Genetic consequences of a severe population bottleneck in the Guadalupe fur seal (Arctocephalus townsendi)

Population bottlenecks may lead to diminished genetic variability and correlative effects on fitness. The Guadalupe fur seal was nearly exterminated by commercial sealers during the late 18th and early 19th centuries. To determine the genetic consequences of this population bottleneck, we compared the variation at a 181 bp section of the mitochondrial DNA (mtDNA) control region from the bones of 26 prebottleneck fur seals versus variation in the extant population. We found 25 different mtDNA genotypes in the prebottleneck fur seals and only 7 genotypes among 32 extant fur seals, including only one of the ancient genotypes. These data demonstrate a substantial loss of genetic variability correlating with the recent population bottleneck. We also found from several genetic measures that the prehistoric population of Guadalupe fur seals was robust and that it had been increasing at some time during the late prehistoric period. Continued recovery of this species may, however, owe more to more immediate nongenetic factors, such as poaching and local availability of food resources during the breeding season and consequent effects on pup survival, than on the reduced genetic variability.     

Genetic consequences of a demographic bottleneck in the Scandinavian arctic fox

Demographic bottlenecks can result in a loss of genetic variation due to the bottleneck effect and subsequent genetic drift. The arctic fox population in Scandinavia went through a severe demographic bottleneck in the early 20th century, and is today classified as critically endangered. In this study, we investigated the pre-bottleneck genetic variation in Scandinavia and compared it to modern samples from Scandinavia and North Russia. Variation in the mtDNA control region and five microsatellite loci was examined through ancient DNA analysis on museum specimens. The microsatellite data from the museum specimens was further used to simulate the expected effect of the bottleneck. The arctic foxes in Scandinavia have lost approximately 25% of the microsatellite alleles and four out of seven mtDNA haplotypes. The results also suggest that the genetic differentiation between North Russia and Scandinavia has doubled over the last 100 years. However, the level of heterozygosity was significantly higher than expected from the simulations. This highlights both the advantage of using museum specimens and the importance of generating specific predictions in conservation genetics.     

Variation in the mitochondrial control region in the Juan Fernández fur seal (Arctocephalus philippii)

The Juan Fernandez fur seal (Arctocephalus philippii was allegedly extremely abundant, numbering as many as 4 million prior to sealing which continued from the late 17th to the late 19th century. By the end of the sealing era the species was thought to be extinct until they were rediscovered at Alejandro Selkirk Island in 1965. Historic records would suggest that the species underwent a substantial population bottleneck as a result of commercial sealing, and from population genetic theory we predicted that the genetic variability in the species would be low. We compared the mtDNA control region sequence from 28 Juan Fernandez fur seals from two islands in the Juan Fernandez Archipelago (Chile). Contrary to expectation, we found that variation in the Juan Fernandez fur seals is not greatly reduced in comparison to other pinniped taxa, especially given the apparent severity of the bottleneck they underwent. We also determined minor, but significantly different haplotype frequencies among the populations on the two islands (Alejandro Selkirk and Robinson Crusoe Islands), but no difference in their levels of variability. Such differences may have arisen stochastically via a recent founder event from Alejandro Selkirk to Robinson Crusoe Island or subsequent genetic drift.     

The strength and timing of the mitochondrial bottleneck in salmon suggests a conserved mechanism in vertebrates

