Knowledge Of Population Structure Research Articles

Population structure and genetic connectivity reveals distinctiveness of Irish harbour seals (Phoca vitulina) and implications for conservation management

Abstract The identification of discrete intraspecific units, such as genetically informed management units (MUs), is important to effectively develop and implement conservation strategies for protected species. Harbour seals (Phoca vitulina) occurring in Irish waters are currently viewed as a single nationwide panmictic population (and hence MU), although this assumption is not based on any knowledge of population structure because of the lack of available genetic data. Thus, the present study used mitochondrial control region sequences and between nine and 11 microsatellite loci from harbour seals from Ireland and Northern Ireland (up to n = 123) and adjacent UK/European waters (up to n = 289) to provide insights into the genetic population structure and diversity of harbour seals in the areas studied. Within the island of Ireland, genetic analyses revealed the presence of three genetically distinct local populations, characterized by high genetic diversity, hereby defined as: East Ireland (EI), North‐west & Northern Ireland (NWNI), and South‐west Ireland (SWI). Using previously published and newly generated data, a subsequent wider scale analysis revealed that the EI and SWI local populations were genetically distinct from neighbouring UK/European areas, whereas seals from the NWNI area could not be distinguished from a previously identified Northern UK metapopulation. Migration rate estimates showed that NWNI receives migrants from North‐west Scotland, with NWNI acting as a genetic source for both SWI and EI. The present study provides the most comprehensive genetic assessment of harbour seals in European waters to date, with findings indicating that conservation strategies for harbour seals in Irish waters should be amended to accommodate at least three genetically distinct local populations/MUs. The use of approaches considering both ecological and genetic parameters is recommended for future assessments and delineation of units of ecological relevance for conservation management purposes.

Population structure and genetic variability in wild and farmed Mediterranean populations of gilthead seabream and European seabass inferred from a 60K combined species SNP array

Knowledge of population structure and genetic diversity within and between wild and farmed populations of gilthead sea bream (Sparus aurata) and European seabass (Dicentrarchus labrax) is important to achieve sustainable aquaculture production of these species and to assess the risk of genetic impacts of fish escaped from farms. Previous population genetic studies on these species have been based on a limited number of genetic markers and samples. In this study, these features were assessed using samples from 24 seabream and 25 seabass populations distributed throughout the Mediterranean Sea, and 3 wild seabream Atlantic populations. Samples were genotyped with a newly developed combined species SNP array that includes ~60K SNPs. Data from sequencing pools of individual DNA from the same populations were also used. Different approaches were employed for identifying the extent of population stratification within species. The effective population size (a parameter inversely related to the rate at which genetic variability is lost) was estimated for each population based on linkage disequilibrium. Population structure results revealed a clear differentiation between wild and farmed populations in both species. Wild populations showed a low degree of differentiation, particularly in seabream. Despite this, a slight differentiation was observed between Atlantic and Mediterranean seabream populations and between western and eastern Mediterranean seabass populations. However, farmed populations were quite heterogeneous and showed a high degree of differentiation. Some farmed populations of both species showed a genetic makeup similar to that found in wild populations. In general, the effective population size was large (> 1000) for wild and small (< 100) for farmed populations of both species. About 40% of the seabream and 80% of the seabass farmed populations had estimates of effective population size smaller than 50 highlighting the need of applying measures to control the rate at which genetic variability is lost.

A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut

Abstract Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.

