Phylogeography,Population Structure,and Conservation of the Javan Gibbon (<Emphasis Type="Italic">Hylobates moloch</Emphasis>)

An understanding of phylogeography and population genetics is needed for a comprehensive long-term conservation management strategy. The Javan gibbon (Hylobates moloch), an Endangered species endemic to the island of Java, has been protected since 1924 but is threatened by ongoing habitat loss, habitat degradation, and the wildlife trade. We studied the phylogeography and population genetic structure of the Javan gibbon, to define the number of Evolutionary Significant Units (ESUs) in the species, and the population genetic structure in each ESU. We sampled 47 individuals, analyzing 35 for variation in mitochondrial DNA control region, 41 for variation in 8 nuclear DNA microsatellites, and 13 for variation in 45 nuclear DNA single nucleotide polymorphisms (SNPs). We found support for two ESUs across the species range: a western ESU, extending from Ujung Kulon to Gunung Gede–Pangrango, and a central ESU, extending from Gunung Masigit–Simpang–Tilu to Gunung Slamet. Analysis of molecular variance and population structure analysis indicate significant structuring in the western ESU between Ujung Kulon and Gunung Halimun–Salak–Gede–Pangrango, and little to moderate structure in the central ESU, underscoring the importance of conserving as many populations as possible to preserve the full array of genetic diversity in this species. Our results will inform future more comprehensive population genetic surveys and the conservation genetic management of the Javan gibbon. This study demonstrates the importance of genetics when designing conservation management strategies for endangered primates.     

Minimum population size,genetic diversity,and social structure of the Asian elephant in Cat Tien National Park and its adjoining areas,Vietnam, based on molecular genetic analyses

Vietnam’s elephant population that has suffered severe declines during the past three decades is now believed to number 60–80 individuals in the wild. Cat Tien National Park is thought to be one of the key areas for the recovery of Vietnam’s elephants. We carried out a molecular genetic study of elephants in Cat Tien National Park and its adjoining areas with the objectives of estimating minimum population size, assessing genetic diversity, and obtaining insights into social organization. We obtained a minimum population size of 11 elephants based on a combination of unique nuclear microsatellite genotypes and mitochondrial haplotypes. While mitochondrial diversity based on a 600-base pair segment was high in this small sample of individuals, the six microsatellite loci examined showed low diversity and the signature of a recent population bottleneck. Along with nuclear genetic depauperation of Cat Tien’s elephants, we also report disruption of normal social organization, with different matrilines having coalesced into a single social group because of anthropogenic disturbance. The results emphasize the critical condition of this elephant population and the need for urgent conservation measures if this population is to be saved.     

The yellow-cheeked gibbon (Hylobates gabriellae) in nam bai cat tien (southern vietnam) revisited

Data concerning the status, habitat, and vocalizations of yellow-cheeked crested gibbons (Hylobates gabriellae) were collected during a short field trip to the Nam Bai Cat Tien National Park (southern Vietnam). Nam Bai Cat Tien may be the southernmost locality where crested gibbons (i.e. theHylobates concolor group) still survive. Fewer songs were heard at Nam Bai Cat Tien National Park than at other crested gibbon sites visited by the author. At least two gibbon groups appear to have been greatly reduced in number since previous surveys in the park. There is some evidence that both the gibbon population and the gibbon habitat in Nam Bai Cat Tien are disturbed. The first case of a great call solo song in wild gibbons of theconcolor group is reported. Great calls ofH. gabriellae are described and documented with sonagrams for the first time. They differ from those previously described forH. leucogenys.     

The rebuilding of an isolated rain forestassemblage: how disharmonicis the flora of Krakatau?