In most species mitochondrial DNA (mtDNA) is inherited maternally in an apparently clonal fashion, although how this is achieved remains uncertain. Population genetic studies show not only that individuals can harbor more than one type of mtDNA (heteroplasmy) but that heteroplasmy is common and widespread across a diversity of taxa. Females harboring a mixture of mtDNAs may transmit varying proportions of each mtDNA type (haplotype) to their offspring. However, mtDNA variants are also observed to segregate rapidly between generations despite the high mtDNA copy number in the oocyte, which suggests a genetic bottleneck acts during mtDNA transmission. Understanding the size and timing of this bottleneck is important for interpreting population genetic relationships and for predicting the inheritance of mtDNA based disease, but despite its importance the underlying mechanisms remain unclear. Empirical studies, restricted to mice, have shown that the mtDNA bottleneck could act either at embryogenesis, oogenesis or both. To investigate whether the size and timing of the mitochondrial bottleneck is conserved between distant vertebrates, we measured the genetic variance in mtDNA heteroplasmy at three developmental stages (female, ova and fry) in chinook salmon and applied a new mathematical model to estimate the number of segregating units (N(e)) of the mitochondrial bottleneck between each stage. Using these data we estimate values for mtDNA Ne of 88.3 for oogenesis, and 80.3 for embryogenesis. Our results confirm the presence of a mitochondrial bottleneck in fish, and show that segregation of mtDNA variation is effectively complete by the end of oogenesis. Considering the extensive differences in reproductive physiology between fish and mammals, our results suggest the mechanism underlying the mtDNA bottleneck is conserved in these distant vertebrates both in terms of it magnitude and timing. This finding may lead to improvements in our understanding of mitochondrial disorders and population interpretations using mtDNA data.     

Population genetic structure of the spotted seal Phoca largha along the Coast of Hokkaido,based on mitochondrial DNA sequences

Population genetic structure of the spotted seal, Phoca largha, along coastal regions of Hokkaido was investigated, using mitochondrial DNA (mtDNA) sequences. A 571-bp fragment of the mtDNA control region and adjacent threonine and proline transfer RNA genes was sequenced from 66 seals. We categorized all individuals into three groups considering sampling area and season: twenty-four seals from the Sea of Okhotsk in winter, 11 seals from the Sea of Okhotsk coast in fall, and 31 seals from the Sea of Japan coast in winter. From the 66 animals, 57 haplotypes were identified. Compared with the harbor seal sequence, all spotted seals examined shared two deletions in the control region, which distinguished between the two species. Forty-nine haplotypes were represented by a single individual, and haplotypes shared by more than two animals were generally restricted to same sampling-groups. Phylogenetic trees did not indicate clear geographic differences among the three groups. An Analysis of molecular variances (AMOVA) did not showed any significant population genetic structure in Hokkaido spotted seals (Phi(st )= -0.003). Our results showed a high level of diversity but no genetic structure, and did not deny the possibility that seals in the Okhotsk breeding concentration mainly stayed in the fall Okhotsk and also inhabited in the winter Sea of Japan.     

Colonization history of the high-arctic pink-footed goose Anser brachyrhynchus

Population structure and phylogeography of the pink-footed goose, Anser brachyrhynchus Baillon 1833, was studied using mtDNA control region sequences (221 bp) from 142 individuals. Present breeding areas of the species in Greenland, Iceland, and Svalbard were largely covered by ice during the late Pleistocene. In pairwise comparisons phiST estimates showed significant differentiation among eastern and western populations, whereas sampling localities within both areas were not differentiated. The mtDNA data indicate that the populations have separated recently (less than 10 000 years ago) and present breeding areas were colonized from one refugial population. The levels of haplotype and nucleotide diversity were approximately five times higher for the eastern population compared to the western population and suggest that the latter was colonized by a subset of eastern birds. Time to the most recent common ancestor of the species is 32 000-46 000 years, i.e. the present mtDNA variation of the pink-footed goose has accumulated during the last 0.1 My. Estimates of the long-term female effective population size (5400-7700 for the eastern population) imply that the refugial population of the pink-footed goose has been large. Tundra habitats were more extensive in cold periods of the late Pleistocene than today and may have sustained population sizes that allowed the accumulation of extant genetic polymorphism. It is not probable that the postulated small refugial areas in the high latitudes had a significant role in maintaining this diversity.     

