversity but similarly affects productivity

Background and AimsThe observed positive diversity effect on ecosystem functioning has rarely been assessed in terms of intraspecific trait variability within populations. Intraspecific phenotypic variability could stem both from underlying genetic diversity and from plasticity in response to environmental cues. The latter might derive from modifications to a plant’s epigenome and potentially last multiple generations in response to previous environmental conditions. We experimentally disentangled the role of genetic diversity and diversity of parental environments on population productivity, resistance against environmental fluctuations and intraspecific phenotypic variation.MethodsA glasshouse experiment was conducted in which different types of Arabidopsis thaliana populations were established: one population type with differing levels of genetic diversity and another type, genetically identical, but with varying diversity levels of the parental environments (parents grown in the same or different environments). The latter population type was further combined, or not, with experimental demethylation to reduce the potential epigenetic diversity produced by the diversity of parental environments. Furthermore, all populations were each grown under different environmental conditions (control, fertilization and waterlogging). Mortality, productivity and trait variability were measured in each population.Key ResultsParental environments triggered phenotypic modifications in the offspring, which translated into more functionally diverse populations when offspring from parents grown under different conditions were brought together in mixtures. In general, neither the increase in genetic diversity nor the increase in diversity of parental environments had a remarkable effect on productivity or resistance to environmental fluctuations. However, when the epigenetic variation was reduced via demethylation, mixtures were less productive than monocultures (i.e. negative net diversity effect), caused by the reduction of phenotypic differences between different parental origins.ConclusionsA diversity of environmental parental origins within a population could ameliorate the negative effect of competition between coexisting individuals by increasing intraspecific phenotypic variation. A diversity of parental environments could thus have comparable effects to genetic diversity. Disentangling the effect of genetic diversity and that of parental environments appears to be an important step in understanding the effect of intraspecific trait variability on coexistence and ecosystem functioning.     

Conservation genetics and phylogeography of southern dunlins Calidris alpina schinzii

Breeding populations of southern dunlin Calidris alpina schinzii in South Fennoscandia and the Baltic are severely fragmented and declining dramatically. Information on the genetic structure and diversity is therefore of importance for the conservation and management of these populations. Here we present the results of comparative genetic analyses of these populations with other populations of the schinzii , alpina and arctica subspecies in northern Europe. We sequenced the mitochondrial DNA control region and the Z-chromosome intron VLDLR-9, and analyzed microsatellites and AFLPs, for analyses of within-population genetic diversity. We also extended previous analyses of the phylogeographic structure of dunlins in northern Europe with a larger sample of individuals and populations. Our results revealed no evidence of reduced genetic diversity or increased levels of inbreeding in the small and fragmented populations around the Baltic Sea as compared to the more vital and larger populations elsewhere. Nevertheless, their small population sizes and presumably high degree of isolation may lead to local extinctions, indicating that demographic and ecological factors may pose a greater threat to the survival of these populations than purely genetic factors. Phylogeographically, the schinzii populations in Scandinavia and the Baltic do not form a separate genetic clade, but are part of larger cline of genetic variation encompassing several recognized subspecies of dunlins in the western Palearctic region. Only the Icelandic population showed some distinctiveness in genetic structure and might therefore be considered a separate management unit. Our study highlights the general problem of lack of genetic support for subspecies in avian taxonomy and conservation genetics.     

Gene flow and population structure of a solitary top carnivore in a human‐dominated landscape

While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free‐roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human–carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human‐caused extinctions.     

Measures of divergence between populations and the effect of forces that reduce variability

Wright's FST and related statistics are often used to measure the extent of divergence among populations of the same species relative to the net genetic diversity within the species. This paper compares several definitions of FST which are relevant to DNA sequence data, and shows that these must be used with care when estimating migration parameters. It is also pointed out that FST is strongly influenced by the level of within-population diversity. In situations where factors such as selection on closely linked sites are expected to have stronger effects on within-population diversity at some loci than at others, differences among loci can result entirely from differences in within- population diversities. It is shown that several published cases of differences in FST among regions of high and low recombination in Drosophila may be caused in this way. For the purpose of comparisons of levels of between-population differences among loci or species which are subject to different intensities of forces that reduce variability within local populations, absolute measures of divergence between populations should be used in preference to relative measures such as FST.      

