Microsatellite variation and microevolution in the critically endangered San Clemente Island loggerhead shrike (Lanius ludovicianus mearnsi)

Polymorphic nuclear microsatellite loci were used to characterize genetic variation in contemporary and historic populations of the San Clemente Island loggerhead shrike (Lanius ludovicianus mearnsi), an endangered bird with a current population of 30 individuals that is endemic to to one of the California Channel Islands. We also compared the population of the shrike with two contemporary populations of the still abundant subspecies, L. l. gambeli, which live 120 km away on the adjacent mainland. The current population of L. l. mearnsi has 60 per cent of the genetic variation of the mainland shrike populations and is strongly differentiated from them. Comparison of living birds with 19 birds collected in 1915 shows that most of the variation within the island population was lost before the recent 90 per cent decline in population size, and the 20 per cent decrease in variation this century is probably attributable to genetic drift. Mitochondrial DNA control region sequence data from 80 year old specimens show that there may have been limited introgression to L. l. mearnsi, this century, from another island subspecies, L. l. anthonyi, found in the northern Channel Islands. Today, gene flow between L. l. mearnsi and mainland L. l. gambel is very low, even though a few mainland birds visit the island annually. The island subspecies population has evolved sufficient genetic independence to justify ongoing conservation efforts to counter demographic collapse and genetic erosion; the course of genetic erosion can now be monitored non-invasively, as demonstrated by this study, based on DNA amplified from feathers.     

Developing population models for guiding reintroductions of extirpated bird species back to the New Zealand mainland

Population models are useful tools to guide management as they allow us to project growth and persistence of wildlife populations under different scenarios. Nevertheless, good data are needed to produce reliable models, and this requirement is problematic in some situations. North Island saddlebacks (Philesturnus rufusater) were reintroduced to Boundary Stream Mainland Island in September 2004, and this was the first time this species had occurred in an unfenced mainland area since their extirpation in the 19th century. This situation creates a challenging scenario for population modelling, as this species has never been studied in the presence of mainland predators, and management of these predators will be the key factor determining whether the population survives. In this paper we present an approach for developing a “prior model” before a reintroduction takes place. We use data from the reintroduced saddleback population on Mokoia Island to develop a model of how saddleback populations are regulated in the absence of mammalian predators. We use this model to project growth of a reintroduced population when vital rates are reduced by predation and also to project responses of source populations to harvesting of birds for translocation. We then incorporate data from the reintroduced North Island robin (Petroica longipes) population at Paengaroa Mainland Island to model the relationship between population parameters and predator tracking rates. The combined model can be used to predict the level of predator control needed to ensure growth of the saddleback population, but the prediction is contingent on guessing the relative vulnerability of robins and saddlebacks to predation. We envision using a Bayesian approach to update such prior models as site-specific data become available after reintroduction.     

A strong genetic footprint of the re‐introduction history of Alpine ibex (Capra ibex ibex)

A population’s neutral genetic variation is a composite of its size, degree of isolation and demographic history. Bottlenecks and founder events increase genetic drift, leading to the loss of genetic variation and increased genetic differentiation among populations. Gene flow has the opposite effects. Thus, gene flow can override the genetic patterns caused by founder events. Using 37 microsatellite loci, we investigated the effects of serial bottlenecks on genetic variation and differentiation among 42 Alpine ibex populations in Switzerland with known re‐introduction histories. We detected a strong footprint of re‐introduction events on contemporary genetic structure, with re‐introduction history explaining a substantial part of the genetic differentiation among populations. As a result of the translocation of a considerable number of individuals from the sole formerly surviving population in northern Italy, most of the genetic variation of the ancestral population is now present in the combined re‐introduced Swiss populations. However, re‐introductions split up the genetic variation among populations, such that each contemporary Swiss population showed lower genetic variation than the ancestral population. As expected, serial bottlenecks had different effects on the expected heterozygosity (He) and standardized number of alleles (sNa). While loss of sNa was higher in the first bottlenecks than in subsequent ones, He declined to a similar degree with each bottleneck. Thus, genetic drift was detected with each bottleneck, even when no loss of sNa was observed. Overall, more than a hundred years after the beginning of this successful re‐introduction programme, re‐introduction history was the main determinant of today’s genetic structure.     