Ontogenetic development underlies population response to mortality

Understanding demographic responses to mortality is crucial to predictive ecology. While classic ecological theory posits reductions in population biomass in response to extrinsic mortality, models containing realistic developmental change predict the potential for counterintuitive increase in stage‐specific biomass, i.e. biomass overcompensation. Patterns of biomass overcompensation should be predictable based on differences in the relative energetic efficiencies of juvenile maturation and adult reproduction. Specifically, in populations where reproduction is the limiting process, adult‐specific mortality should enhance total reproduction and thus juvenile biomass. We tested this prediction by inducing an array of stage‐specific harvesting treatments across replicate populations of Daphnia pulex. In accordance with reproductive regulation, the greatest biomass response occurred in the juvenile Daphnia stage and this response occurred most strongly in response to adult mortality. Nevertheless, we failed to detect significant biomass overcompensation and instead report largely compensatory effects. In total, our work demonstrates that knowledge of population structure is necessary to accurately predict population dynamics, but cautions that further research is needed to illuminate the factors generating over‐compensatory versus compensatory responses across natural populations.

Population Genetic Structure and Connectivity of the European Lobster Homarus gammarus in the Adriatic and Mediterranean Seas.

Highly selective fishing has the potential to permanently change the characteristics within a population and could drive the decline of genetic diversity. European lobster is an intensively fished crustacean species in the Adriatic Sea which reaches high market value. Since knowledge of population structure and dynamics is important for effective fisheries management, in this study, we used 14 neutral microsatellites loci and partial mitochondrial COI region sequencing to explore population connectivity and genetic structure by comparing samples from the Adriatic Sea and the adjacent basins of the Mediterranean Sea. The obtained results suggest that neutral genetic diversity has not been significantly affected by decrease in population size due to overfishing, habitat degradation and other anthropogenic activities. Global genetic differentiation across all populations was low (FST = 0.0062). Populations from the Adriatic Sea were panmictic, while genetic differentiation was found among populations from different Mediterranean basins. Observed gene flow for European lobster suggest that populations in the north eastern Adriatic act as a source for surrounding areas, emphasizing the need to protect these populations by establishing interconnected MPAs that will be beneficial for both fisheries and conservation management.

Population structure and regeneration dynamics of Firmiana major, a dominant but endangered tree species

Firmiana major (Malvaceae) is a dominant tree species endemic in arid-hot and arid-warm valleys in Southwest China. Human disturbance, mainly the use of its bark to produce rope, caused a sharp decline in F. major populations before 1980s. The plant was declared extinct in 1998 but reappeared in 2001. Knowledge of population structure, regeneration characteristics, and current threats is fundamental for its conservation and recovery. In this study, we conducted field surveys and identified fourteen F. major localities, including eleven new localities. Fewer than 4,000 individuals were present in six populations. In four populations, the recruitment of new plants was low, while the other two populations had positive regeneration of seedlings and saplings. Grazing pressure might have caused a reduction in the number of younger trees. The case found in a national nature reserve proved that in situ protection over decades was essential in restoring and regenerating F. major (Panzhihua population). Although sprouting can promote F. major regeneration, it didn’t revert the decline of the populations. The number of individuals and occupancy are highly likely to decline in the near future. Therefore, F. major falls into the Vulnerable (VU) category and should be classified as a Plant Species with Extremely Small Populations (PESEP) of China. The conservation implications and actions were introduced.

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance.

Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, FST), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise FST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number.

Population structure and breed composition prediction in a multi-breed sheep population using genome-wide single nucleotide polymorphism genotypes