Mitochondrial phylogeography of the Eurasian beaver Castor fiber L

Nucleotide variation in an approximately 490 bp fragment of the mitochondrial DNA control region (mtDNA CR) was used to describe the genetic variation and phylogeographical pattern in the Eurasian beaver (Castor fiber) over its entire range. The sampling effort was focused on the relict populations that survived a drastic population bottleneck, caused by overhunting, at the end of the 19th century. A total of 152 individuals grouped into eight populations representing all currently recognized subspecies were studied. Sixteen haplotypes were detected, none of them shared among populations. Intrapopulation sequence variation was very low, most likely a result of the severe bottleneck. Extreme genetic structure could result from human-mediated extinction of intermediate populations, but it could also be an effect of prior substantial structuring of the beaver populations with watersheds of major Eurasian rivers acting as barriers to gene flow. Phylogenetic analysis revealed the presence of two mtDNA lineages: eastern (Poland, Lithuania, Russia and Mongolia) and western (Germany, Norway and France), the former comprising more divergent haplotypes. The low level of sequence divergence of the entire cytochrome b gene among six individuals representing six subspecies suggests differentiation during the last glacial period and existence of multiple glacial refugia. At least two evolutionary significant units (ESU) can be identified, the western and the eastern haplogroup. The individual relict populations should be regarded as management units, the eastern subspecies possibly also as ESUs. Guidelines for future translocations and reintroductions are proposed.     

Low genetic diversity in the vulnerable Goitred Gazelle,Gazella subgutturosa (Cetartiodactyla: Bovidae), in Iran: potential genetic consequence of recent population declines

The Goitered Gazelle, Gazella subgutturosa, is the most widespread gazelle species in the Middle East and central Asia inhabiting desert and semi-desert habitats. Today it is threatened and its geographic range and population size have experienced significant decline in the last decades. In Iran, the remnant populations are confined to fragmented habitats. We aimed to characterise genetic diversity and phylogenetic status of the populations of Goitered Gazelle in Central Iran and to evaluate the potential effect of a historic population bottleneck on the genetic variation of today’s population. We used noninvasive sampling to uncover structure and level of genetic variation in a fragment of the cytochrome-b gene from 170 samples. Genealogical analyses were performed using HKY+I model and phylogenetic trees reconstructed using Bayesian inference and maximum likelihood. We found extremely low levels of genetic variation, with altogether only five haplotypes in samples from different populations. Overall haplotype diversity was 0.081 and nucleotide diversity 0.0003. The mean observed mismatch between any two sequences was 0.093 with the largest peak for small numbers. The mismatch distribution fit the model of population expansion and suggested that gazelles had experienced a sudden expansion. An unrooted median-joining network analysis of mtDNA haplotypes showed a star-like structure which few mutations steps separating the haplotypes from other regions. Our findings strengthen the urgency of preserving the species’ genetic diversity to prevent local extinction.     

Striking differentiation of sub-populations within a genetically homogeneous isolate (Ogliastra) in Sardinia as revealed by mtDNA analysis

Since the reduced genetic diversity found in isolates should simplify the study of complex traits, analyses of patterns of homogeneity within populations are of particular interest. We analysed the mtDNA haplogroups and hypervariable segment I (HVS-I) sequences of 475 individuals from a geographically restricted and isolated area (Ogliastra) within Sardinia, comprehending 175 random samples from 20 out of 23 villages. The remaining 300 subjects were chosen from the other three villages, Talana, Urzulei and Perdasdefogu, by sampling all maternal lineages. A comparison with other European populations reveals that Ogliastra ranks among the most genetically homogenous population and that it has been small and isolated throughout its history. The lack of variation and the high genetic homogeneity indicate that an important founder event and a demographic expansion took place during the Neolithic (~ 7,700 years before present) in Ogliastra's mtDNA gene pool. We present highly resolved phylogenetic networks for Ogliastra and for the three sub-isolates. MtDNA differentiation in the sub-populations versus Ogliastra is revealed by a strong demarcation in their genetic pools due to distinctive founder effects and genetic drift. We found that genetic homogeneity strictly depends on a scale factor in population size and on sampling methodology. The outstanding homogeneity and the reduced female gene pool observed in Ogliastra, in the European context, hide an extremely marked differentiation in sub-isolates originated from the same archaic population. Although Ogliastra can be considered a genetically homogeneous isolate, small villages' divergent genetic histories underline the importance of more systematic analysis of DNA variation between and within populations.C. Fraumene and E. Petretto contributed equally to this work     