The genetic underpinnings of population cyclicity: establishing expectations for the genetic anatomy of cycling populations

Despite extensive research into the mechanisms underlying population cyclicity, we have little understanding of the impacts of numerical fluctuations on the genetic variation of cycling populations. Thus, the potential implications of natural and anthropogenically‐driven variation in population cycle dynamics on the diversity and evolutionary potential of cyclic populations is unclear. Here, we use Canada lynx Lynx canadensis matrix population models, set up in a linear stepping‐stone, to generate demographic replicates of biologically realistic cycling populations. Overall, increasing cycle amplitude predictably reduced genetic diversity and increased genetic differentiation, with cyclic effects increased by population synchrony. Modest dispersal rates (1–3% of the population) between high and low amplitude cyclic populations did not diminish these effects suggesting that spatial variation in cyclic amplitude should be reflected in patterns of genetic diversity and differentiation at these rates. At high dispersal rates (6%) groups containing only high amplitude cyclic populations had higher diversity and lower differentiation than those mixed with low amplitude cyclic populations. Negative density‐dependent dispersal did not impact genetic diversity, but did homogenize populations by reducing differentiation and patterns of isolation by distance. Surprisingly, temporal changes in diversity and differentiation throughout a cycle were not always consistent with population size. In particular, negative density‐dependent dispersal simultaneously decreased differences in genetic diversity while increasing differences in genetic differentiation between numerical peaks and nadirs. Combined, our findings suggest demographic changes at fine temporal scales can impact genetic variation of interacting populations and provide testable predictions relating population cyclicty to genetic variation. Further, our results suggest that including realistic demographic and dispersal parameters in population genetic models and using information from temporal changes in genetic variation could help to discern complex demographic scenarios and illuminate population dynamics at fine temporal scales.     

Spatiotemporal structure of genetic variation of a spreading plant metapopulation on dynamic riverbanks along the Meuse River

Long-distance seed dispersal is a crucial determinant of within-population genetic variability and among-population genetic differentiation in plant metapopulations undergoing recurrent local extinctions and (re-)colonization. We investigated the spatial and temporal structure of genetic variation in a metapopulation of Sisymbrium austriacum located along a dynamic river system using dominant AFLP markers. Data on riverbank dynamics and colonization history allowed separating populations based on their age (< or =5 vs >5 years old). Bayesian analysis of population genetic structure indicated that populations were significantly differentiated from each other, but Mantel tests revealed that there was no relationship between pairwise geographic and genetic distances, suggesting that long-distance seed dispersal partly determines spatial genetic structure. Recent populations were less differentiated from each other than old populations. Analysis of molecular variance (AMOVA) indicated that both spatial factors and population age significantly determined genetic diversity, the effects of age being more important than spatial location. Clustering analysis revealed five large clusters, which were related primarily to population age and to a minor extent to geographical location. Our results indicate that the recurrent formation and destruction of riverbank habitats following peak flow events have a large impact on genetic diversity of riparian plant species.     

Post-colonization temporal genetic variation of an introduced fly, Rhagoletis completa

Evolutionary biologists have been puzzled by the success of introduced species: despite founder effects that reduce genetic variability, invasive species are still successful at colonizing new environments. It is possible that the evolutionary processes during the post-colonization period may increase the genetic diversity and gene flow among invasive populations over time, facilitating their long-term success. Therefore, genetic diversity and population structure would be expected to show greater temporal variation for successful introduced populations than for native populations. We studied the population genetics of the walnut husk fly, Rhagoletis completa, which was introduced into California from the Midwestern US in the early 1900s. We used microsatellites and allozymes to genotype current and historic fly populations, providing a rare perspective on temporal variability in population genetic parameters. We found that introduced populations showed greater temporal fluctuations in allele frequencies than native populations. Some introduced populations also showed an increase in genetic diversity over time, indicating multiple introductions had occurred. Population genetic structure decreased in both native and introduced populations over time. Our study demonstrates that introduced species are not at equilibrium and post-colonization processes may be important in ameliorating the loss of genetic diversity associated with biological invasions.     

Founder events predict changes in genetic diversity during human‐mediated range expansions

Intentional or accidental introduction of species to new locations is predicted to result in loss of genetic variation and increase the likelihood of inbreeding, thus reducing population viability and evolutionary potential. However, multiple introductions and large founder numbers can prevent loss of genetic diversity and may therefore facilitate establishment success and range expansion. Based on a meta‐analysis of 119 introductions of 85 species of plants and animals, we here show a quantitative effect of founding history on genetic diversity in introduced populations. Both introduction of large number of individuals and multiple introduction events significantly contribute to maintaining or even increasing genetic diversity in introduced populations. The most consistent loss of genetic diversity is seen in insects and mammals, whereas introduced plant populations tend to have higher genetic variation than native populations. However, loss or gain of genetic diversity does not explain variation in the extent to which plant or animal populations become invasive outside of their native range. These results provide strong support for predictions from population genetics theory with respect to patterns of genetic diversity in introduced populations, but suggest that invasiveness is not limited by genetic bottlenecks.     

