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Despite containing the largest extent of unfragmented landscape in the Asian elephant (Elephas maximus) range, Myanmar has high levels of human–elephant conflict. The Bago Yoma mountain region of central Myanmar has previously been identified as an elephant conflict hotspot, characterized by high levels of crop-raiding and illegal killing of elephants for the ivory and skin trades. We used non-invasive fecal sampling to evaluate the population structure and demography of wild and captive elephants in the Bago Yoma using microsatellite loci and mitochondrial DNA in combination with crop-raiding status, age, and sex. We were able to collect 252 samples from wild elephants –119 directly following conflict events– and 25 from captive elephants from which we identified 127 unique wild and 21 captive individuals. The population was biased toward subadults, which could be an important contributor to the high rates of conflict, as these individuals may lack the experience to avoid dangerous behaviors. Conflict elephants were primarily male, although both sexes and all ages engaged in crop-raiding, including females with juveniles. We found that elephants that commit solo raids were all male, while larger raiding parties often included both related and unrelated individuals of both sexes. Repeat offenders were common. These wild elephants contained high levels of genetic diversity, differentiated from local captive populations, and valuable for the species’ conservation. Overall, the elephants of Bago Yoma, Myanmar have been heavily affected by conflict, and managers could utilize the knowledge presented to aid in the preservation of this population.

Aim For many endemic species with limited dispersal capacities, the relationship between landscape changes and species distributions is still unclear. We characterized the population structure of the endemic ringed salamander (Ambystoma annulatum) across its distribution in the Central Interior Highlands (CIH) of North America, an area of high species endemism, to infer the ecological and evolutionary history of the species. Methods We sampled 498 individuals across the species distribution and characterized the population genetic structure using nuclear microsatellite and mitochondrial DNA (mtDNA) markers. Results Ambystoma annulatum exist in two strongly supported nuclear genetic clusters across the CIH that correspond to a northern cluster that includes the Missouri Ozark populations and a southern cluster that includes the Arkansas and Oklahoma Ozarks and the Ouachita Mountains. Our demographic models estimated that these populations diverged approximately 2,700 years ago. Pairwise estimates of genetic differentiation at microsatellite and mtDNA markers indicated limited contemporary gene flow and suggest that genetic differentiation was primarily influenced by changes in the post‐Pleistocene landscape of the CIH. Main Conclusions Both the geologic history and post‐European settlement history of the CIH have influenced the population genetic structure of A. annulatum. The low mtDNA diversity suggests a retraction into and expansion out of refugial areas in the south‐central Ozarks, during temperature fluctuations of the Pleistocene and Holocene epochs. Similarly, the estimated divergence time for the two nuclear clusters corresponds to changes in the post‐Pleistocene landscape. More recently, decreased A. annulatum gene flow may be a result of increased habitat fragmentation and alteration post‐European settlement., We characterized the population structure of the endemic ringed salamander (Ambystoma annulatum) across its distribution in the Central Interior Highlands of North America, an area of high species endemism, to infer the ecological and evolutionary history of the species. Both the geologic history and post‐European settlement history of the CIH have influenced the population genetic structure of A. annulatum.

Patterns of human development are shifting from concentrated housing toward sprawled housing intermixed with natural land cover, and wildlife species increasingly persist in close proximity to housing, roads, and other anthropogenic features. These associations can alter population dynamics and evolutionary trajectories. Large carnivores increasingly occupy urban peripheries, yet the ecological consequences for populations established entirely within urban and exurban landscapes are largely unknown. We applied a spatial and landscape genetics approach, using noninvasively collected genetic data, to identify differences in black bear spatial genetic patterns across a rural‐to‐urban gradient and quantify how development affects spatial genetic processes. We quantified differences in black bear dispersal, spatial genetic structure, and migration between differing levels of development within a population primarily occupying areas with >6 houses/km2 in western Connecticut. Increased development disrupted spatial genetic structure, and we found an association between increased housing densities and longer dispersal. We also found evidence that roads limited gene flow among bears in more rural areas, yet had no effect among bears in more developed ones. These results suggest dispersal behavior is condition‐dependent and indicate the potential for landscapes intermixing development and natural land cover to facilitate shifts toward increased dispersal. These changes can affect patterns of range expansion and the phenotypic and genetic composition of surrounding populations. We found evidence that subpopulations occupying more developed landscapes may be sustained by male‐biased immigration, creating potentially detrimental demographic shifts.