The compositional balance of the flora of the Krakatau Islands, Indonesia, is examined in order to identify taxonomic and/or ecological groups which are under-represented in this recovering island ecosystem in relation to regional analogues and potential source areas in the Sunda Strait (Ujung Kulon and Sebesi Island). Interpretations are conditioned by the limited availability of comparative data, the uncertainty surrounding dispersal classifications, the problem of determining habitat suitability for missing elements, and thus the unsuitability of a formal statistical approach. Analysis by dispersal syndrome supports predictions that species with large, winged, wind-scattered propagules, or those with no particular dispersal potential, are under-sampled. However, some species with winged propagules have colonized, in most cases probably by thalassochory (sea-dispersal). Although zoochorous (animal-dispersed) trees and shrubs are well represented on Krakatau, those large-seeded species which are primarily dependent on dispersal by animals other than birds are under-represented. Large-seeded zoochores are probably highly dependent on two species of Ducula (large fruit-pigeons) for transport to Krakatau and their colonization has been relatively slow. Comparison with Christmas and Jarak Islands yields differing degrees of overlap for thalassochorous, zoochorous, and anemochorous (wind-dispersed) spermatophytes and for pteridophytes, interpretable in terms of dispersability and size of the respective species pools. Particular families and genera can be identified which are seemingly under-sampled on Krakatau, as can some which are over-represented in relation to the principal comparative site, the Ujung Kulon peninsular, West Java. The latter are mostly very small-seeded wind-dispersed epiphytic herbs (especially orchids). Ferns are also very well represented in relation to the West Javan source pool. It is concluded that the flora of Krakatau remains disharmonic, in a predictable fashion, although it is certainly becoming less so. The data provide empirical evidence for the abilities of particular functional guilds of rain forest plants to disperse across significant barriers: the implications of these findings are discussed in relation to current concerns with forest fragmentation in the tropics. This revised version was published online in August 2006 with corrections to the Cover Date.     

A genetically distinct wild redband trout (<Emphasis Type="Italic">Oncorhynchus mykiss gairdneri</Emphasis>) population in Crane Prairie Reservoir,Oregon, persists despite extensive stocking of hatchery rainbow trout (<Emphasis Type="Italic">O. m. irideus</Emphasis>)

Crane Prairie Reservoir in the upper Deschutes River Basin has historically supported a wild population of migratory Deschutes River redband trout. Owing to its status as a premier destination for recreational angling in Oregon, the reservoir has been stocked with domesticated hatchery rainbow trout since 1955. In recent years the wild redband trout population has experienced a substantial decline. Effects on productivity related to genetic interaction with naturally spawning hatchery-origin fish (fitness risks) have not been determined. The species Oncorhynchus mykiss has been characterized with substantial genetic diversity throughout the Deschutes River Basin that further heightens the challenge of identifying specific conservation needs of wild populations. A conservation plan for Crane Prairie wild redband trout requires a better understanding of the natural reproductive success of out-of-basin hatchery trout in the reservoir tributaries, and the similarity between Crane Prairie redband trout with other extant redband trout populations in the basin. Using a suite of 17 microsatellite nuclear DNA markers, we evaluated the genetic structure among Crane Prairie Reservoir redband trout, hatchery rainbow trout, and two adjacent populations of redband trout from within the Upper Deschutes River Basin. We observed significant heterogeneity between the hatchery and wild Crane Prairie populations that may reflect differences in life histories, differential productivity and assortative mating. The genetic distinctions observed among the three redband trout populations suggest restricted gene flow and genetic drift within the upper basin. Temporally stratified sampling and larger numbers of samples will be necessary to confirm these conclusions.     