Solutions for PCR,cloning and sequencing errors in population genetic analysis

PCR and sequencing artefacts can seriously bias population genetic analyses, particularly of populations with low genetic variation such as endangered vertebrate populations. Here, we estimate the error rates, discuss their population genetics implications, and propose a simple detection method that helps to reduce the risk of accepting such errors. We study the major histocompatibility complex (MHC) class IIB of guppies, Poecilia reticulata and find that PCR base misincorporations inflate the apparent sequence diversity. When analysing neutral genes, such bias can inflate estimates of effective population size. Previously suggested protocols for identifying genuine alleles are unlikely to exclude all sequencing errors, or they ignore genuine sequence diversity. We present a novel and statistically robust method that reduces the likelihood of accepting PCR artefacts as genuine alleles, and which minimises the necessity of repeated genotyping. Our method identifies sequences that are unlikely to be a PCR artefact, and which need to be independently confirmed through additional PCR of the same template DNA. The proposed methods are recommended particularly for population genetic studies that involve multi-template DNA and in studies on genes with low genetic diversity.     

Multi-annual density fluctuations and habitat size enhance genetic variability in two northern voles

In order to gain a better understanding of the consequences of population density cycles and landscape structure for the genetic composition in time and space of vole populations, we analyzed the multiannual genetic structure of the two numerically dominant, sympatric small rodent species of northernmost Fennoscandia. Red voles Myodes rutilus and grey-sided voles M. rufocanus were trapped in the subarctic birch forest along three fjords over five years. Along each fjord, there were four or five altitudinal transects each with five trapping stations. Spring and fall population densities were estimated from mark–recapture data. Grey-sided voles exhibited higher amplitude density fluctuations than red voles. Polymorphism at eight or nine microsatellite loci, determined in 1228 voles, was used to estimate local genetic diversity and differentiation among samples. Genetic diversity was higher in grey-sided voles than in red voles. Spring densities had no effect on local genetic diversity or on differentiation. The amplitude of density fluctuations and the extent of favorable habitat (sub-arctic birch forest) surrounding each site had a positive effect on genetic diversity, and the amplitude of density fluctuations had a negative effect on differentiation in red voles, for which fluctuating populations were compared with more stable populations. The harmonic mean of densities, reflecting average population sizes, had a negative effect on genetic diversity in red voles, but a positive effect in grey-sided voles, for which only fluctuating populations were compared. No other effects were significant for grey-sided voles. A temporal assignment test showed that the spatial structure was more stable in time for populations with more stable population dynamics. Altogether our results suggest that high amplitude density fluctuations lead to more gene flow and higher genetic diversity in vole populations.     

Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California

Identifying historic patterns of population genetic diversity and connectivity is a primary challenge in efforts to re‐establish the processes that have generated and maintained genetic variation across natural landscapes. The challenge of reconstructing pattern and process is even greater in highly altered landscapes where population extinctions and dramatic demographic fluctuations in remnant populations may have substantially altered, if not eliminated, historic patterns. Here, we seek to reconstruct historic patterns of diversity and connectivity in an endangered subspecies of woodrat that now occupies only 1–2 remnant locations within the highly altered landscape of the Great Central Valley of California. We examine patterns of diversity and connectivity using 14 microsatellite loci and sequence data from a mitochondrial locus and a nuclear intron. We reconstruct temporal change in habitat availability to establish several historical scenarios that could have led to contemporary patterns of diversity, and use an approximate Bayesian computation approach to test which of these scenarios is most consistent with our observed data. We find that the Central Valley populations harbour unique genetic variation coupled with a history of admixture between two well‐differentiated species of woodrats that are currently restricted to the woodlands flanking the Valley. Our simulations also show that certain commonly used analytical approaches may fail to recover a history of admixture when populations experience severe bottlenecks subsequent to hybridization. Overall our study shows the strength of combining empirical and simulation analyses to recover the history of populations occupying highly altered landscapes.     

Unique genetic variation at a species' rear edge is under threat from global climate change

Global climate change is having a significant effect on the distributions of a wide variety of species, causing both range shifts and population extinctions. To date, however, no consensus has emerged on how these processes will affect the range-wide genetic diversity of impacted species. It has been suggested that species that recolonized from low-latitude refugia might harbour high levels of genetic variation in rear-edge populations, and that loss of these populations could cause a disproportionately large reduction in overall genetic diversity in such taxa. In the present study, we have examined the distribution of genetic diversity across the range of the seaweed Chondrus crispus, a species that has exhibited a northward shift in its southern limit in Europe over the last 40 years. Analysis of 19 populations from both sides of the North Atlantic using mitochondrial single nucleotide polymorphisms (SNPs), sequence data from two single-copy nuclear regions and allelic variation at eight microsatellite loci revealed unique genetic variation for all marker classes in the rear-edge populations in Iberia, but not in the rear-edge populations in North America. Palaeodistribution modelling and statistical testing of alternative phylogeographic scenarios indicate that the unique genetic diversity in Iberian populations is a result not only of persistence in the region during the last glacial maximum, but also because this refugium did not contribute substantially to the recolonization of Europe after the retreat of the ice. Consequently, loss of these rear-edge populations as a result of ongoing climate change will have a major effect on the overall genetic diversity of the species, particularly in Europe, and this could compromise the adaptive potential of the species as a whole in the face of future global warming.     

