Quantifying and managing the loss of genetic variation in a free-ranging population of takahe through the use of pedigrees

Pedigree analysis has clear benefits for the genetic management of threatened populations through the evaluation of inbreeding, population structure and genetic diversity. The use of pedigrees is usually restricted to captive populations and few examples exist of their exclusive use in managing free-ranging populations. One such example is the management of the takahe (Porphyrio hochstetteri), a highly endangered, flightless New Zealand rail at risk from introduced mammalian predators and habitat loss. During the 1980’s and 90’s, as part of the takahe recovery programme, birds were translocated from the sole remnant population in Fiordland to four offshore islands from which introduced predators had been eradicated. The subsequent “island” population, now numbering 83 and thought to be at carrying capacity, has been closely monitored since founding. Detailed breeding records allow us to analyse the island pedigree, which is up to 7 generations deep. Gene-drop analysis indicated that 7.5% of genetic diversity has been lost over the relatively short timeframe since founding (2.1 generations on average; total genetic founders = 31) due to both a failure to equalise founder representation early on and subsequent disproportionate breeding success (founder equivalents = 12.5; founder genome equivalents = 6.6). A high prevalence of close inbreeding will have also impacted on genetic diversity. Predictions from pedigree modelling suggest that 90% genetic diversity will be maintained for only 12 years, but by introducing a low level of immigration from the Fiordland population and permitting the population to grow, 90% GD could be maintained over the next 100 years. More generally, the results demonstrate the value of maintaining pedigrees for wild populations, especially in the years immediately after a translocation event.     

Demography of takahe (

The last remaining natural population of the critically endangered takahe (Porphyrio hochstetteri) is confined to the Murchison Mountains in Fiordland, New Zealand. This mainland population contains about half of the c.?300 remaining takahe and benefits from one of the costliest recovery programmes in the country. Management activities include deer culling, stoat trapping, nest manipulation (e.g. removal of infertile eggs) and captive rearing of chicks. To determine what effect this intensive management has had on the recovery of the Fiordland takahe population, we modelled 25 years of survival and breeding success data as a function of environmental factors (e.g. precipitation, temperature, beech seedfall, tussock flowering) and specific management activities (egg manipulation, captive rearing, stoat control). Annual adult survival, estimated at 78% (credibility interval (CI) = 75?81%), is significantly increased to 85% (76?92% CI) in presence of stoat trapping, but is still low relative to introduced takahe populations on offshore islands and other large New Zealand bird species in predator-free environments. This suggests that the harsh environment of Fiordland may be suboptimal habitat in terms of survival for takahe. On the other hand, reproductive output in Fiordland is similar to that for introduced island populations, and is improved even further by management. Number of chicks per pair fledged with nest manipulation and captive rearing is estimated at 0.66 compared with 0.43 in the absence of nest management. The difference is explained mainly by low fledging success in the wild, especially for double clutches, which justifies the practice of removing one of two viable eggs and transferring it to a captive-rearing facility. The results of this study indicate that current management activities such as stoat trapping and captive rearing have a strong positive effect on population growth of the Murchison Mountains takahe population.     

Estimating the home range and carrying capacity for takahe (

Predator-free offshore islands play an important role in the conservation of many of New Zealand's endemic species. Takahe (Porphyrio mantelli) have small populations established on four offshore islands and although hatching success is lower than that of the wild mainland population in Fiordland, juvenile and adult survival is high and populations are growing exponentially. Accurate estimates of home range size and potential carrying capacities are therefore essential for the future management of the population as a whole. The mean home range size of takahe pairs in one study population on Mana Island (217 ha) was 2.8 ± 1.9 ha. The island was assessed for current and maximum available area for takahe and the potential carrying capacity was estimated at 22—53 pairs. Current and maximum available areas were also used to calculate carrying capacities on each of three other islands using two different estimates of mean home range size for Maud Island (7—34 pairs) and Kapiti Island (5—33 pairs) and one estimate of home range size for Tiritiri Matangi Island (25 pairs). A model of the population growth of takahe on islands predicted that estimated carrying capacities would be reached between 1997 and 2009. The urgency of planning to make use of the considerable potential of island populations of takahe is stressed.     

Investigation of genetic diversity in fragmented geometric tortoise (Psammobates geometricus) populations

Microsatellite DNA was used to investigatelevels of genetic variability in severelyfragmented populations of the geometrictortoise, Psammobates geometricus, themost endangered tortoise on mainland Africa.Eight microsatellite markers were used toassess genetic variability within and betweenthree naturally occurring populations of P. geometricus. These populations areseparated by the Cape Fold mountain ranges inthe western Cape region of South Africa. Levels of variability were quantified usingallelic diversity, genotypic frequencies andheterozygosity. Evidence for populationsub-structuring was examined using Fstatistics, R_st and ².High levels of variability were found in allthree populations. Low levels of populationdifferentiation were found suggestingsignificant gene flow between the populations.     