— Understanding sex-specific differences in behavior and survival is essential for informative population modeling and evolutionary biology in animal populations. Uneven sex ratios are common in many migrant passerine species; however, the underlying mechanisms remain unclear. We used molecular sex determination, nest monitoring, and radio telemetry of fledgling Ovenbirds (Seiurus aurocapilla), to determine if sex-specific patterns of production, survival or behavior were present prior to the first migration. We tested whether: 1) sex ratios were skewed towards males at fledging; 2) postfledging survival of males was higher than females; 3) distances moved over time were equal between sexes; and 4) if observed parental care was equal between sexes over time. We determined the sex of 33 hatch-year Ovenbirds in central Missouri in 2015 and followed 19 individuals using radio telemetry. We found no difference in sex ratios within broods, overall numbers of male (n = 18) and female (n = 15) nestlings...

Understanding metapopulation dynamics requires knowledge about local population dynamics and movement in both space and time. Most genetic metapopulation studies use one or two study species across the same landscape to infer population dynamics; however, using multiple co‐occurring species allows for testing of hypotheses related to different life history strategies. We used genetic data to study dispersal, as measured by gene flow, in three ambystomatid salamanders (Ambystoma annulatum, A. maculatum, and A. opacum) and the Central Newt (Notophthalmus viridescens louisianensis) on the same landscape in Missouri, USA. While all four salamander species are forest dependent organisms that require fishless ponds to reproduce, they differ in breeding phenology and spatial distribution on the landscape. We use these differences in life history and distribution to address the following questions: (1) Are there species‐level differences in the observed patterns of genetic diversity and genetic structure? and (2) Is dispersal influenced by landscape resistance? We detected two genetic clusters in A. annulatum and A. opacum on our landscape; both species breed in the fall and larvae overwinter in ponds. In contrast, no structure was evident in A. maculatum and N. v. louisianensis, species that breed during the spring. Tests for isolation by distance were significant for the three ambystomatids but not for N. v. louisianensis. Landscape resistance also contributed to genetic differentiation for all four species. Our results suggest species‐level differences in dispersal ability and breeding phenology are driving observed patterns of genetic differentiation. From an evolutionary standpoint, the observed differences in dispersal distances and genetic structure between fall breeding and spring breeding species may be a result of the trade‐off between larval period length and size at metamorphosis which in turn may influence the long‐term viability of the metapopulation. Thus, it is important to consider life history differences among closely related and ecologically similar species when making management decisions.

By the early 1900s, black bears were believed to be almost extinct in Missouri and Arkansas, presumably due to extensive logging and overharvest. To reestablish Arkansas populations, the Arkansas Game and Fish Commission conducted a translocation program from 1958 to 1968, moving 254 bears from Minnesota and Manitoba, Canada, to the Ozark and Ouachita National Forests. This remains one of the most successful large mammal translocations ever conducted, and the Arkansas population grew rapidly into the thousands. However, bear sightings and nuisance reports suggested that 50 years after the translocations, populations in Missouri were small, and densities were low. We conducted a spatially explicit genetic capture-recapture study to estimate the size and density of the black bear population in south-central Missouri. We genotyped hair samples collected over two years using 15 microsatellite loci and estimated the population size at 279 ± 54 (SE) and the density at 1.7 bears/km2. To infer the source of bears colonizing Missouri, we analyzed the resulting genotypes in the Bayesian clustering program STRUCTURE along with genotypes from Arkansas, Oklahoma, and source populations. The results revealed unique genetic clusters in the Ouachitas, the Ozarks, and the source populations and found that Missouri bears were divided between those that clustered with the Ozarks and a unique cluster. The presence of the unique cluster in Missouri supports the hypothesis that black bears in the Missouri Ozarks were not extirpated but were reduced to very low densities during European settlement and have subsequently become admixed with bears that trace their ancestry to the reintroduction. While some might suggest that the unique Missouri population should be designated as a separate management unit, we caution that this might not be beneficial to the preservation of the Missouri bear population as we have no evidence that it is ecologically or geographically distinct, it has low genetic diversity, and the genetic differentiation may not be related to adaptive differences.

Elephants, which are among the most high-profile of the charismatic megafauna, are increasingly found in the human-dominated landscapes outside protected areas, creating the potential for serious economic impacts and tragic consequences for both humans and elephants. Managing elephants and other wide-ranging species requires information about population and group sizes, demography, distribution and habitat connectivity. Although we can view African savannah elephants (Loxodonta africana) from the air and estimate population sizes and movements through direct observations, these data are especially difficult to obtain for African forest elephants (Loxodonta cyclotis) and Asian elephants (Elephas maximus), as aerial surveys cannot detect animals under the closed canopy and ground surveys cannot be performed due to the dense vegetation. The case studies presented here illustrate the power of genetic studies using DNA obtained from non-invasively collected samples to provide biologists with important insights at the individual and population levels. In the Rift Valley of southern Kenya, the use of these methods allowed researchers to infer the movement patterns, demography and stress levels of a recently reestablished population of African savannah elephants on Maasai community land. Although behavioral studies of African forest elephants have suggested that social groups are predominately made up of a single female and her offspring, genetic analyses revealed evidence of weak, but significant, kin-based social structure comparable to the family groups observed in African savannah elephants. For the Asian elephant population of the Nakai Plateau, Lao PDR, genetic analyses allowed researchers to infer population size and demographic structure, and to estimate the level of genetic diversity. Despite having a considerably smaller population size than those found in India and Sri Lanka, the genetic diversity of the Nakai elephants continues to be among the highest reported in Asian elephants, highlighting the conservation value of this and other small, isolated populations in southeast Asia. These studies illustrate the breadth of information that can be obtained and highlight the use of genetic data in the conservation of these keystone species.

