Genetic differentiation between Apis cerana cerana populations from Damen Island and adjacent mainland in China

Geographic isolation interrupted gene flow between populations leading to population differentiation during the long evolutionary period. In this paper, 33 colonies from Damen Island and 100 colonies from adjacent mainland populations, Juxi and Chixi, were analyzed with both mitochondrial tRNA^leu-COII sequences and five microsatellite loci. The results showed that Apis cerana cerana population from Damen Island significantly differentiated from its adjacent mainland populations. In addition, Damen Island population showed a lower level of genetic diversity in terms of the number of mitochondrial haplotypes while both island and mainland populations showed a low level of genetic diversity with mutilocus analysis. The divergent small island population A.c. cerana might probably have suffered inbreeding and genetic drift as well as limited gene flow across the strait. Our data provides useful information for management and preservation for the Damen Island population.     

Assessment of clinical pathology and pathogen exposure in sea otters (Enhydra lutris) bordering the threatened population in Alaska

Northern sea otter (Enhydra lutris kenyoni) abundance has decreased dramatically over portions of southwest Alaska, USA, since the mid-1980s, and this stock is currently listed as threatened under the Endangered Species Act. In contrast, adjacent populations in south central Alaska, USA, and Russia have been stable to increasing during the same period. Sea otters bordering the area classified in the recent decline were live-captured during 2004-2006 at Bering Island, Russia, and the Kodiak Archipelago, Alaska, USA, to evaluate differences in general health and current exposure status to marine and terrestrial pathogens. Although body condition was lower in animals captured at Bering Island, Russia, than it was at Kodiak, USA, clinical pathology values did not reveal differences in general health between the two regions. Low prevalences of antibodies (<5%) were found in Kodiak, USA, and on Bering Island, Russia, to Toxoplasma gondii, Sarcocystis neurona, and Leptospira interrogans. Exposure to phocine herpesvirus-1 was found in both Kodiak, USA (15.2%), and Bering Island, Russia (2.3%). Antibodies to Brucella spp. were found in 28% of the otters tested on Bering Island, Russia, compared with only 2.7% of the samples from Kodiak, USA. Prevalence of exposure to Phocine distemper virus (PDV) was 41% in Kodiak, USA, but 0% on Bering Island, Russia. Archived sera from southwest and south-central Alaska dating back to 1989 were negative for PDV, indicating exposure occurred in sea otters in Kodiak, USA, in recent years. Because PDV can be highly pathogenic in na?ve and susceptible marine mammal populations, tissues should be examined to explore the contribution of this virus to otter deaths. Our results reveal an increase in exposure to pathogens in sea otters in Kodiak, Alaska, USA, since the 1990 s.     

Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.     

Gene flow between insular, coastal and interior populations of brown bears in Alaska

The brown bears of coastal Alaska have been recently regarded as comprising from one to three distinct genetic groups. We sampled brown bears from each of the regions for which hypotheses of genetic uniqueness have been made, including the bears of the Kodiak Archipelago and the bears of Admiralty, Baranof and Chichagof (ABC) Islands in southeast Alaska. These samples were analysed with a suite of nuclear microsatellite markers. The 'big brown bears' of coastal Alaska were found to be part of the continuous continental distribution of brown bears, and not genetically isolated from the physically smaller 'grizzly bears' of the interior. By contrast, Kodiak brown bears appear to have experienced little or no genetic exchange with continental populations in recent generations. The bears of the ABC Islands, which have previously been shown to undergo little or no female-mediated gene flow with mainland populations, were found not to be genetically isolated from mainland bears. The data from the four insular populations indicate that female and male dispersal can be reduced or eliminated by water barriers of 2–4 km and 7km in width, respectively.     

Genetic assessment of captive Chinese water deer populations in Zhoushan Archipelago,China

Chinese water deer is a rare and vulnerable animal in China because of the poaching for medical use and the habitat loss. In this study, the genetic diversity and population genetic structure of 40 Chinese water deer from three populations in Zhoushan Archipelago were investigated with ten highly polymorphic microsatellite loci, including 4 screened from the nuclear DNA in the study, and 6 selected from the literature. According to the results, these captive populations had a higher genetic diversity than other rare cervid species, such as forest musk deer. No signs of inbreeding were detected. Low genetic differentiation among these populations was found. The probable reasons included the isolation by distance, the exchange among islands, or the supplement of the wild Chinese water deer. We proposed the deer raisers to strengthen the exchanges from different islands or mainland, and if possible, some deer would be returned to the wild to expand the wild population.     