Moderate multiple parentage and low genetic variation reduces the potential for genetic incompatibility avoidance despite high risk of inbreeding

Background

Polyandry is widespread throughout the animal kingdom. In the absence of direct benefits of mating with different males, the underlying basis for polyandry is enigmatic because it can carry considerable costs such as elevated exposure to sexual diseases, physical injury or other direct fitness costs. Such costs may be balanced by indirect genetic benefits to the offspring of polyandrous females. We investigated polyandry and patterns of parentage in the spider Stegodyphus lineatus. This species experiences relatively high levels of inbreeding as a result of its spatial population structure, philopatry and limited male mating dispersal. Polyandry may provide an opportunity for post mating inbreeding avoidance that reduces the risk of genetic incompatibilities arising from incestuous matings. However, multiple mating carries direct fitness costs to females suggesting that genetic benefits must be substantial to counter direct costs.

Methodology/Principal Findings

Genetic parentage analyses in two populations from Israel and a Greek island, showed mixed-brood parentage in approximately 50% of the broods. The number of fathers ranged from 1–2 indicating low levels of multiple parentage and there was no evidence for paternity bias in mixed-broods from both populations. Microsatellite loci variation suggested limited genetic variation within populations, especially in the Greek island population. Relatedness estimates among females in the maternal generation and potentially interacting individuals were substantial indicating full-sib and half-sib relationships.

Conclusions/Significance

Three lines of evidence indicate limited potential to obtain substantial genetic benefits in the form of reduced inbreeding. The relatively low frequency of multiple parentage together with low genetic variation among potential mates and the elevated risk of mating among related individuals as corroborated by our genetic data suggest that there are limited actual outbreeding opportunities for polyandrous females. Polyandry in S. lineatus is thus unlikely to be maintained through adaptive female choice.     

Reduced MHC class II diversity in island compared to mainland populations of the black-footed rock-wallaby (<Emphasis Type="Italic">Petrogale lateralis lateralis</Emphasis>)

Many animal populations that are endangered in mainland areas exist in stable island populations, which have the potential to act as an “ark” in case of mainland population declines. Previous studies have found neutral genetic variation in such species to be up to an order of magnitude lower in island compared to mainland populations. If low genetic variation is prevalent across fitness-related loci, this would reduce the effectiveness of island populations as a source of individuals to supplement declining mainland populations or re-establish extinct mainland populations. One such species, the black-footed rock-wallaby (Petrogale lateralis lateralis), exists within fragmented mainland populations and small island populations off Western Australia. We examined sequence variation in this species within a fitness-related locus under positive selection, the MHC class II DAB β1 locus. The mainland populations displayed greater levels of allelic diversity (4–7 alleles) than the island population, despite being small and isolated, and contained at least two DAB gene copies. The island population displayed low allelic diversity (2 alleles) and fewer alleles per individual in comparison to mainland populations, and probably possesses only one DAB gene copy. The patterns of DAB diversity suggested that the island population has a markedly lower level of genetic variation than the mainland populations, in concordance with results from microsatellites (genotyped in a previous study), but preserved unique alleles which were not found in mainland populations. Where possible, conservation actions should pool individuals from multiple populations, not only island populations, for translocation programs, and focus on preventing further declines in mainland populations.     

Large mainland populations of South Island robins retain greater genetic diversity than offshore island refuges

For conservation purposes islands are considered safe refuges for many species, particularly in regions where introduced predators form a major threat to the native fauna, but island populations are also known to possess low levels of genetic diversity. The New Zealand archipelago provides an ideal system to compare genetic diversity of large mainland populations where introduced predators are common, to that of smaller offshore islands, which serve as predator-free refuges. We assessed microsatellite variation in South Island robins (Petroica australis australis), and compared large mainland, small mainland, natural island and translocated island populations. Large mainland populations exhibited more polymorphic loci and higher number of alleles than small mainland and natural island populations. Genetic variation did not differ between natural and translocated island populations, even though one of the translocated populations was established with five individuals. Hatching failure was recorded in a subset of the populations and found to be significantly higher in translocated populations than in a large mainland population. Significant population differentiation was largely based on heterogeneity in allele frequencies (including fixation of alleles), as few unique alleles were observed. This study shows that large mainland populations retain higher levels of genetic diversity than natural and translocated island populations. It highlights the importance of protecting these mainland populations and using them as a source for new translocations. In the future, these populations may become extremely valuable for species conservation if existing island populations become adversely affected by low levels of genetic variation and do not persist.     