Impact of population bottlenecks on genetic variation and the importance of life-history; a case study of the northern elephant seal

This paper reviews some of the important factors related to the impact of population bottlenecks, using the northern elephant seal (Mirounga angustirostrus) as a case study for illustration. The northern elephant seal was hunted extensively in the 19th century and forced through a bottleneck of approximately 10–20 seals. All measures of molecular genetic variation show current levels for the northern elephant seal to be low. Levels of genetic variation were compared with expectations based on a simulation model that recapitulates demographic growth, based on age-specific data on reproduction and mortality. Predictions from the simulation model are then presented to illustrate the importance of differences in life-history strategy and skewed reproductive success. Either high reproductive skew (e.g. polygyny) or a low growth rate in a population can increase the impact of a bottleneck on molecular variation. Severe population bottlenecks can also disrupt aspects of developmental stability and thereby increase the fluctuating asymmetry and variability of quantitative traits. A comparison of skulls collected before and after the bottleneck showed this to have occurred for some elephant seal quantitative characters.     

Reduced genetic variation in Norwegian Peregrine Falcons Falco peregrinus indicated by minisatellite DNA fingerprinting

The Scandinavian Peregrine Falcon Falco peregrinus population went through a severe population bottleneck during the second half of the twentieth century, and was almost extinct during the 1970s. This event may have reduced the amount of genetic variation in the population. With this background, a comparative study, using multilocus, minisatellite DNA fingerprinting, was carried out on broods of the Peregrine Falcon, the Merlin Falco columbarius and the Eurasian Hobby Falco subbuteo from south-east Norway. Band-sharing analysis of DNA fingerprints was used to test whether broods of Peregrine Falcons showed a greater between-nest similarity in their fingerprint profiles than did broods of the two congeneric species breeding in the same region, which have not undergone any recent population bottlenecks. The results show that broods of Peregrine Falcons were significantly more similar to each other genetically than were broods of either Merlins or Eurasian Hobbies. Furthermore, there was a positive correlation between the similarity in minisatellite DNA and the similarity in a set of 11 microsatellite loci analysed for a subset of the Peregrine Falcon samples. The correlation supports the assumption that minisatellite fingerprints provide a reliable indicator of overall genetic similarity, i.e. relatedness, between breeding pairs in the population. Hence we can conclude that broods of Peregrine Falcons were genetically more related to each other than were broods of the other two species. The high similarity in minisatellite DNA between broods indicates a loss of genetic variation in the Peregrine Falcon population caused by the bottleneck, but this explanation can only be verified through a comparative genetic study of individuals sampled before and after the bottleneck event.     

Historical demography, selection, and coalescence of mitochondrial and nuclear (genes in Prochilodus species of northern South America

Fishes of the genus Prochilodus are ecologically and commercially important, ubiquitous constituents of large river biota in South America. Recent ecologic and demographic studies indicate that these fishes exist in large, stable populations with adult census numbers exceeding one million individuals. Abundance data present a stark contrast to very low levels of genetic diversity (theta) and small effective population sizes (Ne) observed in a mitochondrial (mt) DNA dataset obtained for two species, Prochilodus mariae, and its putative sister taxon, Prochilodus rubrotaeniatus. Both species occupy major river drainages (Orinoco, Essequibo, and Negro) of northeastern South America. Disparity between expectations based on current abundance and life history information and observed genetic data in these lineages could result from historical demographic bottlenecks, or alternatively, natural selection (i.e., a mtDNA selective sweep). To ascertain underlying processes that affect mtDNA diversity in these species we compared theta and Ne estimates obtained from two, unlinked nuclear loci (calmodulin intron-4 and elongation factor-1alpha intron-6) using an approach based on coalescent theory. Genetic diversity and Ne estimated from mtDNA and nuclear sequences were uniformly low in P. rubrotaeniatus from the Rio Negro, suggesting that this population has encountered a historical bottleneck. For all P. mariae populations, theta and Ne based on nuclear sequences were comparable to expectations based on current adult census numbers and were significantly greater than mtDNA estimates, suggesting that a selective mtDNA sweep has occurred in this species. Comparative genetic analysis indicates that a suite of evolutionary processes involving historical demography and natural selection have influenced patterns of genetic variation and speciation in this important Neotropical fish group.     