Decreased immunocompetence in a severely bottlenecked population of an endemic New Zealand bird

Inbreeding resulting from severe population bottlenecks may impair an individual's immune system and render it more susceptible to disease. Although a reduced immune response could threaten the survival of highly endangered species, few studies have assessed the effect of population bottlenecks on immunocompetence. We compared the counts of leucocytes and external, blood and gastrointestinal parasite loads in two populations of the endemic New Zealand robin Petroica australis to assess the immunocompetence of birds in a severely bottlenecked population relative to its more genetically diverse source population. Despite similar parasite loads in both populations, robins in the severely bottlenecked population showed lower counts of both total leucocyte and total lymphocyte numbers. When the immune system was experimentally challenged using the phytohaemagglutinin skin test, robins in the severely bottlenecked population exhibited a significantly lower immune response than the source population, suggesting that birds passing through a severe bottleneck have a compromised immunocompetence. Our results confirm that severe bottlenecks reduce the immune response of birds and highlight the need to avoid severe bottlenecks in the recovery programmes of endangered species.     

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.     

Moderate inbreeding depression in a reintroduced population of North Island robins

Reintroductions of threatened species are increasingly common in conservation. The translocation of a small subset of individuals from a genetically diverse source population could potentially lead to substantial inbreeding depression due to the high genetic load of the parent population. We analysed 12 years of data from the reintroduced population of North Island robins Petroica longipes on Tiritiri Matangi Island, New Zealand, to determine the frequency of inbreeding and magnitude of inbreeding depression. The initial breeding population consisted of 12 females and 21 males, which came from a large mainland population of robins. The frequency of mating between relatives ( f >0; 39%, n =82 pairs) and close relatives ( f =0.25; 6.1%) and the average level of inbreeding ( f =0.027) were within the range reported for other small island populations of birds. The average level of inbreeding fluctuated from year to year depending on the frequency of close inbreeding (e.g. sib–sib pairs). We found evidence for inbreeding depression in juvenile survival, with survival probability estimated to decline from 31% among non-inbred birds ( f =0) to 11% in highly inbred juveniles ( f =0.25). The estimated number of lethal equivalents based on this relationship (4.14) was moderate compared with values reported for other island populations of passerines. Given that significant loss of fitness was only evident in highly inbred individuals, and such individuals were relatively rare once the population expanded above 30 pairs, we conclude that inbreeding depression should have little influence on this robin population. Although the future fitness consequences of any loss of genetic variation due to inbreeding are uncertain, the immediate impact of inbreeding depression is likely to be low in any reintroduced population that expands relatively quickly after establishment.     

MHC variation reflects the bottleneck histories of New Zealand passerines

Most empirical evidence suggests that balancing selection does not counter the effects of genetic drift in shaping postbottleneck major histocompatibility complex (MHC) genetic diversity when population declines are severe or prolonged. However, few studies have been able to include data from historical specimens, or to compare populations/species with different bottleneck histories. In this study, we examined MHC class II B and microsatellite diversity in four New Zealand passerine (songbird) species that experienced moderate to very severe declines. We compared diversity from historical samples (collected c. 1884–1938) to present‐day populations. Using a Bayesian framework, we found that the change in genetic diversity from historical to contemporary samples was affected by three main factors: (i) whether the data were based on MHC or microsatellite markers, (ii) species (as a surrogate for bottleneck severity) and (iii) whether the comparison between historical and contemporary samples was made using historical samples originating from the mainland, or using historical samples originating from islands. The greatest losses in genetic diversity occurred for the most severely bottlenecked species, particularly between historical mainland and contemporary samples. Additionally, where loss of diversity occurred, the change was greater for MHC genes compared to microsatellite loci.     

Genetic variation and structure of house sparrow populations: is there an island effect?

Population genetic structure and intrapopulation levels of genetic variation have important implications for population dynamics and evolutionary processes. Habitat fragmentation is one of the major threats to biodiversity. It leads to smaller population sizes and reduced gene flow between populations and will thus also affect genetic structure. We use a natural system of island and mainland populations of house sparrows along the coast of Norway to characterize the different population genetic properties of fragmented populations. We genotyped 636 individuals distributed across 14 populations at 15 microsatellite loci. The level of genetic differentiation was estimated using F‐statistics and specially designed Mantel tests were conducted to study the influence of population type (i.e. mainland or island) and geographic distance on the genetic population structure. Furthermore, the effects of population type, population size and latitude on the level of genetic variation within populations were examined. Our results suggest that genetic processes on islands and mainland differed in two important ways. First, the intrapopulation level of genetic variation tended to be lower and the occurrence of population bottlenecks more frequent on islands than the mainland. Second, although the general level of genetic differentiation was low to moderate, it was higher between island populations than between mainland populations. However, differentiation increased in mainland populations somewhat faster with geographical distance. These results suggest that population bottleneck events and genetic drift have been more important in shaping the genetic composition of island populations compared with populations on the mainland. Such knowledge is relevant for a better understanding of evolutionary processes and conservation of threatened populations.     