Isolation and characterization of microsatellite loci from the endangered New Zealand takahe (Gruiformes; Rallidae; Porphyrio hochstetteri)

Nineteen polymorphic microsatellite loci were characterized from the endangered takahe (Porphyrio hochstetteri). Like many of New Zealand's other native avian species, levels of polymorphism were low, with variation detected at only 19 of 110 (17.3%) loci, and most polymorphic loci (78.9%) were diallelic (mean number of alleles = 2.3). Despite these low levels of variation, the microsatellites developed here will be useful for parentage assignment for confirming pedigrees, and investigating relationships between genetic variation, pedigree‐based inbreeding and reproductive success in this highly endangered species.     

Strong genetic differentiation of the East-Himalayan <Emphasis Type="Italic">Megacodon stylophorus</Emphasis> (Gentianaceae) detected by Inter-Simple Sequence Repeats (ISSR)

Megacodon stylophorus (Clarke) Smith is a perennial alpine herb endemic to the species-rich eastern Himalayan region. Its populations are locally scattered as isolated patches throughout this region. Genetic variation within and among six populations of this species was assessed using ISSR fingerprinting with 13 primers. High levels of genetic diversity exist within species (P = 69.83%, H_T = 0.1949 and H_sp = 0.3047), while the within-population diversity is low (P = 11.21%, H_E = 0.0532 and H_pop = 0.0792). Extraordinarily high levels of genetic differentiation were detected among populations based on various statistics, including Neis genetic diversity analysis (72.7%), Shannons diversity index (74.01%) and AMOVA (80.70%). That is, populations shared low levels of genetic identity (I = 0.8203 ± 0.0430). This genetic structure was probably due to severe genetic drift of the small-sized patchy populations resulting from postglacial habitat fragmentations. The observed genetic structure of the populations implies that as many populations as possible should be considered for any in situ and ex situ conservation practice on this species.     

Genetically depauperate in the continent but rich in oceanic islands: Cistus monspeliensis (Cistaceae) in the Canary Islands

Background

Population genetic theory holds that oceanic island populations are expected to have lower levels of genetic variation than their mainland counterparts, due to founder effect after island colonization from the continent. Cistus monspeliensis (Cistaceae) is distributed in both the Canary Islands and the Mediterranean region. Numerous phylogenetic results obtained in the last years allow performing further phylogeographic analyses in Cistus.

Methodology/Principal Findings

We analyzed sequences from multiple plastid DNA regions in 47 populations of Cistus monspeliensis from the Canary Islands (21 populations) and the Mediterranean basin (26 populations). The time-calibrated phylogeny and phylogeographic analyses yielded the following results: (1) a single, ancestral haplotype is distributed across the Mediterranean, whereas 10 haplotypes in the Canary Islands; (2) four haplotype lineages are present in the Canarian Islands; (3) multiple colonization events across the archipelago are inferred; (4) the earliest split of intraspecific lineages occurred in the Early to Middle Pleistocene (<930,000 years BP).

Conclusions/Significance

The contrasting pattern of cpDNA variation is best explained by genetic bottlenecks in the Mediterranean during Quaternary glaciations, while the Canarian archipelago acted as a refugium of high levels of genetic diversity. Active colonization across the Canarian islands is supported not only by the distribution of C. monspeliensis in five of the seven islands, but also by our phylogeographic reconstruction in which unrelated haplotypes are present on the same island. Widespread distribution of thermophilous habitats on every island, as those found throughout the Mediterranean, has likely been responsible for the successful colonization of C. monspeliensis, despite the absence of a long-distance dispersal mechanism. This is the first example of a plant species with higher genetic variation among oceanic island populations than among those of the continent.     