Knowledge of population structure and breed composition of a population can be advantageous for a number of reasons; these include designing optimal (cross)breeding strategies in order to maximise non-additive genetic effects, maintaining flockbook integrity by authenticating animals being registered and as a quality control measure in the genotyping process. The objectives of the present study were to 1) describe the population structure of 24 sheep breeds, 2) quantify the breed composition of both flockbook-recorded and crossbred animals using single nucleotide polymorphism BLUP (SNP-BLUP), and 3) quantify the accuracy of breed composition prediction from low-density genotype panels containing between 2000 and 6000 SNPs. In total, 9334 autosomal SNPs on 11 144 flockbook-recorded animals and 1172 crossbred animals were used. The population structure of all breeds was characterised by principal component analysis (PCA) as well as the pairwise breed fixation index (Fst). The total number of animals, all of which were purebred, included in the calibration population for SNP-BLUP was 2579 with the number of animals per breed ranging from 9 to 500. The remaining 9559 flockbook-recorded animals, composite breeds and crossbred animals represented the test population; three breeds were excluded from breed composition prediction. The breed composition predicted using SNP-BLUP with 9334 SNPs was considered the gold standard prediction. The pairwise breed Fst ranged from 0.040 (between the Irish Blackface and Scottish Blackface) to 0.282 (between the Border Leicester and Suffolk). Principal component analysis revealed that the Suffolk from Ireland and the Suffolk from New Zealand formed distinct, non-overlapping clusters. In contrast, the Texel from Ireland and that from New Zealand formed integrated, overlapping clusters. Composite animals such as the Belclare clustered close to its founder breeds (i.e., Finn, Galway, Lleyn and Texel). When all 9334 SNPs were used to predict breed composition, an animal that had a majority breed proportion predicted to be ≥0.90 was defined as purebred for the present study. As the panel density decreased, the predicted breed proportion threshold, used to identify animals as purebred, also decreased (≥0.85 with 6000 SNPs to ≥0.60 with 2000 SNPs). In all, results from the study suggest that breed composition for purebred and crossbred animals can be determined with SNP-BLUP using ≥5000 SNPs.

Population structure, connectivity, and demographic history of an apex marine predator, the bull shark Carcharhinus leucas.

Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large‐bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, and cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC‐RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.

Evaluating spatial structure of a mixed broad-leaved/Korean pine forest based on neighborhood relationships in Mudanfeng National Nature Reserve, China

China’s 13th 5-year forestry plan explicitly requires the end of commercial harvesting and the improved management of natural forests by means of adjusting and optimizing forest structure and developing high-quality forest production. This requires the quantification of stand structure and species diversity. In this study, species distribution, association and size differentiation in a mixed broad-leaved/Korean pine (Pinus koraiensis Siebold & Zucc.) forest in Mudanfeng National Nature Reserve were analyzed using three spatial structure indices: uniform angle index, complete mingling index, and size differentiation index. The results show that the species were randomly distributed, with a moderate size differentiation and high mixed structure. Three dominant species exhibited different patterns in terms of the three indices and their bivariate distribution. Overall, Korean pine showed an opposite trend to Manchurian maple (Acer mandshuricum Maxim.), whereas the distribution pattern of Manchurian linden (Tilia mandshurica Rupr. & Maxim.) was similar to that of the entire stand. Our work contributes to further the knowledge of population structure in order to optimize the structure of secondary forests and plantations.

Population structure of Han nationality in Central-Southern China

Knowledge of population structure is very important for forensic genetics. However, the population substructure in Central-Southern China Han nationality has still not been fully described. In this study, we investigated the genetic diversity of 15 forensic autosomal STR loci from 6879 individuals in 12 Han populations subdivided by administrative provinces in Central-Southern China. The statistical analysis of genetic variation showed that genetic differentiation among these populations was very small with a Fst value of 0.0009. The Discriminant Analysis of Principal Components (DAPC) showed that there were no obvious population clusters in Central-Southern China Han population. In practice, the population structure effect in Central-Southern China Han population can be negligible in forensic identification and paternity testing.

Isolation and characterisation of 16 polymorphic microsatellite loci for bight redfish, Centroberyx gerrardi (Actinopterygii : Berycidae), and cross-amplification in two other Centroberyx species