Amphibian metapopulations have become increasingly fragmented in the Midwestern United States, with wetland-breeding salamanders being especially dependent on intact, high-quality forested landscapes. However, the degree to which amphibian populations are isolated, the factors that influence dispersal and, ultimately, functional connectivity remain areas in need of investigation. We combined population demographic and genetic approaches to assess how a landscape fragmented by agriculture influences functional connectivity and metapopulation dynamics of a locally threatened salamander (Ambystoma jeffersonianum). We found that the allelic richness and heterozygosity of this species was significantly related to the level of connectivity with other occupied breeding wetlands and that decreased connectivity resulted in increased genetic differentiation. We also found that effective population size appears to be declining and, while correlative, our focal landscape has experienced significant losses of forested upland habitats and potential wetland breeding habitats over the last 200 years. By combining population and landscape genetic analyses with an assessment of regional wetland occupancy, our study has uniquely synthesized genetic and metapopulation processes, while also incorporating the effects of the landscape matrix on dispersal, connectivity, and population differentiation. The significant relationship between connectivity with heterozygosity, allelic richness, and genetic divergence observed in this study reinforces empirical observations of long distance dispersal and movements in ambystomatid salamanders. However, our results show that protection of core habitat around isolated wetlands may not sufficiently minimize genetic differentiation among populations and preserve critical genetic diversity that may be essential for the long-term persistence of local populations.

Analysis of multilocus genotypes is fundamental to conservation genetics, allowing inference ranging from population delineation to identification of dispersers; additionally, the natal range of a sample of unknown origin may be assigned. We investigated the accuracy and precision of two methods (spatial smoothing and principal components regression) for natal assignment with five datasets that varied in marker type (microsatellites or SNPs), number of loci, and number of training samples. Accuracy varied between datasets where the median difference between true and estimated geographic locations ranged from 192 to 902 km. A dataset using 1000 SNP loci and the spatial smoothing method was both the most accurate and precise. We observed that natal inference from SNPs was more accurate and precise than when estimated using microsatellites, and that large numbers of SNP loci could overcome having few samples in the training dataset. Our results suggest cautious interpretation of natal assignments, as 52% or fewer test samples were assigned to the correct management jurisdiction. In addition, samples from continuous habitat had less accurate assignments than samples from isolated areas whether due to landscape barriers or anthropogenic fragmentation. The use of natal inference as a tool for management agencies may work well at the regional level, given sufficient input data; however, we clearly observed limits on the spatial scale of inference and consequently on the effectiveness of genotypes as a sole source for natal inference.

Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species.

Habitat fragmentation plays a major role in the reduction of genetic diversity among wildlife populations. The African savannah elephant population of the Ruaha-Rungwa and Katavi-Rukwa ecosystems in south-western Tanzania, comprises one of the world’s largest remaining elephant populations, but is increasingly threatened by loss of connectivity and poaching for ivory. We investigate whether there are incipient signs of genetic isolation (loss of heterozygosity) within the younger cohort as a result of habitat loss between the two ecosystems. To investigate the genetic structure of populations, we compared the genotypes for 11 microsatellite loci in the western (n = 81 individuals from Katavi-Rukwa), central (n = 36 individuals from Lukwati and Piti), and eastern populations (n = 193, individuals from Ruaha-Rungwa). We found evidence of significant genetic differentiation among the three populations, but the levels were low, suggesting recent divergence. Furthermore, we identified weak isolation by distance, suggesting higher gene flow among nearer individuals with samples within 50km of each other being more genetically similar to one another than beyond. Although sample sizes were small, a further analysis of genetic differences across populations and in separate age classes revealed evidence of increasing genetic structure among younger age classes across the landscape. In a long-lived species with overlapping generations, it takes a long time to develop genetic substructure even when there are substantial obstacles to migration. Thus, in these recently fragmented populations, inbreeding (and the loss of heterozygosity) may be less of an immediate concern than demography (the loss of adults due to illegal hunting).