Mitochondrial DNA sequence variation and phylogeographic patterns in harbour porpoises (Phocoena phocoena) from the North Atlantic

The harbour porpoise (Phocoena phocoena)experiences high rates of incidental mortalityin commercial fisheries, and in some areasthese rates are sufficiently high to justifyconcern over population sustainability. Giventhe high incidental mortality, the resolutionof population structure will be important toconservation and management, but in the NorthAtlantic the relationships among many of theputative populations remain unclear. Aprevious genetic study demonstrated substantialgenetic differences between eastern and westernNorth Atlantic populations, however thelocation of this break remained unresolved. Inthe present study, we addressed this issue byincluding new samples from Iceland. Toinvestigate population structure, variation inthe mitochondrial DNA of 370 porpoises wascompared among six locations corresponding toseveral of the putative populations (Gulf ofMaine, Gulf of St. Lawrence, Newfoundland, WestGreenland, Iceland, Norway). The first 342base pairs of the control region were sequencedand genetic variation investigated by analysisof molecular variance (F _ST and _ST ) and ² withpermutation. Although some fine scalepopulation structure was detected, porpoisesfrom Iceland were found to be more similar tothe western populations (W. Greenland, Gulf ofSt. Lawrence, Newfoundland, Gulf of Maine) thanto Norway. Furthermore, porpoises from Norwaywere different from all other regions. Thesepatterns suggest the existence of adiscontinuity between Iceland and Norway,possibly the result of isolating events causedby repeated range contractions and expansionsthroughout Quaternary glaciation events withinthe North Atlantic. These results suggest thatharbour porpoise populations within the NorthAtlantic are distinguishable, but patterns mustbe interpreted in light of their historicalbiogeography.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Lack of genetic polymorphism among peregrine falcons Falco peregrinus of Fiji

We compared levels of genetic diversity and isolation among peregrine falcons Falco peregrinus from two South Pacific island complexes (Fiji and Vanuatu: F. p. nesiotes), relative to other island and mainland populations. Fragment data from 12 microsatellite loci and sequence information from the control region of the mitochondrial DNA indicated levels of genetic variation in the South Pacific populations were lower than other island and mainland populations. Indeed, diversity varied from extremely low (Vanuatu) to completely absent (Fiji). We find little support for a hypothesis that populations on Fiji or Vanuatu were colonized via Australia. The complete lack of polymorphism in peregrine falcons of Fiji is remarkable, and to our knowledge has not been observed in a natural avian population. This lack of polymorphism, and the inability to test for decrease in polymorphism using museum samples, precludes testing whether the lack of genetic diversity in the population on Fiji is due to a recent bottleneck, or sustained isolation over evolutionary time. Increased fertility in eggs of Fiji peregrines upon outbreeding with males from other areas is consistent with inbreeding depression within a population typified by heterozygote deficiency.     

Genetic variability in migratory and endemic island songbirds (genus Vireo): A comparative assessment using molecular and morphological traits

Low genetic variation is thought to increase the risk of extinction in island species; however, these species can differ both in terms of endemism and gene flow. In a previous study, the endemic species of Puerto Rico (V. latimeri) and Jamaica (V. modestus and V. osburni) were shown to have less genetic variability than a continental relative, V. griseus. In this study, a migratory island species, V. altiloquus, is analyzed together with the endemics in order to (1) compare levels of genetic variation in migratory and endemic island species, and (2) assess this variation using both molecular markers and morphological traits. Each island species is also compared to a continental relative (V. griseus for the endemic species, and V. olivaceus for the migratory species). Variability in random amplified polymorphic DNA markers was significantly lower in the endemic species than in either migratory population. All island populations had significantly lower levels of variation than their respective continental relatives, but with significantly greater reduction in the endemic species. In contrast, the morphological measures revealed only two cases with a significantly lower CV in an endemic species compared to V. altiloquus or V. griseus. All others exhibited either no differences in CV or greater levels in the island populations. While the molecular results generally correspond to predictions of lower variability in endemic vs. migratory island species and island vs. continental species, the morphological comparisons do not, and therefore may not be useful for quick, field-based assessments of underlying genetic variability. This revised version was published online in July 2006 with corrections to the Cover Date.     

Contrasting Levels of Variation in Neutral and Quantitative Genetic Loci on Island Populations of Moor Frogs (<Emphasis Type="Italic">Rana arvalis</Emphasis>)

Reduced levels of genetic variability and a prominent differentiation in both neutral marker genes and phenotypic traits are typical for many island populations as compared to their mainland conspecifics. However, whether genetic diversity in neutral marker genes reflects genetic variability in quantitative traits, and thus, their evolutionary potential, remains typically unclear. Moreover, the phenotypic differentiation on islands could be attributable to phenotypic plasticity, selection or drift; something which seldom has been tested. Using eight polymorphic microsatellite loci and quantitative genetic breeding experiments we conducted a detailed comparison on genetic variability and differentiation between Nordic islands (viz. Gotland, Öland and Læsø) and neighbouring mainland populations of moor frogs (Rana arvalis). As expected, the neutral variation was generally lower in island than in mainland populations. But as opposed to this, higher levels of additive genetic variation (V _A) in body size and tibia length were found on the island of Gotland as compared to the mainland population. When comparing the differentiation seen in neutral marker genes (F _ST) with the differentiation in genes coding quantitative traits (Q _ST) two different evolutionary scenarios were found: while selection might explain a smaller size of moor frogs on Gotland, the differentiation seen in tibia length could be explained by genetic drift. These results highlight the limited utility of microsatellite loci alone in inferring the causes behind an observed phenotypic differentiation, or in predicting the amount of genetic variation in ecologically important quantitative traits.     