History and fate of a small isolated population of Weddell seals at White Island,Antarctica

Weddell seals (Leptonychotes weddellii Lesson) at White Island, Antarctica form a small, completely enclosed, natural population hypothesized to be of recent origin, likely founded by individuals from nearby Erebus Bay. This population constitutes an ideal model to document a founder event and ensuing genetic drift, with implications for conservation. Here we combined historical accounts, census and tagging data since the late 1960s, and genetic data (41 microsatellite loci and mitochondrial DNA sequences) from 84 individuals representing nearly all individuals present between 1990 and 2000 to investigate the history of the founding of the White Island population, document its population dynamics and evaluate possible future threats. We fully resolved parental relationships over three overlapping generations. Cytonuclear disequilibrium among the first generation suggested that it comprised the direct descendants of a founding group. We estimated that the White Island population was founded by a small group of individuals that accessed the island during a brief break in the surrounding sea ice in the mid-1950s, consistent with historical accounts. Direct and indirect methods of calculating effective population size were highly congruent and suggested a minimum founding group consisting of three females and two males. The White Island population showed altered reproductive dynamics compared to Erebus Bay, including highly skewed sex ratio, documented inbred mating events, and the oldest known reproducing Weddell seals. A comparison with the putative source population showed that the White Island population has an effective inbreeding coefficient (F _e) of 0.29. Based on a pedigree analysis including the hypothesized founding group, 86% of the individuals for whom parents were known had inbreeding coefficients ranging 0.09–0.31. This high level of inbreeding was correlated with reduced pup survival. Seals at White Island therefore face the combined effects of low genetic variability, lack of immigration, and inbreeding depression. Ultimately, this study provides evidence of the effects of natural isolation on a large, long-lived vertebrate and can provide clues to the potential effects of anthropogenic-caused isolation of similar taxa.     

Inbreeding and surnames: a projection into Easter Island's past

The population of Easter Island is one of the most interesting extant human communities due to its unique demographic history, its geographic isolation, and the development of an incomparable culture characterized by the towering "Moais" and its enigmatic writing. Following the colonization of its population by Polynesians from the Mangarevan Islands in the 5th century AD, the island remained isolated up until the middle of the 20th century. Under these conditions, with endogamy levels fluctuating between 61.04-96.54% and given such a small population, a high rate of inbreeding, and consequently, an elevated level of genetic relationships would be expected. Using data from church and civil records, we calculated the consanguinity of the population of Rapa Nui. The results of this analysis do not support the hypothesis of a high level of consanguinity (alpha = 0.00028 and F(t) = 0.0007, with F(r) = 0.00586 and F(n) = -0.00519), suggesting instead the existence of a strategy used to avoid marriage between close relatives. To explain these observations, the structure and exchange dynamics of the population were studied in the tribes, known locally as "Mata." The results of this analysis suggest a tendency toward the avoidance of inbreeding within tribes, in order to decrease the rate of endogamy in each group. This is consistent with ethnographic observations from the beginning of the 20th century that support the existence of strict regulations to prevent inbreeding between closely related individuals. Furthermore, we confirm that this situation dates back to a period before the "refounding" of Easter Island. Our results demonstrate that conditions of geographical isolation are not in themselves sufficient to produce an elevated inbreeding coefficient, revealing Easter Island as an interesting example of how cultural rules can shape the genetic structure of a population.     

Strong spatial genetic structure in five tropical Piper species: should the Baker–Fedorov hypothesis be revived for tropical shrubs?

Fifty years ago, Baker and Fedorov proposed that the high species diversity of tropical forests could arise from the combined effects of inbreeding and genetic drift leading to population differentiation and eventually to sympatric speciation. Decades of research, however have failed to support the Baker-Fedorov hypothesis (BFH), and it has now been discarded in favor of a paradigm where most trees are self-incompatible or strongly outcrossing, and where long-distance pollen dispersal prevents population drift. Here, we propose that several hyper-diverse genera of tropical herbs and shrubs, including Piper (>1,000 species), may provide an exception. Species in this genus often have aggregated, high-density populations with self-compatible breeding systems; characteristics which the BFH would predict lead to high local genetic differentiation. We test this prediction for five Piper species on Barro Colorado Island, Panama, using Amplified Fragment Length Polymorphism (AFLP) markers. All species showed strong genetic structure at both fine- and large-spatial scales. Over short distances (200-750 m) populations showed significant genetic differentiation (Fst 0.11-0.46, P < 0.05), with values of spatial genetic structure that exceed those reported for other tropical tree species (Sp = 0.03-0.136). This genetic structure probably results from the combined effects of limited seed and pollen dispersal, clonal spread, and selfing. These processes are likely to have facilitated the diversification of populations in response to local natural selection or genetic drift and may explain the remarkable diversity of this rich genus.     