Post-bottleneck mtDNA diversity in a free-living population of European bison: implications for conservation

A free-living population of European bison Bison bonasus in the Białowieża Primeval Forest originated from only seven founder animals after a severe bottleneck that occurred at the beginning of the 20th century. Consequently, the contemporary population of the species is characterized by low genetic diversity. We studied a total of 195 individuals (127 males and 68 females). A 1429 bp fragment of mitochondrial DNA (mtDNA) including the D-loop region was analyzed in 87 individuals and revealed only three distinct haplotypes. Nucleotide ( π ) and haplotype ( H _d) diversity values were estimated for the European bison and were compared with π and H _d estimated from three individuals of American bison Bison bison . Very low diversity values were found in the European bison in comparison with the diversity values found in the American bison. The low mtDNA variability in the European bison is in concordance with theoretical expectations for a species that has undergone a severe and recent bottleneck. A management strategy for the preservation of the rare and very rare haplotypes present in the Białowieża population of the European bison is discussed. Furthermore, all 195 individuals were investigated for heteroplasmy involving these three haplotypes, in order to detect a possible association between heteroplasmy and the incidence of males affected by posthitis , a disease that affects the male reproductive organs, leading to necrotic lesions. Heteroplasmy was found in 15 females, in 17 males affected by posthitis and in 11 non-affected males, and no significant association was found.     

Molecular Population Genetics of Mtdna Size Variation in Crickets

Nucleotide sequence analysis of a region of cricket (Gryllus firmus) mtDNA showing discrete length variation revealed tandemly repeated sequences 220 base pairs (bp) in length. The repeats consist of 206 bp sequences bounded by the dyad symmetric sequence 5'GGGGGCATGCCCCC3'. The sequence data showed that mtDNA size variation in this species is due to variation in the number of copies of tandem repeats. Southern blot analysis was used to document the frequency of crickets heteroplasmic for two or more different-sized mtDNAs. In New England populations of G. firmus and a close relative Gryllus pennsylvanicus approximately 60% of the former and 45% of the latter were heteroplasmic. From densitometry of autoradiographs the frequencies of mtDNA size classes were determined for the population samples and are shown to very different in the two species. However, in populations where hybridization between the two species has occurred, the frequencies of size classes and cytoplasmic genotypes in each species' distinct mtDNA lineage were shifted in a manner suggesting nuclear-cytoplasmic interactions. The data were applied to reported diversity indices and hierarchical statistics. The hierarchical statistics indicated that the greatest proportion of variation for mtDNA size was due to variation among individuals in their cytoplasmic genotypes (heteroplasmic or homoplasmic state). The diversity indices were used to estimate a per-generation mutation rate for size variants of 10(-4). The data are discussed in light of the relationship between genetic drift and mutation in maintaining variation for mtDNA size.     

Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus)

Genetic analyses of bird subspecies designated as conservation units can address whether they represent units with independent evolutionary histories and provide insights into the evolutionary processes that determine the degree to which they are genetically distinct. Here we use mitochondrial DNA control region sequence and six microsatellite DNA loci to examine phylogeographical structure and genetic differentiation among five North American grasshopper sparrow (Ammodramus savannarum) populations representing three subspecies, including a population of the endangered Florida subspecies (A. s. floridanus). This federally listed taxon is of particular interest because it differs phenotypically from other subspecies in plumage and behaviour and has also undergone a drastic decline in population size over the past century. Despite this designation, we observed no phylogeographical structure among populations in either marker: mtDNA haplotypes and microsatellite genotypes from floridanus samples did not form clades that were phylogenetically distinct from variants found in other subspecies. However, there was low but significant differentiation between Florida and all other populations combined in both mtDNA (FST = 0.069) and in one measure of microsatellite differentiation (theta = 0.016), while the non-Florida populations were not different from each other. Based on analyses of mtDNA variation using a coalescent-based model, the effective sizes of these populations are large (approximately 80,000 females) and they have only recently diverged from each other (< 26,000 ybp). These populations are probably far from genetic equilibrium and therefore the lack of phylogenetic distinctiveness of the floridanus subspecies and minimal genetic differentiation is due most probably to retained ancestral polymorphism. Finally, levels of variation in Florida were similar to other populations supporting the idea that the drastic reduction in population size which has occurred within the last 100 years has not yet had an impact on levels of variation in floridanus. We argue that despite the lack of phylogenetic distinctiveness of floridanus genotypes the observed genetic differentiation and previously documented phenotypic differences justify continued designation of this subspecies as a protected population segment.     

Admixture promotes genetic variation in bottlenecked moose populations in eastern Poland

Human activity has led to severe bottlenecks in many wildlife species in the recent past. This usually increases the strength of genetic drift, leading to loss of genetic variation. Gene flow may however counteract the genetic consequences of small population size. Using 11 of 38 tested microsatellite loci and five moose populations in eastern Poland, we investigated the effects of two phenomena: bottlenecks that occurred in the nineteenth century and the first half of twentieth century, and admixture after moose populations expanded demographically and spatially in eastern Poland after the Second World War. The statistical tests indicated a recent bottleneck in all the studied samples with respect to H _E and low Garza–Williamson index values. The Biebrza population, which consists of autochthonous moose representing a branch of the Central Europe mitochondrial DNA (mtDNA) clade and immigrants belonging to the Ural clade, is one of the most variable populations of this species. AMOVA, PCA, and STRUCTURE analyses all revealed significant population structuring, with most probable existence of K?=?2 genetically distinct clusters that exhibited a relatively high level of admixture. Analysis of recent dispersal rates demonstrated that population from the Biebrza Valley may supply individuals to the other four studied moose populations. We also found female-biased sex ratio in nonharvested moose populations inhabiting eastern Poland.     

The population genetics of a biological control introduction: mitochondrial DNA and microsatellie variation in native and introduced populations of Aphidus ervi, a parisitoid wasp

Introductions of biological control agents may cause bottlenecks in population size despite efforts to avoid them. We examined the population genetics of Aphidius ervi (Hymenoptera: Braconidae), a parasitoid that was introduced to North America from Western Europe in 1959 to control pea aphids. To explore the phylogeographical relationships of A. ervi we sequenced 1249 bp of mitochondrial DNA (mtDNA) from 27 individuals from the native range and 51 individuals from the introduced range. Most individuals from Western Europe, the Middle East and North America shared one of two common haplotypes, consistent with the known history of the introduction. However, some A. ervi from the Pacific Northwest have a haplotype that is most similar to haplotypes found in Japan, raising the possibility of a second accidental introduction. To examine population structure and assess whether a bottleneck occurred upon introduction to North America, we assayed variation at 5 microsatellite loci in 62 individuals from 2 native populations and 230 individuals from 6 introduced populations. Introduced samples had fewer rare alleles than native samples (F1,34 = 13.5, P = 0.0008), but heterozygosity did not differ significantly. These results suggest that a mild bottleneck occurred in spite of the introduction of over 1000 individuals. Using a hierarchical Bayesian approach, the founding population size was estimated to be 245 individuals. amova showed significant genetic differentiation between the European and North American samples, and a Bayesian assignment approach clustered individuals into four groups, with most European individuals in one group and most North American individuals in the other three. These results highlight that genetic changes are associated with founder events in rapidly growing natural populations, even when the founding population size is relatively large.     