GENETIC VARIABILITY AND POPULATION DIFFERENTIATION INFERRED FROM DNA FINGERPRINTING IN SILVEREYES (AVES: ZOSTEROPIDAE)

This study evaluated DNA fingerprinting as a tool for estimating population genetic diversity and differentiation by comparing minisatellite variation in island and mainland populations of silvereyes (Aves: Zosterops lateralis). Three populations with different recent histories were compared: (1) Heron Island and neighboring islands, colonized 3000 to 4000 yr ago; (2) Lady Elliot Island, colonized within the past two decades; and (3) an adjacent mainland population, which presumably has existed for thousands of years. The degree of genetic variability within the three populations reflected both their size and the time since their colonization. Minisatellite diversity was highest in the mainland population, intermediate in the Capricorn Island group (which was shown to represent a single admixture), and lowest in the Lady Elliot Island population, possibly because of a recent population bottleneck during colonization. Mean band sharing between any two populations was less than the mean within either of those populations, and four fingerprint bands common to island birds were rare or absent in the fingerprints of mainland birds. In the absence of significant gene flow between the mainland and the islands, the populations have apparently become distinct at minisatellite loci, as evidenced by differences in both allelic diversity and in the frequencies of specific fragments. Within the Heron Island population, cohort analyses demonstrated the temporal stability of the fingerprint profile over 6 yr. This study demonstrates that length polymorphisms at minisatellite loci may be stable enough over time to retain information about recent historical and demographic effects on the relative genetic variability and differentiation of small, closely related populations.     

Habitat selection in reintroduced bird populations: a case study of Stewart Island robins and South Island saddlebacks on Ulva Island

An understanding of the mechanisms influencing habitat selection in reintroduced bird populations is fundamental for successful translocation programmes. Plant species composition, abundance, structure and food availability are likely to influence animal movement and habitat choice, but few studies have evaluated their combined effect on habitat selection of translocated birds. Stewart Island robins (Petroica australis rakiura) and South Island saddlebacks (Philesturnus carunculatus carunculatus) are two threatened New?Zealand bird species that have been reintroduced to Ulva Island (Stewart Island). We hypothesised that their initial settlement patterns were driven by habitat quality. We tested this hypothesis by comparing habitat components between occupied and unoccupied habitats as the population grew after initial tanslocation. We also modelled probabilities of site selection as a function of the composition and structure of vegetation, availability of food (invertebrate composition) and nesting resources (cavity type). Founding pairs of both species first established territories in coastal habitat in the western part of the island, which is characterised by structurally complex broadleaved vegetation. Birds also selected sites with a greater abundance and diversity of food resources. Thus in the early stages of population establishment robins and saddlebacks appear to select high quality habitat that offers enhanced cover and foraging opportunities.     

Significant genetic admixture after reintroduction of peregrine falcon (<Emphasis Type="Italic">Falco peregrinus</Emphasis>) in Southern Scandinavia

The peregrine falcon (Falco peregrinus) population in southern Scandinavia was almost extinct in the 1970’s. A successful reintroduction project was launched in 1974, using captive breeding birds of northern and southern Scandinavian, Finnish and Scottish origin. We examined the genetic structure in the pre-bottleneck population using eleven microsatellite markers and compared the data with the previously genotyped captive breeding population and contemporary wild population. Museum specimens between 53 and 130 years old were analyzed. Despite an apparent loss of historical genetic diversity, the contemporary population shows a relatively high level of genetic variation. Considerable gene introgression from captive breeding stock used to repopulate the former range of southern Scandinavian peregrines may have altered the genetic composition of this population. Both the historical and contemporary northern and southern Scandinavian populations are genetically differentiated. The reintroduction project implemented in the region and the use of non-native genetic stock likely prevented the southern Scandinavian population from extinction and thus helped maintain the level of genetic diversity and prevent inbreeding depression. The population is rapidly increasing in numbers and range and shows no indication of reduced fitness or adaptive capabilities in the wake of the severe bottleneck and the reintroduction.     

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.     