Cultural remains in local and regional context on the central Alaska Peninsula: housepits, language, and cultural affinities at Marraatuq after 1000 B.P

Professor Dumond's research on the Alaska Peninsula provided information that prior to 1,000 years ago people of both sides of the Alaska Peninsula shared material culture and exhibited subsistence interests that persisted into historic times, During the Late Precontact Era (ca. 1100 A.D. to mid-1700s) these Alutiiq societies shared cultural traits including language, house styles, and material culture with their relatives and neighbors on Kodiak Island. Until recently, few data were available regarding potential variability in house construction techniques, or styles and functions of Alutiiq semi-subterranean houses of this era found on the Alaska Peninsula, This paper provides examples of a few known prehistoric and historic Alaska Peninsula and Kodiak Alutiiq houses and presents previously unreported data from archaeological tests at Marraatuq on the Central Alaska Peninsula, Taken together with Dumond's 1998-1999 field work at Leader Creek and archaeological research on Kodiak Island, the work provides further evidence that interregional interaction was strong during the Late Precontact Era. However, large population centers and ranked political hierarchies probably were not hallmarks of central Alaska Peninsula communities during the Late Precontact Era and historic times as they were on the Kodiak and Aleutian islands.     

Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer (Odocoileus virginianus)

Islands are generally colonized by few individuals which could lead to a founder effect causing loss of genetic diversity and rapid divergence by strong genetic drift. Insular conditions can also induce new selective pressures on populations. Here, we investigated the extent of genetic differentiation within a white‐tailed deer (Odocoileus virginianus) population introduced on an island and its differentiation with its source mainland population. In response to their novel environmental conditions, introduced deer changed phenotypically from mainland individuals, therefore we investigated the genetic bases of the morphological differentiation. The study was conducted on Anticosti Island (Québec, Canada) where 220 individuals were introduced 120 years ago, resulting in a population size over 160,000 individuals. We used genotyping‐by‐sequencing (GBS) to generate 8,518 filtered high‐quality SNPs and compared patterns of genetic diversity and differentiation between the continental and Anticosti Island populations. Clustering analyses indicated a single panmictic island population and no sign of isolation by distance. Our results revealed a weak, albeit highly significant, genetic differentiation between the Anticosti Island population and its source population (mean F_ST = 0.005), which allowed a population assignment success of 93%. Also, the high genetic diversity maintained in the introduced population supports the absence of a strong founder effect due to the large number of founders followed by rapid population growth. We further used a polygenic approach to assess the genetic bases of the divergent phenotypical traits between insular and continental populations. We found loci related to muscular function and lipid metabolism, which suggested that these could be involved in local adaptation on Anticosti Island. We discuss these results in a harvest management context.     

Genetic analysis of an isolated red deer (<Emphasis Type="Italic">Cervus elaphus</Emphasis>) population showing signs of inbreeding depression

In the present study, we analysed 18 red deer specimens from a small (N = 50) and isolated population in Schleswig-Holstein, northern Germany, with respect to variability at nine polymorphic microsatellite loci and 439 bp of the mitochondrial DNA control region. Several cases of brachygnathy (shortened lower jaw), commonly associated with inbreeding depression, have been recorded in the population. Genetic variability was very low compared with other European red deer populations including the neighbouring population from which the population under study was derived some 130 years ago. The effective population size was estimated to be seven individuals corresponding to an increase in inbreeding (or a loss of heterozygosity) of 7% each generation. This value is seven times higher than the theoretical threshold level up to which natural selection is believed to counteract the fixation of deleterious alleles in the gene pool. As a consequence, the population urgently needs genetic input from other populations to overcome the negative effects of random drift and inbreeding. To our knowledge, this study is one of the first to genetically analyse a red deer population showing strong signs of inbreeding depression.     