For animal species with dynamic interactions, understanding social patterns can be difficult. Social network analysis quantifies associations and their intensity between individuals within a population, revealing the overall patterns of the society. We used networks to test the hypothesis that the elusive African forest elephant Loxodonta cyclotis exhibits fission−fusion social dynamics, similar to other elephant species. We observed associations between individuals in savanna clearings in Lope National Park, Gabon, in 2006, 2008, and 2010. When possible, dung was collected from individuals for genetic analyses using 10 microsatellite loci and the mitochon- drial DNA control region. Using simple ratio association indices, networks were created for each year, wet and dry seasons, individuals detected at least twice, and for all females. We identified 118 unique adult females, for 40 of which we obtained genetic information. Networks had low densities, many disconnected components, short average path lengths, and high clustering coeffi- cients. Within components, average relatedness was 0.093 ± 0.071 (SD) and females appeared to share mitochondrial haplotypes. We detected 1 large component consisting of 22 adult females, but there were few preferred associations (8 of 65, 12.3%). No seasonal or yearly differences were observed. Our results substantiate fission−fusion dynamics in forest elephants; however, the net- works are more disconnected than those for other elephant species, possibly due to poaching and ecological constraints in the forest environment.

Reintroduction is an effective tool for restoring endangered populations. There is increasing concern, however, that demographic restoration may not equate with genetic restoration. We examine the demographic-genetic contrast in the context of one of the world's most successful carnivore population restorations. Beginning in 1982, a total of 835 river otters Lontra canadensis were reintroduced to Missouri, USA, more than 50 years after extirpation. Most otters were translocated from Louisiana, USA, and released at 43 sites across the state. An estimated population of 11 000–18 000 otters existed by 2000, and density estimates for Missouri otters are now similar to those reported for populations across the continent, indicating demographic recovery. We used microsatellite genotyping and mitochondrial sequence analysis of DNA extracted from fecal samples from eight southern Missouri rivers, in conjunction with mitochondrial DNA (mtDNA) analyses from several native Louisiana otter populations, to evaluate the genetic diversity and population structure of otters within Missouri as compared with Louisiana. The Missouri population showed moderate to high heterozygosity and allelic diversity, similar to that of the source populations, but low mtDNA haplotype diversity. We detected five distinct genetic clusters distributed throughout the eight rivers, with no evidence of isolation by distance. These data collectively suggest that 30 years after restoration efforts commenced, Missouri river otters have retained genetic diversity levels similar to those of the source populations, but that genetic structure has not reached an equilibrium between migration and genetic drift. Thus, the Missouri otter population has made a robust recovery despite retaining the genetic signature of the reintroduction.

Understanding patterns of dispersal, gene flow, and population differentiation are critical to making informed management and conservation decisions. By assessing these processes in multiple sympatric species, we can increase the generality and applicability of management plans. In this study, we assess patterns of genetic differentiation and pop- ulation structure in two ecologically similar ambystomatid salamanders in Missouri, USA. Ambystoma annulatum (rin- ged salamander) and A. maculatum (spotted salamander) are both dependent upon forested habitats and fishless ponds for reproduction, but differ in their breeding phenology. In comparing these species, we assessed the support for five different processes that we hypothesized to affect genetic differentiation: (1) resistance of landscape features to move- ment, (2) distribution of breeding habitat, (3) dispersal pro- pensity, (4) dispersal ability, and (5) breeding habitat quality. Of these hypotheses, we found support for differences in dispersal ability and propensity. In both species, there was a strong pattern of isolation-by-distance. However, A. annula- tum exhibited greater overall differentiation (F 0 ¼ 0:31 ), had a greater rate of differentiation increase with distance, and were grouped into three spatially congruent genetic clusters. In contrast, A. maculatum consisted of a single population cluster and overall F 0 ST was 0.047. We estimated the mean genetic dispersal distance of A. annulatum and A. maculatum to be 1,693 m and 2,050 m, respectively. Our results under- score the importance of considering multiple species when developing management criteria to better account for differ- ences in dispersal ability.

Understanding how populations are genetically and demographically connected is beneficial for species management, since gene flow and dispersal contribute to genetic diversity and population persistence. For hellbenders (Cryptobranchus alleganiensis), an aquatic salamander species experiencing dramatic declines in population size, fine-scale (i.e. within river) patterns of genetic diversity and gene flow are not well understood. Previous findings indicate that hellbenders are habitat specialists that exhibit extreme site fidelity and low vagility, suggesting that gene flow is restricted among the several, discrete habitat patches within a river. Using 15 polymorphic microsatellite loci and 497 hellbender samples from four Missouri rivers, we assessed fine-scale patterns of genetic diversity in order to infer population connectivity and aid in population management. Results indicate moderate levels of genetic variation (HO = 0.66–0.78) with little differentiation among habitat patches (avg. FST = 0.002) and no evidence of isolation by distance. Our data suggest that hellbender gene flow has been extensive even among habitat patches separated by distances greater than >100 km. These results are useful for hellbender management, especially in terms of making informed decisions regarding restorative releases of captively propagated individuals.