How closely do measures of mitochondrial DNA control region diversity reflect recent trajectories of population decline in birds?

Monitoring levels of genetic diversity in wildlife species is important for understanding population status and trajectory. Knowledge of the distribution and level of genetic diversity in a population is essential to inform conservation management, and help alleviate detrimental genetic impacts associated with recent population bottlenecking. Mitochondrial DNA (mtDNA) markers such as the control region have become a common means of surveying for within-population genetic diversity and detecting signatures of recent population decline. Nevertheless, little attention has been given to examining the mtDNA control region’s sensitivity and performance at detecting instances of population decline. We review genetic studies of bird populations published since 1993 that have used the mtDNA control region and reported haplotype diversity, number of haplotypes and nucleotide diversity as measures of within-population variability. We examined the extent to which these measures reflect differences in known demographic parameters such as current population size, severity of any recent bottleneck and IUCN Red List status. Overall, significant relationships were observed between two measures of genetic diversity (haplotype diversity and the number of haplotypes), and population size across a number of comparisons. Both measures gave a more accurate reflection of recent population history in comparison to nucleotide diversity, for which no significant associations were found. Importantly, levels of diversity only correlated with demographic declines where population sizes were known to have fallen below 500 individuals. This finding suggests that measures of mtDNA control region diversity should be used with a degree of caution when inferring demographic history, particularly bottleneck events at population sizes above N = 500.     

Mitochondrial DNA and nuclear microsatellites reveal high diversity and genetic structure in an avian top predator,the white‐tailed sea eagle,in central Europe

We analysed 123 white‐tailed sea eagles (Haliaeetus albicilla) from (primarily central) Europe with respect to variability and differentiation based on 499 bp of the mitochondrial control region and genotypes at seven unlinked nuclear microsatellites. Variability was high (overall expected heterozygosity, haplotype and nucleotide diversity being 0.70, 0.764 and 0.00698, respectively) and both marker systems showed a subdivision into two main genetic clusters (microsatellites) or haplogroups (mtDNA). In line with earlier analyses focusing on populations from northern and eastern Europe, as well as from Asia, we found a high level of admixture in Europe and no signs of a bottleneck – despite a severe decline of white‐tailed sea eagle populations during the 20^th century. Europe is thus a global stronghold for this species not only with respect to the number of breeding pairs but also regarding the proportion of species‐wide genetic diversity. Our dense sampling revealed a possibly clinal variation within central Europe from north‐west to south‐east that was reflected by the distribution of mtDNA haplotypes as well as the two microsatellite‐based clusters. This population differentiation in central Europe probably originated from a geographically structured postglacial colonization and was later enhanced by recent demographic fluctuations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 727–737.     

Extremely low genetic diversity in the endangered Hawaiian monk seal (Monachus schauinslandi)

Hunted to near extinction in the late 19th century, the endangered and endemic Hawaiian monk seal (Monachus schauinslandi) exhibits low variation at all molecular markers tested to date. Here we confirm extreme paucity of genetic diversity, finding polymorphisms at only 8 of 154 microsatellite loci tested (143 novel species-specific loci, 10 loci from Antarctic seals, and 1 previously characterized locus). This screening revealed unprecedentedly low levels of allelic diversity and heterozygosity (A = 1.1, H(e) = 0.026). Subsequent analyses of 2409 Hawaiian monk seals at the 8 polymorphic loci provide evidence for a bottleneck (P = 0.002), but simulations indicate low genetic diversity (H(e) < 0.09) prior to recorded human influence. There is little indication of contemporary inbreeding (F(IS) = 0.018) or population structure (K = 1 population). Minimal genetic variation did not prevent partial recovery by the late 1950s and may not be driving the current population decline to approximately 1200 seals. Nonetheless, genotyping nearly every individual living during the past 25 years sets a new benchmark for low genetic diversity in an endangered species.