Effects of population size on genetic diversity and seed production in the rare <Emphasis Type="Italic">Dictamnus albus</Emphasis>(Rutaceae) in central Germany

It is widely assumed that population size significantly affects the dynamics of plant populations. Smaller populations are threatened by genetic drift and inbreeding depression, both of which may result in a decrease of genetic variation and a resulting negative impact on plant fitness. In our study we analysed the patterns of random amplified polymorphic DNA (RAPD) variation among 10 Dictamnus albuspopulations of varying size. The aim was to examine local differentiation in relation to spatial isolation resulting from limited population size and geographical distancing between populations. Significant correlations were noted between population size and both percentage of polymorphic loci (P <0.01) and genetic diversity (P<0.01). The matrix correlation between genetic and geographical distances revealed that geographical differentiation was reflected in the RAPD profile (Mantel test: r²=0.34, P<0.001). We found the highest level of molecular variance of RAPD patterns among individuals within the populations (72.6%), whereas among-population variation accounted for only 21.6% of variation. These results were highly significant in that they indicated a restricted population differentiation, as would be expected from outcrossing species. An additional analysis of seed production showed that there was significant variation among populations in terms of mean seed number per flower and mean seed mass per population which could be attributed to differences in population size as well as levels of genetic variation.     

A Contrast in Extra-Pair Paternity Levels on Mainland and Island Populations of Mediterranean Blue Tits

Extra‐pair copulation (EPC) is a widespread behaviour amongst birds, yet the rate of occurrence of extra‐pair offspring is highly variable both within and across species. Two populations of Mediterranean blue tits, Parus caeruleus, one on the mainland and the other on the island of Corsica, are characterized by high levels of extra‐pair paternity (EPP), with 14 and 25% of extra‐pair offspring (in 46 and 68% of the nests), respectively. The rate of EPP is significantly higher in the island population. Such high rates on Corsica contradict the predictions of higher mate fidelity and lower levels of EPP on islands. Despite expressing several traits that characterize an insular syndrome, blue tits of Corsica do not exhibit lower genetic variation which could be associated with low levels of EPP on islands. Furthermore, our results do not support any of the hypotheses that have been proposed so far to explain variation in EPP rates at the local level. We tentatively suggest that proximate Mediterranean constraints, especially consistent food shortage, prompt females to seek better breeding opportunities through a two‐step process including high rates of EPC and divorce.     

Genetic Diversity in Remnant Mainland and “Pristine” Island Populations of Three Endemic Australian Macropodids (Marsupialia): Macropus Eugenii, Lagorchestes Hirsutus and Petrogale Lateralis

Since European settlement, mainland Australia has experienced a wave of mammal extinctions and population declines. However, some species have persisted on off-shore islands, which are now viewed as important wildlife refuges. In this study, we assessed the level of genetic diversity, at 7–11 microsatellite loci, in island and remnant mainland populations of three endemic species of macropodid marsupial; the tammar wallaby Macropus eugenii(n = 92); rufous hare-wallaby Lagorchestes hirsutus(n = 40) and black-footed rock-wallaby Petrogale lateralis(n = 164). There was a consistent pattern of significantly higher levels of microsatellite diversity in the remnant mainland population (A= 4.9–13.9; He= 0.61–0.86) of each species compared to conspecific pristine island populations (A= 1.2–3.7; He= 0.05–0.44). These marked differences are even apparent where island populations currently have a substantially larger census size. In addition, island populations were substantially inbred (Fe= 0.49–0.91). Although island populations have been insulated from the relatively recent threatening processes operating on the mainland, they have nevertheless been significantly impacted by increased inbreeding and the substantial erosion of genetic diversity. Despite the difficulties of ensuring the survival of remnant mainland populations, they appear to retain substantially more genetic diversity than their island counterparts and therefore are more likely to contribute to the long-term persistence of their species. These data also demonstrate that small remnant mainland populations (n < 10–20) are often capable of rapid recovery and are not necessarily genetically depauperate.     

Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates

Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island–mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long‐standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.     

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.