Harvest can affect the size and composition of wildlife populations. American black bear (Ursus americanus) populations in the Central Interior Highlands, Arkansas, USA, were nearly extirpated as a result of harvest and habitat change, but have expanded geographically and demographically since reintroduction in the late 1950s and early 1960s. Harvest levels have increased since baiting was permitted on private land in 2001; therefore, we initiated demographic analyses of 2 black bear populations to evaluate the effect of this policy change. We evaluated composition of harvest in response to baiting and used noninvasive genetic sampling in conjunction with capture–recapture methods to estimate density, survival, and population growth rate (λ) of black bear populations at locations within the Ouachita (2006–2008) and Ozark (2009–2011) national forests, Arkansas. More males were harvested than females with the use of bait. Capture probability varied annually; thus, multi-year data were valuable for capturing accurate population parameters. Density was approximately 14 bears/100 km2 in the Ouachitas and approximately 26/100 km2 for the Ozarks, which was greater than estimates from historical data (1989–1990). Thus, these populations maintained or exceeded previous density estimates while the use of bait was allowed on private land. However, as with any harvested population, it will be important to continue to monitor the population to be able make decisions about appropriate harvest policies going forward.

Although black bears (Ursus americanus) were believed to be extirpated from the Interior Highlands of North America by the early 1900s, populations have recently recovered, aided in part by reintroductions in Arkansas. Today black bears can be found in the Ozark and Ouachita National Forests of northern and western Arkansas, the White River National Wildlife Refuge in eastern Arkansas, and the Ozark region of southern Missouri. Previous genetic studies have investigated the effects of translocating black bears from Minnesota and Manitoba, Canada, into the Ozark and Ouachita National Forests between 1958 and 1968, with differing results. We used nuclear microsatellite loci to infer the genetic structure of black bears across the Interior Highlands and to investigate the sources of bears found today in southern Missouri. Our results suggest that the Ozark population was strongly influenced by the reintroductions, whereas the Ouachita population was influenced to a lesser degree. Although the majority of bears in the Ozark region of Arkansas and Missouri represent a single genetic unit, bears in Webster County, Missouri, may represent a remnant of the historical population of the region. Our results confirm that the bear population in the White River National Wildlife Refuge is strongly differentiated genetically from other Arkansas populations and support previous reports that the Ouachita bear population may have resulted from an admixture of a remnant population and reintroduced bears.

Non-invasive DNA-based capture–mark–recapture (CMR) methods have been developed to estimate population size and other parameters and have the advantage that samples can be collected without the need to see or disturb the animals. There are, however, few comparisons of DNA-based CMR estimates of animal population size with estimates from non-genetic methods. We compared the results of a dung-density based survey of an Asian elephant ( Elephas maximus ) population with a simultaneous fecal DNA-based CMR survey of the same population. We found 545 dung-piles along 116 line transects, converted dung-pile density to elephant density using rates of defecation and dung disappearance, and derived a population estimate of 141 (95% CI = [95, 208]) elephants. We collected 267 fecal samples during three CMR sampling sessions: 215 (81%) yielded sufficient genotypic information for analysis and gave an estimated population size of 132 (95% CI = [120,149]) elephants, closely matching the estimate produced by the dung-density method but with greater precision. The DNA-based method also provided information on population structure. We conclude that DNA-based CMR methods provide more precise abundance estimates, and more data about population structure and dynamics, than dung density-based methods. Fecal DNA-based CMR methods also require less time in the field and can be used when dung density methods are impracticable. Finally, fecal DNA based CMR methods are now cheaper than dung density based methods when line transect survey costs are approximately equal to CMR survey costs and dung decay rate monitoring costs are greater than laboratory costs (which will usually be the case).

Peripheral populations of wide-ranging species are often of special conservation concern, and knowledge of genetic diversity, gene flow, and historical population dynamics are critical to informed management of these populations. In this study we evaluate patterns of genetic diversity and gene flow among a series of wood frog populations in east-central Missouri where it is a species of conservation concern. Because these populations are on the periphery of the species’ range and are isolated from one another by fragmented landscapes, we expected to see population subdivision with signatures of range-edge effects and isolation by resistance. Our analyses reveal significant interpopulation differentiation and a distinct gradient in diversity where levels of allelic richness and heterozygosity decline as the species boundary is approached. These patterns likely stem from factors characteristic of peripheral populations, including reduced population size, reduced gene flow, and more frequent extinction–recolonization events. Population structure was evident, but isolation by resistance (i.e. fragmentation) was not a significant factor in our focal landscape. Isolation by distance was significant, but the level of population differentiation suggests that gene flow among populations is limited. We hypothesize that the lack of gene flow is due to the absence of available fishless breeding habitats outside of protected, managed lands, and recommend that future management efforts of the wood frog include increasing population connectivity at the landscape scale via the creation and maintenance of fishless aquatic breeding habitat.