Comparison of genetic variation in populations of wild rice, Oryza rufipogon, plants and their soil seed banks

Wild rice, Oryza rufipogon, has endangered species conservation status and it is subject to in situ conservation in China. To understand the potential of the seed bank in species conservation and population restoration, this study compared the genetic diversity of O. rufipogon plants with that of its soil seed banks in two marshes. A total of 11 pairs of rice SSR primers were used and 9 were polymorphic. Allele frequencies of the seeds differed significantly from those of surface plants and varied between soil layers. Relatively more alleles and higher genetic diversity (H _e) were found in plant populations, relative to seed banks. The numbers of germinable seeds and the level of genetic variation in seed banks decreased with the increasing of soil depth, indicating a rapid seed loss. Genetic differentiation was detected between sites and between plant and seed populations, as well as among seeds of different soil strata. Rapid seed loss, partly dormancy loss, and nonrandom seed mortality are discussed as the possible contributors to the pattern of reduced genetic variation within seed banks, compared to plants. These could also be responsible for the considerable genetic differentiation between populations. The seed population held about 72% of the total genetic variation of O. rufipogon in each marsh, indicating the potential of seed banks for restoring population variabilities if the plant populations were lost.     

Stand Biomass and Tree Mortality from Permanent Forest Plots on Krakatau,Indonesia, 1989–19951

Forest closure on the three original Krakatau Islands (Panjang, Rakata, and Sertung) took place ca 1930, about 50 yr after the apparent sterilization of the islands due to volcanic eruptions. Two permanent forest plots were established on each of these islands in 1989. A full enumeration of these plots, of two additional Rakata plots, and of two “mainland”plots from the Ujung Kulon National Park, West Java, was undertaken in 1992. These data provide the first estimates of aboveground biomass from Krakatau. The values reported for Krakatau are below the local West Javan figures, with considerable variation occurring within the islands. In 1992, the fourth Krakatau island, Anak Krakatau, began an eruption sequence which continued through the study period, depositing ash on the study sites of Panjang and Sertung. A further partial survey of these plots in 1994–1995 revealed a significant increase in mortality since the volcanic activity recommenced, with an increase in deaths of larger stems. Although Rakata has not been influenced directly by volcanism, three sites surveyed on Rakata in 1994–1995 have experienced increased tree mortality, in two cases as a consequence of storm damage and in particular, of lightning strikes. Stand dynamics on Krakatau thus appear to be strongly influenced by episodic environmental disturbance with varying degrees of dependence on the volcanic activity of Anak Krakatau.     

Trio under threat: can we secure the future of rhinos,elephants and tigers in Malaysia?

Three of Malaysia’s endangered large mammal species are experiencing contrasting futures. Populations of the Sumatran rhino (Dicerorhinus sumatrensis) have dwindled to critically low numbers in Peninsular Malaysia (current estimates need to be revised) and the state of Sabah (less than 40 individuals estimated). In the latter region, a bold intervention involving the translocation of isolated rhinos is being developed to concentrate them into a protected area to improve reproduction success rates. For the Asian elephant (Elephas maximus), recently established baselines for Peninsular Malaysia (0.09 elephants/km² estimated from one site) and Sabah (between 0.56 and 2.15 elephants/km² estimated from four sites) seem to indicate globally significant populations based on dung count surveys. Similar surveys are required to monitor elephant population trends at these sites and to determine baselines elsewhere. The population status of the Malayan tiger (Panthera tigris jacksoni) in Peninsular Malaysia, however, remains uncertain as only a couple of scientifically defensible camera-trapping surveys (1.66 and 2.59 tigers/100 km² estimated from two sites) have been conducted to date. As conservation resources are limited, it may be prudent to focus tiger monitoring and protection efforts in priority areas identified by the National Tiger Action Plan for Malaysia. Apart from reviewing the conservation status of rhinos, elephants and tigers and threats facing them, we highlight existing and novel conservation initiatives, policies and frameworks that can help secure the long-term future of these iconic species in Malaysia.     