Bight redfish, Centroberyx gerrardi, is a demersal teleost endemic to continental shelf and upper slope waters of southern Australia. Throughout most of its range, C. gerrardi is targeted by a number of separately managed commercial and recreational fisheries across several jurisdictions. However, it is currently unknown whether stock assessments and management for this shared resource are being conducted at appropriate spatial scales, thereby requiring knowledge of population structure and connectivity. To investigate population structure and connectivity, we developed 16 new polymorphic microsatellite markers using 454 shotgun sequencing. Two to 15 alleles per locus were detected. There was no evidence of linkage disequilibrium between pairs of loci and all loci except one were in Hardy–Weinberg equilibrium. Cross-amplification trials in the congeneric C. australis and C. lineatus revealed that 11 and 16 loci are potentially useful, respectively. However, deviations from Hardy–Weinberg equilibrium and linkage disequilibrium between pairs of loci were detected at several of the 16 markers for C. australis, and therefore the number of markers useful for population genetic analyses with C. lineatus is likely considerably lower than 11.

Molecular genetics to inform spatial management in benthic invertebrate fisheries: a case study using the Australian Greenlip Abalone

Hierarchical sampling and subsequent microsatellite genotyping of >2300 Haliotis laevigata (greenlip abalone) from 19 locations distributed across five biogeographic regions have substantially advanced our knowledge of population structure and connectivity in this commercially important species. The study has found key differences in stock structure of H. laevigata compared with the sympatric and congeneric Haliotis rubra (blacklip abalone) and yielded valuable insights into the management of fisheries targeting species characterized by spatial structure at small scales (i.e. S-fisheries). As with H. rubra, H. laevigata comprise a series of metapopulations with strong self-recruitment. However, the spatial extent of H. laevigata metapopulations (reefal areas around 30 km(2) ; distances of up to 135 km are effective barriers to larval dispersal) was substantially greater than that identified for H. rubra (Miller et al. 2009). Differences in the dynamics and scale of population processes, even between congeneric haliotids as made evident in this study, imply that for S-fisheries, it is difficult to generalize about the potential consequences of life history commonalities. Consequently, species-specific management reflective of the population structure of the target species remains particularly important. This will likely require integration of information about stock structure and connectivity with data on life history and population dynamics to determine the necessary input (e.g. number of fishers, fishing effort) and output (e.g. minimum legal size, total allowable catch) controls to underpin their sustainable management.

Development of microsatellite markers in the rice paddy snake Enhydris plumbea (Colubridae)

The rice paddy snake (also known as Boie’s mud snake) Enhydris plumbea is a viviparous colubrid snake. This is a widely distributed species found from the Andaman Islands (India) and Myanmar eastwards across the Southeast Asian Peninsula and southern China southwards into Indonesia; and it is present on most of the Indonesian islands and eastwards to Sulawesi and the Moluccas. The snake has been overexploited by local people for traditional medicine to treat skin diseases, and is listed on the “Lists of terrestrial wildlife under state protection, which are beneficial or of important economic or scientific value” promulgated by China’s State Forestry Administration in 2000. Knowledge of population structure and genetic diversity is crucial for effective wildlife preservation. Specific molecular markers such as mitochondrial DNA and microsatellites are useful tools for achieving this goal. Here, eight polymorphic microsatellite loci were isolated from an enriched genomic library of E. plumbea. One hundred and twenty individuals were collected from Wenzhou population in Zhejiang, China. These markers revealed a high degree of genetic diversity (4–8 alleles per locus) and heterozygosity (H O ranged from 0.148 to 0.789, and H E ranged from 0.347 to 0.766). No locus exhibited significant deviations from Hardy-Weinberg equilibrium. There was no evidence of linkage disequilibrium among pairs of loci. These loci will be useful for future study of population structure, genetic diversity and conservation strategy design of E. plumbea.