Previously, American black bears (Ursus americanus) were thought to follow the pattern of female philopatry and male-biased dispersal. However, recent studies have identified deviations from this pattern. Such flexibility in dispersal patterns can allow individuals greater ability to acclimate to changing environments. We explored dispersal and spatial genetic relatedness patterns across ten black bear populations-including long established (historic), with known reproduction >50 years ago, and newly established (recent) populations, with reproduction recorded

Recently, a number of papers have addressed the use of pedigrees in the study of wild populations, highlighting the value of pedigrees in conservation management. We used pedigrees to study the horses (Equus caballus) of Assateague Island National Seashore, Maryland, USA, one of a small number of free-ranging animal populations that have been the subject of long-term studies. This population grew from 28 in 1968 to 175 in 2001, causing negative impacts on the island ecosystem. To minimize these effects, an immunocontraception program was instituted, and horse numbers are slowly decreasing. However, there is concern that this program may negatively affect the genetic health of the herd. We found that although mitochondrial DNA diversity is low, nuclear diversity is comparable to that of established breeds. Using genetic data, we verified and amended maternal pedigrees that had been primarily based on behavioral data and inferred paternity using genetic data along with National Park Service records of the historic ranges of males. The resulting pedigrees enabled us to examine demography, founder contributions, rates of inbreeding and loss of diversity over recent generations, as well as the level of kinship among horses. We then evaluated the strategy of removing individuals (using nonlethal means) with the highest mean kinship values. Although the removal strategy increased the retained diversity of founders and decreased average kinship between individuals, it disproportionately impacted sizes of the youngest age classes. Our results suggest that a combined strategy of controlled breeding and immunocontraception would be more effective than removing individuals with high mean kinships in preserving the long-term health and viability of the herd. © 2010 The Wildlife Society.

In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adultAmbystoma maculatumfrom five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FSTandDC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when usingDC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis.

Terrestrial salamanders of the genus Plethodon are closely tied to abiotic environmental habitat features and are particularly sensitive to land use and habitat change. To better understand the effects of land use and habitat fragmentation on population genetic characteristics, we screened 137 primers developed from 454 sequence libraries, and developed 27 microsatellite primers for the western slimy salamander, Plethodon albagula. Twenty-two of these primers cross-amplified in P. shermani. These new loci will be invaluable tools to study habitat variables affecting gene flow, population genetic structure, and genetic diversity across heterogeneous landscapes.

Aim Dispersal is a critical component of animal ecology that is poorly understood for most species. In particular, savanna elephants (Loxodonta africana) have been studied for decades in national parks across Africa, but little is known about their dispersal into new or unused habitats or their population dynamics in human-dominated landscapes. We capitalized on a natural dispersal event of savanna elephants recolonizing communal land in southern Kenya to document their demographic characteristics and genetic relationships. Location Rift Valley province of Kenya. Methods We collected faecal samples and used genetic methods to identify individuals, estimate the sex ratio and evaluate the patterns of relatedness within the female groups and male aggregations. We also measured dung bolus circumference to assign age classes to individuals and estimate the age structure. Results We identified 112 individuals with a sex ratio not different from one (1.32:1.00). The age structure was skewed towards younger elephants (71%), suggesting the potential for rapid growth from reproduction. We detected significantly higher kinship levels within female groups (R = 0.124 ± 0.023), suggesting that family groups colonized the site, but found little support for higher-order genetic relationships among female groups. Males detected together were unrelated (R = 0.003 ± 0.030). Main conclusions Our results suggest that highly social mammals, such as savanna elephants, disperse into unoccupied habitat as family groups and that a young demographic structure and a large number of males might be expected in establishing populations. These findings highlight the potential value of indirect, non-invasive methods for assessing elephant herd and demographic characteristics when direct observations are difficult.