Evidence for a recent genetic bottleneck in the endangered Florida Keys silver rice rat (<Emphasis Type="Italic">Oryzomys argentatus</Emphasis>) revealed by microsatellite DNA analyses

Low levels of genetic variation are thought to contribute significantly to the higher extinction rates of endemic island populations compared to their mainland counterparts. We used six microsatellite loci to compare the genetic structure of the endangered silver rice rat (Oryzomys argentatus) population in Saddlebunch Key, Florida to the mainland population of the closely related marsh rice rat (Oryzomys palustris natator) in Everglades National Park. Allelic richness and gene diversity are significantly lower in Saddlebunch Key than in the larger mainland population, and the two populations are significantly differentiated as measured by both F-statistics and Bayesian clustering methods. These findings support the classification of the Keys population as a “distinct vertebrate population” by the U.S. Fish and Wildlife Service. Current gene diversity (H _E) is higher than expected under mutation-drift equilibrium in Saddlebunch Key, indicating a genetic bottleneck. The Keys population also exhibits a mode shift in its allele frequency distribution which suggests a very recent bottleneck has occurred and is consistent with reports of recent population declines. Although habitat loss and exotic species pose a more immediate and serious threat to silver rice rats, the continued loss of genetic variation may contribute to their long-term extinction risk due to inbreeding or by lowering the population’s ability to adapt to future environmental changes. The protection of habitat and the removal of introduced predators and competitors may help increase the population size of silver rice rats and lower their risk of extinction, both from a demographic and a genetic perspective.     

Habitat fragmentation causes bottlenecks and inbreeding in the European tree frog (Hyla arborea)

A genetic study of the European tree frog, Hyla arborea, in Denmark was undertaken to examine the population structure on mainland Jutland and the island of Lolland after a period of reduction in suitable habitat and population sizes. The two regions have experienced the same rate of habitat loss but fragmentation has been more severe on Lolland. Genetic variation based on 12 polymorphic DNA microsatellites was analysed in 494 tree frogs sampled from two ponds in Jutland and 10 ponds on Lolland. A significant overall deviation from Hardy-Weinberg expectations could be attributed to three ponds, all on Lolland. This was most probably caused by an inbreeding effect reducing fitness, which was supported by the observed significant negative correlation between larva survival and mean F(IS) value and mean individual inbreeding coefficient. A significant reduction in genetic variation (bottleneck) was detected in most of the ponds on Lolland. Population-structure analysis suggested the existence of at least 11 genetically different populations, corresponding to most of the sampled population units. The results indicated that the populations were unique genetic units and could be used to illustrate the migration pattern between newly established ponds arisen either by natural colonization of tree frogs or by artificial introduction. A high degree of pond fidelity in the tree frogs was suggested. A severe fragmentation process reducing population size and fitness within some of the populations probably caused the significant reduction in genetic variation of tree frog populations on Lolland.     

Conservation genetics of the Common Tern (Sterna hirundo) in the North Atlantic region; implications for the critically endangered population at Bermuda

Common Terns nesting at Bermuda are isolated by 1,000–4,000?km from other populations of the species around the North Atlantic Ocean. This population experienced a severe demographic bottleneck as a result of a hurricane in 2003 and was subsequently re-established by four males and four females. Using seven microsatellite loci, we compared the genetic diversity of the pre- and post-bottleneck populations, compared the genetic profile of the Bermuda population with those of other populations around the North Atlantic Ocean and mainland Europe, and assessed the potential contribution of immigration to genetic diversity. We found a loss of genetic diversity (number of alleles and heterozygosity) in the post-bottleneck Bermudian population (4.6–2.9 and 0.56–0.52, respectively). We also report significant differentiation among all sampled locations (global F_ST?=?0.16) with no evidence for immigration into Bermuda. Common Terns from the Azores were genetically more similar to those from mainland North America than to those from Bermuda or mainland Europe. Our results suggest that the critically endangered population in Bermuda is genetically distinct and requires continued and enhanced conservation priority.     