Influence of translocation strategy and mating system on the genetic structure of a newly established population of island ptarmigan

Island populations and populations established by reintroductions are prone to extinction, in part because they are vulnerable to deterministic and stochastic phenomena associated with geographic isolation and small population size. As population size declines, reduced genetic diversity can result in decreased fitness and reduced adaptive potential, which may hinder short- or long-term population viability. We used 32 microsatellite markers to investigate the conservation genetics of a newly established population of Evermann’s Rock Ptarmigan (Lagopus muta evermanni) at Agattu Island, in the western Aleutian Archipelago, Alaska. We found low genetic diversity (observed heterozygosity = 0.41, allelic richness = 2.2) and a small effective population size (N _e  = 28.6), but a relatively large N _e /N ratio = 0.55, which was attributed to multiple paternity in 80% of the broods and low reproductive skew among males (λ = 0.29). Moreover, successful breeding pairs were less related to each other than random male–female pairs. For conservation efforts based on reintroductions, a mating system with high rates of multiple paternity may facilitate retention of genetic diversity, thereby reducing the potential for inbreeding in small or isolated populations. Our results underscore the importance of quantifying genetic diversity and understanding the breeding behavior of translocated populations.     

Genetic structuring among Alaskan Pacific herring populations identified using microsatellite variation

Five highly variable microsatellite loci were used to investigate population structuring in Pacific herring Clupea pallasi collected from Kodiak Island, two sites in the Bering Sea and four sites within Prince William Sound, Alaska. All loci revealed high levels of variability with heterozygosity estimates ranging from 86 to 97% (mean heterozygosity: 89%). The variation was structured significantly among sites suggesting that the samples investigated were genetically distinct from each other. Genetic divergence was greatest between populations from the Bering Sea and those from Prince William Sound. The Kodiak Island and Point Chalmers samples appeared to be distinct from the Prince William Sound and Bering Sea populations. The observed genetic distance relationships among samples could be explained largely in terms of geographical separation.     

Re‐mating across years and intralineage polygyny are associated with greater than expected levels of inbreeding in wild red deer

The interaction between philopatry and nonrandom mating has important consequences for the genetic structure of populations, influencing co‐ancestry within social groups but also inbreeding. Here, using genetic paternity data, we describe mating patterns in a wild population of red deer (Cervus elaphus) which are associated with marked consequences for co‐ancestry and inbreeding in the population. Around a fifth of females mate with a male with whom they have mated previously, and further, females frequently mate with a male with whom a female relative has also mated (intralineage polygyny). Both of these phenomena occur more than expected under random mating. Using simulations, we demonstrate that temporal and spatial factors, as well as skew in male breeding success, are important in promoting both re‐mating behaviours and intralineage polygyny. However, the information modelled was not sufficient to explain the extent to which these behaviours occurred. We show that re‐mating and intralineage polygyny are associated with increased pairwise relatedness in the population and a rise in average inbreeding coefficients. In particular, the latter resulted from a correlation between male relatedness and rutting location, with related males being more likely to rut in proximity to one another. These patterns, alongside their consequences for the genetic structure of the population, have rarely been documented in wild polygynous mammals, yet they have important implications for our understanding of genetic structure, inbreeding avoidance and dispersal in such systems.     

Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago

We assessed genetic differentiation and diversity in 14 populations of sika deer (Cervus nippon) from Japan and four populations of sika deer introduced to the UK, using nine microsatellite loci. We observed extreme levels of differentiation and significant differences in diversity between populations. Our results do not support morphological subspecies designations, but are consistent with previous mitochondrial DNA analyses which suggest the existence of two genetically distinct lineages of sika deer in Japan. The source of sika introduced to the UK was identified as Kyushu. The underlying structure of Japanese populations probably derives from drift in separate glacial refugia and male dispersal limited by distance. This structure has been perturbed by bottlenecks and habitat fragmentation, resulting from human activity from the mid-nineteenth century. Most current genetic differentiation and differences in diversity among populations probably result from recent drift. Coalescent model analysis suggests sika on each of the main Japanese islands have experienced different recent population histories. Hokkaido, which has large areas of continuous habitat, has maintained high levels of gene flow. In Honshu the population is highly fragmented and is likely to have been evolving by drift alone. In Kyushu there has been a balance between gene flow and drift but all the populations have experienced high levels of drift. Habitat fragment size was not significantly associated with genetic diversity in populations but there was a significant correlation between habitat fragment size and effective population size.     

Temporal genetic change in the last remaining population of woolly mammoth

During the Late Pleistocene, the woolly mammoth (Mammuthus primigenius) experienced a series of local extinctions generally attributed to human predation or environmental change. Some small and isolated populations did however survive far into the Holocene. Here, we investigated the genetic consequences of the isolation of the last remaining mammoth population on Wrangel Island. We analysed 741 bp of the mitochondrial DNA and found a loss of genetic variation in relation to the isolation event, probably caused by a demographic bottleneck or a founder event. However, in spite of ca 5000 years of isolation, we did not detect any further loss of genetic variation. Together with the relatively high number of mitochondrial haplotypes on Wrangel Island near the final disappearance, this suggests a sudden extinction of a rather stable population.     

Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment

Populations with spatially restricted gene flow are characterized by genetic differentiation that may be positively correlated with the geographic distance separating populations, a pattern known as isolation by distance (IBD). Here we examined the fine-scale genetic structure of 66 chum salmon (Oncorhynchus keta) populations spawning in Alaska waterways and explored patterns of IBD using 90 nuclear and 3 mitochondrial single nucleotide polymorphisms. Estimating population structure of chum salmon in Alaska is of increasing concern because of fluctuating census sizes and the uncertain effects of harvest on specific populations. We hypothesized that IBD would be present because chum salmon spawn in coastal rivers that are distributed along a linear array and gene flow is spatially restricted due to homing. Evidence of very weak IBD was found throughout the region (R² = 0.06, p < 0.0001) but the strength of the IBD relationship varied greatly over different spatial scales and geographic regions. Decomposed pairwise regression analyses identified nine outlier populations to regional IBD patterns, suggesting that geographic distance is not the only factor influencing genetic differentiation in the region. Instead, population structure appears to be heavily influenced by glacial history of the region and the presence of a glacial refugium on Kodiak Island.     

Evaluation of introgressive hybridization among Cervidae in Japan's Kinki District via two novel genetic markers developed from public NGS data

Hybridization and backcrossing of native populations with introduced species can lead to introgression and genetic alteration. In this study, we evaluated introgression in 43 deer from a potential hybrid zone around Okinoshima Island, Kinki District, Japan. This region witnessed the migration of a hybrid population (cross between the Formosan sika deer [Cervus nippon taiouanus] and other deer species) that could potentially breed with the native Japanese sika deer (C. n. centralis). We used an existing genetic marker for the mitochondrial cytochrome b gene and two novel markers for nuclear DNA, developed using publicly available next‐generation sequencing data. We identified one mainland deer with a mitochondrial haplotype identical to that of the Formosan sika deer as well as nuclear heterozygous sequences identical to those of Formosan and Japanese sika deer. This suggests that the mainland deer is a hybrid offspring of the Okinoshima population and native deer. However, only Japanese sika deer sequences were found in the other 42 samples, indicating limited introgression. Nevertheless, hybridization pre‐ and postintroduction in the Okinoshima population could cause multispecies introgression among Japanese sika deer, negatively affecting genetic integrity. We developed a simple test based on polymerase chain reaction–restriction fragment length polymorphism to detect introgression in natural populations. Our method can accelerate genetic monitoring of Japanese sika deer in Kinki District. In conclusion, to prevent further introgression and maintain genetic integrity of Japanese sika deer, we recommend establishing fences around Okinoshima Island to limit migration, besides a continued genetic monitoring of the native deer.     

Assessing genetic diversity for conservation management: a case study of a threatened reptile

The consequences of inbreeding in small isolated populations are well documented, yet populations are often managed in isolation to avoid irreversibly mixing genetic lineages and to maintain the historic integrity of each population. Three remaining populations of Whitaker's skink ( Cyclodina whitakeri ) in New Zealand, remnants of a once wider distribution, illustrate the conflict between this genetic goal (separate management of populations) with the more tangible and immediate threats of small population size and inbreeding. Middle and Castle Islands harbour populations of C. whitakeri and have been separated from each other and from the mainland for ∼10 000 years. The single mainland population at Pukerua Bay is extremely small, declining and deemed a high priority for management. We sequenced a 550 bp region of mitochondrial DNA (mtDNA,ND2) and genotyped animals from all three populations at 13 microsatellite loci. The population of C. whitakeri at Pukerua Bay showed marked differences from the island populations at both mtDNA (unique, fixed haplotype) and microsatellite loci ( F _ST∼0.20), and private alleles were detected at a high frequency (24% of all alleles). However, we attribute this pattern to an historic genetic gradient coupled with rapid genetic drift. Further, animals in captivity show genetic signatures of both Pukerua Bay and island populations, despite the goal to maintain a pure Pukerua Bay stock. The mixed genetic stock in captivity provides an opportunity for the addition of skinks from Middle Island to evaluate the risks of further population hybridization, including the disruption of potential local adaptation, while mitigating the risks of inbreeding.