The Lao People’s Democratic Republic (PDR) may have the largest Asian elephant population in Indochina. However, elephants on Lao PDR’s Nakai Plateau are potentially threatened by the construction of a hydropower dam that will flood important habitat. We conducted a non-invasive genetic study of elephants in this region to provide baseline data on genetic diversity and social structure prior to dam construction. For the 102 elephants we detected, values of observed heterozygosity (0.711) and allelic diversity (8.0 alleles/locus) at microsatellite loci were higher than those found in elephant populations in India and Vietnam, while mitochondrial diversity (haplotype diversity 0.741; nucleotide diversity 0.011) was similar to that reported for the Lao/Vietnam region. Six mitochondrial haplotypes were detected, representing both major clades previously reported in this species. Relatedness estimates between females and young detected near each other are consistent with familial relationships, and relatedness estimates between adult males and females suggest male locational dispersal. Since family group structure appears to be intact in the Nakai region, these elephants will likely move as relatively large family groups in response to habitat disturbance. These results have positive implications for the viability of the elephant population in this region, demonstrate its conservation significance, and will be valuable for predicting and monitoring the effects of the hydropower dam over time.

We isolated and screened 68 microsatellite loci from the spotted salamander, Ambystoma maculatum, in Missouri, USA. Eighteen polymorphic loci were identified and pooled into two multiplex reactions. These loci are a needed addition to the known loci for A. maculatum, which were developed in a different geographic region and are unsuitable for population or landscape genetic analyses in Missouri. To effectively protect and manage this species, regionally-relevant studies of population genetic structure and connectivity are necessary.

The loggerhead shrike ( Lanius ludovicianus ), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi , was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi , was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.

An isolated population of dark-eyed juncos, Junco hyemalis, became established on the campus of the University of California at San Diego (UCSD), probably in the early 1980s. It now numbers about 70 breeding pairs. Populations across the entire natural range of the subspecies J. h. thurberi are weakly differentiated from each other at five microsatellite loci ( F ST = 0.01). The UCSD population is significantly different from these populations, the closest of which is 70 km away. It has 88% of the genetic heterozygosity and 63% of the allelic richness of populations in the montane range of the subspecies, consistent with a harmonic mean effective population size of 32 (but with 95% confidence limits from four to > 70) over the eight generations since founding. Results suggest a moderate bottleneck in the early establishment phase but with more than seven effective founders. Individuals in the UCSD population have shorter wings and tails than those in the nearby mountains and a common garden experiment indicates that the morphological differences are genetically based. The moderate effective population size is not sufficient for the observed morphological differences to have evolved as a consequence of genetic drift, indicating a major role for selection subsequent to the founding of the UCSD population.

African forest elephants are difficult to observe in the dense vegetation, and previous studies have relied upon indirect methods to estimate population sizes. Using multilocus genotyping of noninvasively collected samples, we performed a genetic survey of the forest elephant population at Kakum National Park, Ghana. We estimated population size, sex ratio and genetic variability from our data, then combined this information with field observations to divide the population into age groups. Our population size estimate was very close to that obtained using dung counts, the most commonly used indirect method of estimating the population sizes of forest elephant populations. As their habitat is fragmented by expanding human populations, management will be increasingly important to the persistence of forest elephant populations. The data that can be obtained from noninvasively collected samples will help managers plan for the conservation of this keystone species.

The hellbender is the only North American member of the aquatic salamander family Cryptobranchidae and is a species of conservation concern across its range. We developed eight polymorphic microsatellite loci for hellbenders using a magnetic bead enrichment protocol and a PCR-based detection technique. Allelic diversity averaged 4.0 (±1.8 SD) per locus and heterozygosity averaged 0.56 (±0.30 SD). The hellbender is rare and difficult to study due to its cryptic life history. These loci will provide a valuable resource for population studies, which could inform future conservation and management decisions.

The endangered Asian elephant is found today primarily in protected areas. We characterized 18 dinucleotide microsatellite loci in this species. Allelic diversity ranged from three to eight per locus, and observed heterozygosity ranged from 0.200 to 0.842 in a wild population. All loci were in Hardy-Weinberg equilibrium, but linkage disequilibrium was detected between two loci in the wild, but not in the zoo elephants. These loci will be useful for the population-level studies of this species.

Bottlenecks, founder events, and genetic drift often result in decreased genetic diversity and increased population differentiation. These events may follow abundance declines due to natural or anthropogenic perturbations, where translocations may be an effective conservation strategy to increase population size. American black bears (Ursus americanus) were nearly extirpated from the Central Interior Highlands, USA by 1920. In an effort to restore bears, 254 individuals were translocated from Minnesota, USA, and Manitoba, Canada, into the Ouachita and Ozark Mountains from 1958 to 1968. Using 15 microsatellites and mitochondrial haplotypes, we observed contemporary genetic diversity and differentiation between the source and supplemented populations. We inferred four genetic clusters: Source, Ouachitas, Ozarks, and a cluster in Missouri where no individuals were translocated. Coalescent models using approximate Bayesian computation identified an admixture model as having the highest posterior probability (0.942) over models where the translocation was unsuccessful or acted as a founder event. Nuclear genetic diversity was highest in the source (AR = 9.11) and significantly lower in the translocated populations (AR = 7.07–7.34; P = 0.004). The Missouri cluster had the lowest genetic diversity (AR = 5.48) and served as a natural experiment showing the utility of translocations to increase genetic diversity following demographic bottlenecks. Differentiation was greater between the two admixed populations than either compared to the source, suggesting that genetic drift acted strongly over the eight generations since the translocation. The Ouachitas and Missouri were previously hypothesized to be remnant lineages. We observed a pretranslocation remnant signature in Missouri but not in the Ouachitas.