Population genetics of Thamnaconus hypargyreus (Tetraodontiformes: Monacanthidae) in the South China Sea

Knowledge of population structure is particularly important for long-term fisheries management and conservation. Lesser-spotted leatherjacket Thamnaconus hypargyreus is an economically important fish species in the South China Sea. Fish specimens (totally 158 individuals) used in this study were collected from five geographical locations in the north of the South China Sea and the southwestern Nansha Islands. The results were as follows: a total of 636 nucleotides of the mitochondrial DNA (mtDNA) control region (CR) of T. hypargyreus were amplified by polymerase chain reaction (PCR) technology. Both 103 mutations of nucleotide acids without inserting or deleting one and 91 haplotypes were found among the examined CR fragment. High haplotype diversity (0.9419 ± 0.0151) and nucleotide diversity (0.0095 ± 0.00506) relatively together with a recent and sudden population expansion which characterizes the genetic population structure of this species. Analysis of molecular variance (AMOVA) and the fixation indices (Fst) of five groups showed that the genetic variance mainly came from individuals within groups, and there was no genetic differentiation between groups. The phylogenetic trees including maximum likelihood (ML) and Bayesian inference (BI) proved no phylogeographic differentiation structure in five groups. The mtDNA marker suggested the five groups should be genetic homogeneity, which implied T. hypargyreus in the north and southwest continental shelf of the South China Sea belongs to one population.

Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping

Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classified as hot, mild, sweet and ornamental types is indispensable for applying association mapping and genomic selection to improve pepper. The current study aimed to resolve the genetic diversity and relatedness of Capsicum annuum germplasm by use of simple sequence repeat (SSR) loci across all chromosomes in samples collected in 2011 and 2012. The physical distance covered by the entire set of SSRs used was 2,265.9 Mb from the 3.48-Gb hot-pepper genome size. The model-based program STRUCTURE was used to infer five clusters, which was further confirmed by classical molecular-genetic diversity analysis. Mean heterozygosity of various loci was estimated to be 0.15. Linkage disequilibrium (LD) was used to identify 17 LD blocks across various chromosomes with sizes from 0.154 Kb to 126.28 Mb. CAMS-142 of chromosome 1 was significantly associated with both capsaicin (CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplified bands of 244, 268, 283 and 326 bp. Alleles 268 and 283 bp had positive effects on both CA and DCA levels, with an average R(2) of 12.15 % (CA) and 12.3 % (DCA). Eight markers from seven different chromosomes were significantly associated with fruit weight, contributing an average effect of 15 %. CAMS-199, HpmsE082 and CAMS-190 are the three major quantitative trait loci located on chromosomes 8, 9, and 10, respectively, and were associated with fruit weight in samples from both years of the study. This research demonstrates the effectiveness of using genome-wide SSR-based markers to assess features of LD and genetic diversity within C. annuum.

USE OF CARROT GENETIC RESOURCES TO UNDERSTAND ROOT CAROTENOID CONTENT: PRELIMINARY STEPS TO AN ASSOCIATION MAPPING STUDY

Association mapping becomes one of the major genetic methods used to understand genetic control of complex traits. This method allows the use of natural populations with high resolution thanks to ancestral recombinations. Resolution is given by linkage disequilibrium (LD) extend. But false positives can be detected when phenotypic traits are correlated with underlying population stratification at non causal loci. Knowledge of population structure is then a preliminary step for association mapping studies. Here we investigated the population structure in cultivated carrot and the LD extend in the carotenoid isomerase gene, a key gene in the carotenoid biosynthesis pathway. An unexpected high LD for outcrossing species was found in this gene. Population stratification analysis confirmed the differentiation of the carrot germplasm in two clusters. The first one comprised European and American accessions, the second one Asian accessions. These are preliminary steps to perform association mapping studies to understand root carotenoid content in cultivated carrot.