Genetic diversity in the northernmost<Emphasis Type="Italic"> Oryza rufipogon</Emphasis> populations estimated by SSR markers

To estimate genetic diversity of the residual northern populations of Oryza rufipogon, a total of 232 individuals from six populations were analyzed using microsatellites (SSRs). The O. rufipogon populations with different status included three from Dongxiang (Jiangxi Province) and three from Chaling (Hunan Province) in China. The 23 rice SSR primer pairs selected from the RiceGenes Database detected a total of 115 alleles, indicating that all the SSR loci were polymorphic in this study. The total gene diversity was 0.919 in the six O. rufipogon populations, and the Donxiang populations showed higher diversity than the Chaling populations. More significant genetic differentiation and less gene flow were found among the Dongxiang populations than those from Chaling. The two putative introgressed populations showed relatively high genetic variation. One in situ conserved population from Dongxiang had the lowest level of genetic diversity. The re-introduced population from Chaling restored about 90% of the genetic variation, compared with the original source population. It is concluded from these results that a relatively high level of genetic variation resided in the northern O. rufipogon populations and continued efforts of conservation of these populations are needed; and that the conservation of some Chaling and Dongxiang populations has been effective in preventing gene flow from cultivated rice. Introgression of cultivated rice demonstrated significant impacts on genetic variability of the O. rufipogon populations, and should be carefully considered in conserving this wild rice. This study also suggested that re-introduction to its original habitats is an effective approach to restore O. rufipogon populations.Communicated by J.S. Heslop-Harrison     

Genetic diversity analysis and conservation of the endangered Chinese endemic herb Dendrobium officinale Kimura et Migo (Orchidaceae) based on AFLP

Dendrobium officinale is a critically endangered perennial herb endemic to China. Determining the levels of genetic diversity and patterns of population genetic structure of this species would assist in its conservation and management. Data of 12 populations were used to assess its genetic diversity and population structure, employing the method of amplified fragment length polymorphism (AFLP). A high level of genetic diversity was detected (H (E) = 0.269) with POPGENE. As revealed by AMOVA analysis, there was moderate variation between pairs of populations with Phi(ST) values ranging from 0.047 to 0.578 and on average 26.97% of the genetic variation occurred among populations. Three main clusters were shown in UPGMA dendrogram using TFPGA, which is consistent with the result of principal coordinate ananlysis (PCO) using NTSYS. Keeping a stable environment is critical for the in situ conservation and management of this rare and endangered plant, and for ex situ conservation it is important to design an integrated germplasm bank.     

Evaluation of the eastern (Centrocercus urophasianus urophasianus) and western (Centrocercus urophasianus phaios) subspecies of Sage-grouse using mitochondrial control-region sequence data

The status of Sage-grouse (Centrocercusurophasianus) is of increasing concern, aspopulations throughout its range havecontracted as a result of habitat loss anddegradation. Historically, Sage-grouse wereclassified into two subspecies: eastern(C. u. urophasianus) and westernSage-grouse (C. u. phaios) based onslight differences in coloration noted amongeight individuals sampled from Washington,Oregon, and California. We sequenced a rapidlyevolving portion of the mitochondrial controlregion in 332 birds from 16 populations. Although our sampling area covers the proposedboundary between the eastern and westernsubspecies, no genetic evidence to support thedelineation of these subspecies was found. However, a population straddling southwesternNevada and eastern California was found tocontain an unusually high proportion of uniquehaplotypes, consistent with its geneticisolation from other Sage-grouse populations. Of additional interest was the lack ofdiversity in the two populations sampled fromWashington, one of which contained only asingle haplotype. We suggest that multiplelines of evidence are valuable for theformulation of conservation strategies andhence the southwestern Nevada/easternCalifornia population merits furthermorphological, behavioral, and molecular investigation.     