Lack of genetic structure among ecologically adapted populations of an Australian rainforest Drosophila species as indicated by microsatellite markers and mitochondrial DNA sequences

Although fragmented rainforest environments represent hotspots for invertebrate biodiversity, few genetic studies have been conducted on rainforest invertebrates. Thus, it is not known if invertebrate species in rainforests are highly genetically fragmented, with the potential for populations to show divergent selection responses, or if there are low levels of gene flow sufficient to maintain genetic homogeneity among fragmented populations. Here we use microsatellite markers and DNA sequences from the mitochondrial ND5 locus to investigate genetic differences among Drosophila birchii populations from tropical rainforests in Queensland, Australia. As found in a previous study, mitochondrial DNA diversity was low with no evidence for population differentiation among rainforest fragments. The pattern of mitochondrial haplotype variation was consistent with D. birchii having undergone substantial past population growth. Levels of nuclear genetic variation were high in all populations while F(ST) values were very low, even for flies from geographically isolated areas of rainforest. No significant differentiation was observed between populations on either side of the Burdekin Gap (a long-term dry corridor), although there was evidence for higher gene diversity in low-latitude populations. Spatial autocorrelation coefficients were low and did not differ significantly from random, except for one locus which revealed a clinal-like pattern. Comparisons of microsatellite differentiation contrasted with previously established clinal patterns in quantitative traits in D. birchii, and indicate that the patterns in quantitative traits are likely to be due to selection. These results suggest moderate gene flow in D. birchii over large distances. Limited population structure in this species appears to be due to recent range expansions or cycles of local extinctions followed by recolonizations/expansions. Nevertheless, patterns of local adaptation have developed in D. birchii that may result in populations showing different selection responses when faced with environmental change.     

Genetic variation and island biogreography: Microsatellite and mitochondrial DNA variation in island populations of the Australian bush rat, Rattus fuscipes greyii

To understand the impact of various factors on the maintenance of genetic variation in natural populations, we need to focus on situations where at least some of these factors are removed or controlled. In this study, we used highly variable, presumably neutral, microsatellite and mtDNA markers to assess the nature of genetic variation in 14 island and two mainland populations of the Australian bush rat, where there is no migration between islands. Thus we are controlling for selection and gene flow. Both marker sets revealed low levels of diversity within the small island populations and extreme differentiation between populations. For six microsatellite loci, all of the small island populations had less genetic variation than the mainland populations; reduction in allelic diversity was more pronounced than loss of heterozygosity. Kangaroo Island, the large island population, had similar levels of diversity to the mainland populations. A 442 base pair (bp) section of the mtDNA control region was screened for variation by outgroup heteroduplex analysis/temperature gradient gel electrophoresis (OHA/TGGE). Only three of the 13 small island populations showed haplotypic diversity: Gambier (2), Waldegrave (2), and Eyere (3). The level of haplotypic diversity in the small island populations was similar to that on the mainland, most likely reflecting a recent population bottleneck on the mainland. In contrast, Kangaroo Island had 9 mtDNA haplotypes. The dominant factor influencing genetic diversity on the islands was island size. No correlation was detected between genetic diversity and the time since isolation or distance form the mainland. The combination of genetic drift within and complete isolation among the small island populations has resulted in rapid and extreme population divergence. Population pair-wise comparisons of allele frequency distributions showed significant differences for all populations for all loci (F _st = 0.11–0.84, R _st = 0.07–0.99). For the mtDNA control region, 92.6% of variation was apportioned between populations; only the Pearson islands shared a haplotype. Mantel tests of pair-wise genetic distance with pair-wise geographic distance showed no significant geographical clustering of haplotypes. However, population substructuring was detected within populations where sampling was conducted over a broader geographical range, as indicated by departures from Hardy-Weinberg equilibrium. Thus substructuring in the ancestral population cannot be ruled out. The dominant evolutionary forces on the islands, after the initial founder event, are stochastic population processes such as genetic drift and mutation. This revised version was published online in July 2006 with corrections to the Cover Date.