News of the Société Botanique de France

Despite its economic, cultural and historical importance, few studies have investigated the evolutionary history of the domesticated apple (Malus domestica) as well as those of its wild relatives. Using new population genetic approaches (approximate Bayesian computation) with microsatellites and nuclear sequences, this thesis aimed to unravel, at different evolutionary scales (phylogeography, speciation, domestication), the natural and artificial diversification processes at play in the Malus genus. Research focused on the four wild apple species distributed across Eurasia [Malus orientalis (Caucasus), Malus sieversii (Central Asia), Malus sylvestris (Europe) and Malus baccata (Siberia)] and on the single domesticated apple species in the genus, Malus domestica. The thesis was divided into four parts: (1) domestication history of the cultivated apple, from its origin in Central Asia to Europe, (2) post-glacial recolonization history of the European crabapple (M. sylvestris), (3) the history of speciation among the five Malus species, (4) crop-to-wild gene flow and dispersal capacities of the closest wild relative species (M. sylvestris, M. sieversii and M. orientalis). By investigating artificial diversification, we found evidence of unique processes of domestication in this fruit tree, with no bottleneck and with extensive post-domestication introgressions by a wild species (M. sylvestris) other than the ancestral progenitor (M. sieversii). Natural diversification patterns (phylogeography, speciation and population structure) revealed large effective population sizes, high dispersal capacities and weak spatial genetic structures. This thesis also revealed high levels of interspecific hybridizations, and a particularly high level of crop-to-wild gene flow in Europe and Central Asia. This study extended our knowledge of population structures for the wild species that contributed to the cultivated apple genome, as well as the extent of hybridization rates. This work is essential for the conservation of wild apple populations, the maintenance of the integrity of wild species facing fragmentation and future breeding programmes concerning the domesticated apple.

Inferring population connectivity across the range of the purple-crowned fairy-wren (Malurus coronatus) from mitochondrial DNA and morphology: implications for conservation management

Knowledge of population structure and patterns of connectivity is required to implement effective conservation measures for the purple-crowned fairy-wren (Malurus coronatus), a threatened endemic of northern Australia. This study aimed to identify barriers to dispersal across the distribution of M. coronatus, investigate the impact that the recent declines may have on population connectivity, and propose conservation actions to maintain natural patterns of gene flow. Analysis of mitochondrial DNA sequences from 87 M. coronatus identified two phylogenetic clusters that corresponded with the phenotypically defined western (M. c. coronatus) and eastern (M. c. macgillivrayi) subspecies. The genetic divergence between these subspecies was consistent with isolation by a natural barrier to gene flow, and supports their separate conservation management. Within the declining M. c. coronatus, the lack of genetic divergence and only slight morphological difference between remnant populations indicates that populations were recently linked by gene flow. It is likely that widespread habitat degradation and the recent extirpation of M. c. coronatus from the Ord River will disrupt connectivity between, and dynamics within, remnant populations. To prevent further declines, conservation of M. coronatus must preserve areas of quality habitat and restore connectivity between isolated populations.

Genetic structure in large, continuous mammal populations: the example of brown bears in northwestern Eurasia

Knowledge of population structure and genetic diversity and the spatio-temporal demographic processes affecting populations is crucial for effective wildlife preservation, yet these factors are still poorly understood for organisms with large continuous ranges. Available population genetic data reveal that widespread mammals have for the most part only been carefully studied at the local population scale, which is insufficient for understanding population processes at larger scales. Here, we provide data on population structure, genetic diversity and gene flow in a brown bear population inhabiting the large territory of northwestern Eurasia. Analysis of 17 microsatellite loci indicated significant population substructure, consisting of four genetic groups. While three genetic clusters were confined to small geographical areas-located in Estonia, southern Finland and Leningrad oblast, Russia-the fourth cluster spanned a very large area broadly falling between northern Finland and the Arkhangelsk and Kirov oblasts of Russia. Thus, the data indicate a complex pattern where a fraction of the population exhibits large-scale gene flow that is unparalleled by other wild mammals studied to date, while the remainder of the population appears to have been structured by a combination of demographic history and landscape barriers. These results based on nuclear data are generally in good agreement with evidence previously derived using mitochondrial markers, and taken together, these markers provide complementary information about female-specific and population-level processes. Moreover, this study conveys information about spatial processes occurring over multiple generations that cannot be readily gained using other approaches, e.g. telemetry.