Microsatellite variation in China’s Hainan Eld’s deer (<Emphasis Type="Italic">Cervus eldi hainanus</Emphasis>) and implications for their conservation

Hainan Eld’s deer (Cervus eldi hainanus) experienced a dramatic decline in the late 1960s through early 1970s and by 1976 only 26 deer remained in Datian of Hainan Island, China. Since then, conservation efforts have successfully rescued this deer from extinction. We employed 10 microsatellite DNA loci to index genetic variation in the one source (Datian) and two introduced populations (Bangxi and Ganshiling) and suggest implications for the conservation of the species. A total of 40 alleles at 10 loci were examined from 198 deer blood samples. The source population harbored all 40 alleles, while the Bangxi and Ganshiling translocated populations contained 24 and 26 alleles, respectively. The genetic variability was low (H _e ≈ 0.33) for each of the three populations. No significant difference in genetic variability between the three populations was detected (P > 0.05); yet significant differentiation was found among the three populations. Our results suggest that founder effects and genetic drift have affected the two translocated populations. For conservation we recommend the three populations be managed as a meta-population. When establishing future reintroductions, the founder population should have a size larger than the original 26 founders in Datian population or be composed of a cohort of over 20 same-age individuals with 1:1 sex ratio. Genetic monitoring for both the source and translocated populations should be continuously conducted in order to assess the effectiveness of deer conservation in the future.     

Genetic variability and the effect of habitat fragmentation in spotted suslik Spermophilus suslicus populations from two different regions

Endangered species worldwide exist in remnant populations, often within fragmented landscapes. Although assessment of genetic diversity in fragmented habitats is very important for conservation purposes, it is usually impossible to evaluate the amount of diversity that has actually been lost. Here, we compared population structure and levels of genetic diversity within populations of spotted suslik Spermophilus suslicus, inhabiting two different parts of the species range characterized by different levels of habitat connectivity. We used microsatellites to analyze 10 critically endangered populations located at the western part of the range, where suslik habitat have been severely devastated due to agriculture industrialization. Their genetic composition was compared with four populations from the eastern part of the range where the species still occupies habitat with reasonable levels of connectivity. In the western region, we detected extreme population structure (F _ST = 0.20) and levels of genetic diversity (Allelic richness ranged from 1.45 to 3.07) characteristic for highly endangered populations. Alternatively, in the eastern region we found significantly higher allelic richness (from 5.09 to 5.81) and insignificant population structure (F _ST = 0.03). As we identified a strong correlation between genetic and geographic distance and a lack of private alleles in the western region, we conclude that extreme population structure and lower genetic diversity is due to recent habitat loss. Results from this study provide guidelines for conservation and management of this highly endangered species.     

Anthropogenic Influences on Conservation Values of White Rhinoceros

White rhinoceros (rhinos) is a keystone conservation species and also provides revenue for protection agencies. Restoring or mimicking the outcomes of impeded ecological processes allows reconciliation of biodiversity and financial objectives. We evaluate the consequences of white rhino management removal, and in recent times, poaching, on population persistence, regional conservation outcomes and opportunities for revenue generation. In Kruger National Park, white rhinos increased from 1998 to 2008. Since then the population may vary non-directionally. In 2010, we estimated 10,621 (95% CI: 8,767–12,682) white rhinos using three different population estimation methods. The desired management effect of a varying population was detectable after 2008. Age and sex structures in sink areas (focal rhino capture areas) were different from elsewhere. This comes from relatively more sub-adults being removed by managers than what the standing age distribution defined. Poachers in turn focused on more adults in 2011. Although the effect of poaching was not detectable at the population level given the confidence intervals of estimates, managers accommodated expected poaching annually and adapted management removals. The present poaching trend predicts that 432 white rhinos may be poached in Kruger during 2012. The white rhino management model mimicking outcomes of impeded ecological processes predicts 397 rhino management removals are required. At present poachers may be doing “management removals,” but conservationists have no opportunity left to contribute to regional rhino conservation strategies or generate revenue through white rhino sales. In addition, continued trends in poaching predict detectable white rhino declines in Kruger National Park by 2016. Our results suggest that conservationists need innovative approaches that reduce financial incentives to curb the threats that poaching poses to several conservation values of natural resources such as white rhinos.     

Small edge populations at risk: genetic diversity of the green lizard (<Emphasis Type="Italic">Lacerta viridis viridis</Emphasis>) in Germany and implications for conservation management

Edge and central populations can show great differences regarding their genetic variation and thereby also in their probability of extinction. This fact might be of great importance for the conservation strategies of endangered species. In this study we examine the level of microsatellite variability within three threatened edge populations of the green lizard subspecies Lacerta viridis viridis (Laur.) in Brandenburg (Germany) and compare the observed variation to other edge and central populations within the northern species range. We demonstrate that the northernmost edge populations contain less genetic variation in comparison to the central population. However, there were no observable significant differences to the other edge population included in this study. Surprisingly, we observed a high genetic differentiation in a small geographical range between the three endangered populations in Brandenburg, which can be explained by processes like fragmentation, isolation, genetic drift and small individual numbers within these populations. We also detected unique genetic variants (alleles), which only occurred in these populations, despite a low overall genetic variation. This study demonstrates the potential of fast evolving markers assessing the genetic status of endangered populations with a high resolution. It also illustrates the need for a comparative analysis of different regions within the species range, achieving a more exact interpretation of the genetic variation in endangered populations. This will aid future management decisions in the conservation of genetic diversity in threatened species.     

Threatened freshwater pearl mussel <Emphasis Type="Italic">Margaritifera margaritifera</Emphasis> L. in NW Spain: low and very structured genetic variation in southern peripheral populations assessed using microsatellite markers

A genetic analysis of freshwater pearl mussel Margaritifera margaritifera populations from NW Spain, a peripheral area of its European distribution, was carried out using microsatellite markers. These populations were formerly reported as genetically differentiated on the basis of growth and longevity studies. Ten loci previously characterized in populations from central Europe were used to comparatively analyze the genetic variability at the southern edge of the species’ range. Iberian pearl mussel populations showed very low genetic variability and significant high genetic differentiation. Half of the total genetic diversity observed appeared to be distributed between populations, which suggested a highly structured adaptive potential in pearl mussel at the southern peripheral distribution of the species. Population distinctiveness was evidenced by assignment tests, which revealed a high accuracy of individual assignments to their population of origin. All data suggested low effective population size and major effects of genetic drift on population genetic structure. In order to avoid further loss of genetic variation in biologically distinctive populations from NW Spain, prioritization of genetic resources of this species is required for conservation and management.     

Australian lungfish (Neoceratodus forsteri: Dipnoi) have low genetic variation at allozyme and mitochondrial DNA loci: a conservation alert?

Genetic variation at allozyme and mitochondrialDNA loci was investigated in the Australianlungfish, Neoceratodus forsteri Krefft1870. Tissue samples for genetic analysis weretaken non-lethally from 278 individualsrepresenting two spatially distinct endemicpopulations (Mary and Burnett rivers), as wellas one population thought to be derived from ananthropogenic translocation in the 1890's(Brisbane river). Two of 24 allozyme lociresolved from muscle tissue were polymorphic.Mitochondrial DNA nucleotide sequence diversityestimated across 2,235 base pairs in each of 40individuals ranged between 0.000423 and0.001470 per river. Low genetic variation atallozyme and mitochondrial loci could beattributed to population bottlenecks, possiblyinduced by Pleistocene aridity. Limited geneticdifferentiation was detected among rivers usingnuclear and mitochondrial markers suggestingthat admixture may have occurred between theendemic Mary and Burnett populations duringperiods of low sea level when the drainages mayhave converged before reaching the ocean.Genetic data was consistent with theexplanation that lungfish were introduced tothe Brisbane river from the Mary river. Furtherresearch using more variable genetic loci isneeded before the conservation status ofpopulations can be determined, particularly asanthropogenic demands on lungfish habitat areincreasing. In the interim we recommend amanagement strategy aimed at conservingexisting genetic variation within and betweenrivers.     

Patterns of genetic and phenotypic variation in Iris haynei and I. atrofusca (Iris sect. Oncocyclus = the royal irises) along an ecogeographical gradient in Israel and the West Bank

Iris haynei and I. atrofusca are two closely related narrow endemics distributed vicariously along an ecogeographical north-south gradient in Israel and the West Bank. To obtain baseline information of the taxonomic status, conservation and population history of these taxa, we investigated patterns of phenotypic variation and the partitioning of genetic variation within and among populations using dominant random amplified polymorphic DNA (RAPD) markers. Multivariate (principal components analysis) and taxonomic distance analyses based on morphometric traits from eight populations revealed no unambiguous separation into two distinct groups. Results of genetic analyses for nine populations differed only slightly when either allele- or marker-based approaches were employed. Mean within-population diversity was high (0.258 for Nei's expected heterozygosity), but there was no significant relationship between genetic diversity and either population size or latitude. Although the range-wide estimate of GST ( approximately 0.20) revealed relatively high differentiation among populations this value was inflated because of a small, but significant, component of molecular variance among regions viz. taxa ( approximately 5%). Limited long-distance dispersal capabilities in conjunction with a linearized habitat distribution are proposed to contribute to the approximate isolation by distance pattern observed. It also appears that extant populations are currently deviating from equilibrium conditions because of primary divergence of a formerly more widespread ancestral population. Given the absence of deep genetic and phenotypic subdivision among northern (I. haynei) vs. central/southern (I. atrofusca) populations, we argue for a revision of their species status. Nonetheless, we recommend conservation attention to these geographically differentiated segments as separate management units, which can be seen as an instructive example of incipient species formation.     

Reproductive Strategies Explain Genetic Diversity in Atlantic Salmon, Salmo salar

Synopsis We investigated the relationship between conservation status and genetic variability in European and North American Atlantic salmon, Salmo salar, populations, many of which have suffered severe bottlenecks. A negative north--south cline exists for the status of population conservation in this species. A literature review of genetic variability and demographic parameters of wild Atlantic salmon populations resulted in no statistical associations between population conservation status and genetic variation at enzyme or VNTR loci. We found however, a negative relationship between male parr maturation rates and geographical latitude for both American and European populations. The increase in effective population size due to participation by mature male parr and the increased proportions of these males in smaller (southern) populations could explain the lack of expected relationship between genetic variation and conservation status.     

Population differentiation in the redshank (<Emphasis Type="Italic">Tringa totanus</Emphasis>) as revealed by mitochondrial DNA and amplified fragment length polymorphism markers

The redshank (Tringa totanus) is declining throughout Europe and to implement efficient conservation measures, it is important to obtain information about the population genetic structure. The aim of the present study was two-fold. First, we analysed the genetic variation within and between populations in the Baltic region in southern Scandinavia. Evidence of genetic structure would suggest that different populations might require separate management strategies. Second, in an attempt to study large-scale genetic structure we compared the Baltic populations with redshanks from northern Scandinavia and Iceland. This analysis could reveal insights into phylogeography and long-term population history. DNA samples were collected from six breeding sites in Scandinavia presumed to include two subspecies (totanus and britannica) and a further sample from Iceland (subspecies robusta). Two methods were used to study the population genetic structure. Domain II and III of the mitochondrial control region was analysed by DNA sequencing and nuclear DNA was analysed by screening amplified fragment length polymorphism (AFLP) markers. Mitochondrial DNA showed no variation between individuals in domain II. When analysing an 481 bp fragment of domain III seven haplotypes were found among birds. On the basis of mtDNA sequences, redshanks showed some evidence of a recent expansion from a bottlenecked refugial population. Bayesian analyses of AFLP data revealed a significant genetic differentiation between suggested subspecies but not between populations within the Baltic region. Our results indicate that populations of redshanks in Europe constitute at least three separate management units corresponding to the recognised subspecies.