The common raccoon (Procyon lotor) is endemic to Central and North America, although non-native populations have become established around the world. In Spain, growing evidence of the introduction of raccoons has been reported across the country in the last decade, especially in Central Spain where the largest population is thought to occur. We used mitochondrial and microsatellite DNA data to investigate the genetics of invasive raccoons in Central Spain and to infer: the number of introduction events, the number of founders and the genetic variability of the introduced populations compared to a native population. We found that at least two introduction events have occurred along the Jarama and Henares Rivers in Central Spain, which currently constitute two genetically differentiated subpopulations. In both localities the number of effective founders from a native population was estimated as 2–4 individuals. These newly founded populations have expanded and show evidence of incipient contact and reproduction between them. This may allow for an increase in the genetic variability and adaptive potential of the population(s), possibly increasing the difficulty of controlling this invasive species. Our results reveal the ability to longitudinally monitor the genetics of the raccoon range expansion and emphasize the urgent need to control the pet trade of potentially invasive species., This study was partially funded by the Regional Park Parque Regional del Sureste and the Comunidad Autónoma de Madrid. Sampling and genotyping of Missouri raccoons was supported by grants from the National Science Foundation (DEB-0347609 and DEB-0841654).

Inverse correlations between genetic variability and parasitism are important concerns for conservation biologists. We examined correlations between neutral genetic variability and the presence of antibodies to canine distemper virus (CDV) and feline parvovirus (FPV) in a free-ranging population of raccoons. Over 3 years there was a strong relationship between age and seroprevalence rates. Most young animals were seronegative to CDV and FPV, but the oldest age class was greater than 80 per cent seropositive to both viruses. CDV-seropositive animals had greater heterozygosity and lower measures of inbreeding compared with CDV-seronegative animals. This relationship was strongest among the youngest animals and did not occur during a 1 year CDV epidemic. In contrast, FPV-seropositive animals only had significantly lower measures of inbreeding in 1 year, perhaps because FPV-associated mortality is relatively low or primarily occurs among very young individuals that were under-represented in our sampling. These results suggest that even in large outcrossing populations, animals with lower heterozygosity and higher measures of inbreeding are less likely to successfully mount an immune response when challenged by highly pathogenic parasites.

The National Park Service (NPS) manages a culturally significant population of feral horses (Equus caballus) inhabiting the Maryland portion of Assateague Island, a barrier island in the eastern United States. Rapid growth of this population over the past few decades from 28 to 166 horses negatively impacts native species and ecological processes on the island. Since 1994, contraception via porcine zona pellucida vaccine has been used to control horse numbers, although herd reduction has been slower than initially expected, leading NPS to consider other management options. An individual-based stochastic simulation model was developed using the Vortex software program to examine the effects of different management strategies on the population. Data from the managed population were used to populate the model parameters. Model projections over the next 50 years using current management practices show an average rate of population decline of 13% per year, suggesting that the population will reach the management target of 80–100 horses in 5–8 years. The effectiveness of contraception to reduce the herd and maintain it at various target sizes of 20–100 horses was also assessed. The accumulation of inbreeding at each target population size was also modelled.

Non-invasive samples of animal dung are being collected for use with DNA-based capture–recapture analysis to estimate the abundance of the species. A typical sampling strategy involves repeated sampling of transects or grids to search for dung. Searches performed on different transects or on different occasions are often considered the capture sessions for capture–recapture analysis. It is possible that multiple samples of dung from the same individual are found within an occasion. Most current capture–recapture models do not account for this additional data. We present a generalization of the geographically and demographically closed population capture–recapture models that use the numbers of dung found for each individual during each sampling occasion to help estimate heterogeneity in capture probability. We demonstrate that in the face of heterogeneity caused by unequal amounts of dung available per individual, the estimator developed here out performs standard capture–recapture abundance estimation. The estimator allows the benefit of using all data collected while not adding additional costs to the study. We present an example using dung-based capture–recapture data from African elephants to demonstrate the method.

Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r) tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r) tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines, with some individuals having more associates than observed from group sizes alone.

We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p