Comparison of historical bottleneck effects and genetic consequences of re‐introduction in a critically endangered island passerine

Re‐introduction is an important tool for recovering endangered species; however, the magnitude of genetic consequences for re‐introduced populations remains largely unknown, in particular the relative impacts of historical population bottlenecks compared to those induced by conservation management. We characterize 14 microsatellite loci developed for the Seychelles paradise flycatcher and use them to quantify temporal and spatial measures of genetic variation across a 134‐year time frame encompassing a historical bottleneck that reduced the species to ~28 individuals in the 1960s, through the initial stages of recovery and across a second contemporary conservation‐introduction‐induced bottleneck. We then evaluate the relative impacts of the two bottlenecks, and finally apply our findings to inform broader re‐introduction strategy. We find a temporal trend of significant decrease in standard measures of genetic diversity across the historical bottleneck, but only a nonsignificant downward trend in number of alleles across the contemporary bottleneck. However, accounting for the different timescales of the two bottlenecks (~40 historical generations versus <1 contemporary generation), the loss of genetic diversity per generation is greater across the contemporary bottleneck. Historically, the flycatcher population was genetically structured; however, extinction on four of five islands has resulted in a homogeneous contemporary population. We conclude that severe historical bottlenecks can leave a large footprint in terms of sheer quantity of genetic diversity lost. However, severely depleted genetic diversity does not render a species immune to further genetic erosion upon re‐introduction. In some cases, the loss of genetic diversity per generation can, initially at least, be greater across re‐introduction‐induced bottlenecks.     

性选择、配偶外父亲身份确认程度、遗传变异性和保护

岛屿动物中的性选择强度不高,其原因可能是由于岛屿种群的遗传变异性水平较低。本文作者检验了鸟类岛屿种群是否具有较低的遗传变异性、性选择强度大的种群是否具有较高的突变输入率（rate of mutational input),在鸟类岛屿种群中是否具有较低的性选择强度（可以根据配偶外父亲身份的频率来估计）。小卫星共有谱带系数（minisatellite band sharing coefficient)可确定无亲源关系个体之间的遗传变异性,对与遗传变异性有关的雄性个体的父亲（paternity)进行了成对比较以检验如下假说：在具有较多遗传变异的种群中,雌性个体更经常地进行配偶外交配。在小卫星谱带系数较低的鸟类种群中,配偶外父亲的频次较高。对岛屿和大陆鸟类进行的第二个比较分析表明：岛屿种群中的配偶外父亲频次较低,遗传变异性也较低,其部分原因在于突变输入（mutational input)减少。上述发现表明：（1）父亲确认程度（parternity)随遗传变异性的数量而增加;（2）在遗传变异性较大的种群中,突变率较高,性选择的程度更激烈;（3）岛屿种群中性选择的强度一般比大陆种群弱。这对于理解遗传变异性的空间变异、理解岛屿种群和其它隔离种群的保护问题有重要启示。     

Population genetic structure and dispersal across a fragmented landscape in cerulean warblers (<Emphasis Type="Italic">Dendroica cerulea</Emphasis>)

Cerulean warblers (Dendroica cerulea) have experienced significant declines across their breeding range and presently exist in disjunct populations, largely because of extensive loss and fragmentation of their breeding and wintering habitat. Despite this overall decline, a recent north-eastern expansion of the breeding range has been proposed, and some researchers have suggested that the eastern Ontario population may be acting as a source population maintaining sink populations elsewhere. However, little is known about either the geographic distribution of genetic variation or dispersal in these birds. We assayed variation in five microsatellite loci and a 366 base-pair fragment of the mitochondrial control region among 154 cerulean warblers from five populations throughout the breeding range. No evidence of population genetic structure was found. Assignment tests suggested that six individuals were either inter-population migrants or descendants of recent migrants. The lack of population genetic structure is probably due to a combination of historical association and contemporary dispersal. Population decline does not appear to have reduced genetic variation yet. Overall results suggest that cerulean warblers from Ontario, Illinois, Arkansas and Tennessee should be considered a single genetic management unit for conservation.     

Genetic structure of Asian populations of Bombus ignitus (Hymenoptera: Apidae)

The genetic structure of seven mainland and island Asian populations of Bombus ignitus was investigated using nine microsatellite markers and the sequences of part of the mitochondrial cytochrome b (cytb) gene. While microsatellite markers showed high genetic variability, no sequence variation was found in the cytb gene fragment analyzed. The number of microsatellite alleles ranged from 9 to 24. Gene diversities per locus per population ranged from 0.378 to 0.992. Analysis of molecular variance (AMOVA) and most pairwise F(ST) values showed significant genetic differentiation between mainland and island populations. Cytb sequences data and microsatellite bottleneck tests indicated that almost all populations were subjected to recent bottlenecks. Our results suggest that B. ignitus populations diverged due to recent bottlenecks and geographic isolation.     

Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies

Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea ‘mainland’ and two the ‘aquatic islands’ composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control‐region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post‐colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea.