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Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage., In primates, the most colorful of mammals, few have examined the influence the melanocortin 1 receptor (MC1R) has on color variation (light or dark) in primates. Here, we examined how MC1R impacts color variation in a cryptic primate family with high contrasting color variation. We found MC1R is under purifying selection, but there appears to be a link in nucleotide changes and light coat color.

Due to geologic processes and recent anthropogenic introductions, patterns of genetic and morphological diversity within the Smallmouth Bass (Micropterus dolomieu), which are endemic to the central and eastern United States (USA), are poorly understood. We assessed genetic and morphological differentiation between the widespread Northern Smallmouth Bass (M. d. dolomieu) and the more restricted Neosho Smallmouth Bass (M. d. velox) where their ranges meet in the Central Interior Highlands ecoregion (CIH). Data from 14 microsatellite loci were used to conduct Structure and principal components analyses to evaluate diversity across populations and screen for hybridization with sympatric Spotted Bass (M. punctulatus). We also tested for morphological differences using five morphometric traits and one meristic trait. We found support for three genetic clusters corresponding to previously described taxonomic variation; five clusters largely corresponding to river systems; and nine clusters representing hierarchical population structure within both ranges. We found evidence of a unique genetic cluster in tributaries of the White River within the Northern Smallmouth Bass range and admixture between the subspecies throughout the Neosho range. We also found evidence of morphological differentiation between subspecies; Neosho Smallmouth Bass exhibited larger head length than Northern Smallmouth Bass relative to total length, and there was a significant interaction of subspecies and orbital length, possibly indicating differential growth patterns between subspecies. Our results reveal multiple levels of divergence, suggesting the CIH harbors greater and more complex Smallmouth Bass diversity than previously thought.

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.

Recent carnivore distributions in eastern Pakistan are poorly documented. In an effort to fill knowledge gaps, we combined field and laboratory molecular approaches to identify the large- and mid-sized mammalian carnivores in Murree, Kotli Sattian, and Kahuta National Park in Rawalpindi, Punjab. A total of 23 sites, each with a transect of 1–4 km in length, were identified and visited monthly over 24 months in 2016–2018. Fecal samples (n = 317) were collected and identified to species in the field based on morphology, odor, and additional signs. A subset (n = 150) of these samples was genetically identified to species using primers designed to amplify an informative region of the canid, felid, mustelid, and viverrid mitochondrial control region. Identified carnivore species for the park include leopard, leopard cat, jungle cat, red fox, golden jackal, small Indian civet, and Canis spp. For leopard, red fox, and golden jackal, field identification rates were accurate at a true-positive rate ≥ 63%. However, there was a notably high rate of field misidentification of putative jungle cat and yellow-throated marten samples, most of which were genetically identified as leopard cat or non-Carnivora samples. We mapped fecal sample presence points based on both morphological and genetically confirmed samples. For five of six dyadic combinations of pairwise species segregation patterns, there was evidence of high rates of non-random co-occurrence of red fox and jackal (p ≤ 0.05). For the other five pairwise combinations, no statistical support was found for non-random distribution. Such findings reiterate the need to combine field and molecular approaches when using fecal samples to survey communities, and underscore the need for broader studies of the carnivore communities of Pakistan.

Habitat fragmentation can play a major role in the reduction of genetic diversity among wildlife populations. The Ruaha-Rungwa and Katavi-Rukwa ecosystems in south-western Tanzania comprise one of the world’s largest remaining African savannah elephant metapopulation but are increasingly threatened by loss of connectivity and poaching for ivory. To investigate the genetic structure of populations, we compared the genotypes for nine microsatellite loci in the western, central and eastern populations. We found evidence of genetic differentiation among the three populations, but the levels were low and mostly concerned the younger cohort, suggesting recent divergence probably resulting from habitat loss between the two ecosystems. We identified weak isolation by distance, suggesting higher gene flow among individuals located less than 50km apart. 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 the loss of adults due to illegal hunting.

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.

We examined pond-breeding amphibian community composition at 210 ponds in Missouri between 2002 and 2012 using drift fence, dipnet, and funnel trap data. We encountered a total of 20 pond-breeding amphibian species in the combined surveys. We also examined whether the presence of American Bullfrogs, Lithobates catesbeianus, and fish influenced these patterns of diversity. Our results indicate the presence of American Bullfrogs, fish, and their interaction influenced the community composition of amphibians at these sites but in opposite patterns. American Bullfrogs often had a positive relationship with the total number of species, total caudate species, and total anuran species, whereas fish presence was negatively associated overall with species diversity, and the presence of both American Bullfrogs and fish was negatively associated with anuran species diversity. It is important to have baseline community species composition data from wide geographical ranges so spatiotemporal changes in community structure can be noted and assessed.

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).

Extensive phylogenetic studies have found robust phylogenies are modeled by using a multi-gene approach and sampling from the majority of the taxa of interest. Yet, molecular studies focused on the lorises, a cryptic primate family, have often relied on one gene, or just mitochondrial DNA, and many were unable to include all four genera in the analyses, resulting in inconclusive phylogenies. Past phylogenetic loris studies resulted in lorises being monophyletic, paraphyletic, or an unresolvable trichotomy with the closely related galagos. The purpose of our study is to improve our understanding of loris phylogeny and evolutionary history by using a multi-gene approach. We used the mitochondrial genes cytochrome b, and cytochrome c oxidase subunit 1, along with a nuclear intron (recombination activating gene 2) and nuclear exon (the melanocortin 1 receptor). Maximum Likelihood and Bayesian phylogenetic analyses were conducted based on data from each locus, as well as on the concatenated sequences. The robust, concatenated results found lorises to be a monophyletic family (Lorisidae) (PP ≥ 0.99) with two distinct subfamilies: the African Perodictinae (PP ≥ 0.99) and the Asian Lorisinae (PP ≥ 0.99). Additionally, from these analyses all four genera were all recovered as monophyletic (PP ≥ 0.99). Some of our single-gene analyses recovered monophyly, but many had discordances, with some showing paraphyly or a deep-trichotomy. Bayesian partitioned analyses inferred the most recent common ancestors of lorises emerged ∼42 ± 6 million years ago (mya), the Asian Lorisinae separated ∼30 ± 9 mya, and Perodictinae arose ∼26 ± 10 mya. These times fit well with known historical tectonic shifts of the area, as well as with the sparse loris fossil record. Additionally, our results agree with previous multi-gene studies on Lorisidae which found lorises to be monophyletic and arising ∼40 mya ( Perelman et al., 2011 , Pozzi et al., 2014 ). By taking a multi-gene approach, we were able to recover a well-supported, monophyletic loris phylogeny and inferred the evolutionary history of this cryptic family.

Baylisascaris procyonis is a nematode of significant concern to public and domestic animal health as well as wildlife management. The population genetics of B. procyonis is poorly understood. To gain insights into patterns of genetic diversity within (infrapopulation level) and among (component population level) raccoon (Procyon lotor) hosts, and specifically to assess the relative importance of indirect and direct transmission of the parasite for explaining observed population structure, we collected 69 B. procyonis from 17 wild raccoons inhabiting five counties in Missouri and Arkansas, USA. Informative regions of mitochondrial (CO1, CO2) and nuclear (28S, ITS2) genes were amplified and the distribution and genetic variability of these genes were assessed within and across raccoons. Concatenation of the CO1 and CO2 mtDNA sequences resulted in 5 unique haplotypes, with haplotype diversity 0.456 ± 0.068. The most common haplotype occurred in 94% of raccoons and 72.5% of B. procyonis. Sequences for 28S rDNA revealed four unique nuclear genotypes, the most common found in 100% of raccoons and 82.6% of B. procyonis. ITS2 genotypes were assessed using fragment analysis, and there was a 1:1 correspondence between 28S and ITS-2 genotypes. Infrapopulation variation in haplotypes and genotypes was high and virtually all hosts infected with multiple sequenced nematodes also harbored multiple haplotypes and genotypes. There was a positive relationship between the size of the analyzed infrapopulation (i.e., the number of nematodes analyzed) and the number of haplotypes identified in an individual. Collectively this work emphasizes the importance of indirect transmission in the lifecycle to this parasite.

Major Histocompatibility Complex (MHC) variability plays a key role in pathogen resistance, but its relative importance compared to environmental and demographic factors that also influence resistance is unknown. We analyzed the MHC II DRB exon 2 for 165 raccoons (Procyon lotor) in Missouri (USA). For each animal we also determined the presence of immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies to two highly virulent pathogens, canine distemper virus (CDV) and parvovirus. We investigated the role of MHC polymorphism and other demographic and environmental factors previously associated with predicting seroconversion. In addition, using an experimental approach, we studied the relative importance of resource availability and contact rates. We found important associations between IgG antibody presence and several MHC alleles and supertypes but not between IgM antibody presence and MHC. No effect of individual MHC diversity was found. For CDV, supertype S8, one allele within S8 (Prlo-DRB(∗)222), and a second allele (Prlo-DRB(∗)204) were positively associated with being IgG+, while supertype S4 and one allele within the supertype (Prlo-DRB(∗)210) were negatively associated with being IgG+. Age, year, and increased food availability were also positively associated with being IgG+, but allele Prlo-DRB(∗)222 was a stronger predictor. For parvovirus, only one MHC allele was negatively associated with being IgG+ and age and site were stronger predictors of seroconversion. Our results show that negative-frequency dependent selection is likely acting on the raccoon MHC and that while the role of MHC in relation to other factors depends on the pathogen of interest, it may be one of the most important factors predicting successful immune response.

Many carnivores require large ranges to meet their ecological and energetic needs; however, anthropogenic changes threaten species and their habitats. Camera traps have been used to effectively collect data on carnivores in a variety of habitat types; however, a single survey effort is typically limited to species that have similar body size, habitat use, and movement patterns and individual identification of animals is not always possible. We evaluated whether scat detection dogs could effectively survey for four wide-ranging felids that vary in these characteristics: jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), and oncilla (Leopardus tigrinus). From June to October 2009 and May to August 2011, a detection dog-handler team detected 588 scats, from which 176 unique genotypes were detected. We assigned sex to 84.7% of the genotyped scats and identified 55 individuals multiple times. The effectiveness of these noninvasive techniques (detection dogs and genetic analyses of scat) not only opens the door for additional studies in areas that were previously difficult or impossible with standard survey techniques, but also provides conservationists with a set of tools that overcome some of the limitations associated with the use of camera traps alone. Fil: Dematteo, Karen. University of Missouri; Estados Unidos Fil: Rinas, Miguel A.. Provincia de Misiones. Ministerio de Ecología y Recursos Naturales Renovables; Argentina Fil: Argüelles, Carina Francisca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina Fil: Holman, Bernardo E.. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina Fil: Di Bitetti, Mario Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentina Fil: Davenport, Barbara. Packleader Dog Training LLC; Estados Unidos Fil: Parker, Patricia G.. University of Missouri; Estados Unidos Fil: Eggert, Lori S.. University of Missouri; Estados Unidos

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.

Biodiversity conservation strategies are increasingly focused on regions outside national protected areas, where animals face numerous anthropogenic threats and must coexist with human settlements, livestock, and agriculture. The effects of these potential threats are not always clear, but they could have profound implications for population viability. We used savannah elephants (Loxodonta africana) as a case study to assess the physiological stress associated with living in a human-livestock-dominated landscape. We collected samples over two 3-month periods in 2007 and 2008. We used fecal DNA to identify 96 individual elephants in a community conservation area (CCA) and measured fecal glucocorticoid metabolite (FGM) concentrations as a proxy for stress. The CCA is community Maasai land managed for livestock and wildlife. We compared the FGM concentrations from the CCA to FGM concentrations of 40 elephants in Amboseli National Park and 32 elephants in the Maasai Mara National Reserve, where human settlements and intense livestock grazing were absent. In the CCA, we found no significant individual differences in FGM concentrations among the elephants in 2007 (p = 0.312) or 2008 (p = 0.412) and no difference between years (p = 0.616). The elephants in the CCA had similar FGM concentrations to the Maasai Mara population, but Amboseli elephants had significantly lower FGM concentrations than those in either Maasai Mara or the CCA (Tukey pairwise test, p < 0.001), due primarily to females excreting significantly lower FGM relative to males (p = 0.025). In the CCA, there was no relation among female group size, average pairwise group relatedness, and average group FGM concentration. We found no clear evidence of chronic stress in elephants living on CCA communal land, which is encouraging for conservation strategies promoting the protection of animals living outside protected areas. Conservacion Fuera de Areas Protegidas y el Efecto de Paisajes Dominados por Humanos sobre Hormonas del Estres en Elefantes Africanos Resumen Las estrategias de conservacion se enfocan cada vez mas hacia regiones fuera de areas nacionales protegidas, donde los animales enfrentan numerosas amenazas antropogenicas y deben coexistir con asentamientos humanos, ganado y agricultura. Los efectos de esas amenazas potenciales no siempre son claros, pero podrian tener implicaciones profundas para la viabilidad poblacional. Utilizamos elefantes africanos (Loxodonta africana) como un estudio de caso para evaluar el estres fisiologico asociado con vivir en un paisaje dominado por humanos y ganado. Recolectamos muestras en 2 periodos de 3 meses en 2007 y 2008. Utilizamos ADN fecal para identificar a 96 elefantes individuales en un area de conservacion comunitaria (ACC) y medimos las concentraciones del metabolito glucocorticoide fecal (MGF) como un indicador de estres. El ACC es tierra Maasai comunitaria manejada para ganado y vida silvestres. Comparamos las concentraciones de MGF en el ACC con las concentraciones de MGF de 40 elefantes del Parque Nacional Amboseli y 32 elefantes de la Reserva Nacional Maasai Mara, donde no hay asentamientos humanos ni pastoreo intensivo. En el ACC, no encontramos diferencias individuales significativas en las concentraciones de MGF entre los elefantes en 2007 (p = 0.312) ni 2008 (p = 0.412) ni entre anos (p = 0.616). Los elefantes en el ACC tuvieron concentraciones similares de MGF a la poblacion de Maasai Mara, pero los elefantes de Amboseli tuvieron concentraciones de MGF significativamente menores que las de Maasai Mara o el ACC. (prueba pareada de Tukey, p < 0.001), debido principalmente a que las hembras excretan significativamente menos MGF que los machos (p = 0.025). En el ACC, no hubo relacion entre el tamano del grupo de hembras, la similitud promedio de grupos pareados, ni la concentracion de MGF promedio del grupo. No encontramos evidencias claras de estres cronico en elefantes viviendo en el ACC, lo cual es alentador para las estrategias de conservacion que promueven la proteccion de animales que viven fuera de areas protegidas.

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.

We screened 74 published microsatellite primers in Ambystoma annulatum, a species for which no microsatellite markers have been developed. Overall, we had a moderate success rate, identifying 11 polymorphic microsatellites previously developed in four different species of Ambystoma. We also conducted a review of the literature, collecting all published cross-species applications of microsatellite markers within the genus Ambystoma. From this, we identified 20 loci that have amplified in three or more species. Our synthesis of microsatellite use within the genus Ambystoma should prove valuable to future molecular research, especially in species without developed markers and for studies in species that may already have microsatellites, but are being conducted far from the region where individuals were collected for original development of species-specific loci.

The reproductive strategies and variation in reproductive success of ticks are poorly understood. We determined variation in multiple paternity in the American dog tick Dermancentor variabilis . In total, 48 blood-engorged female ticks and 22 male companion ticks were collected from 13 raccoon ( Procyon lotor ) hosts. In the laboratory, 56.3% of blood-engorged females laid eggs, of which 37.0% hatched or showed signs of development. We examined the presence of multiple paternity in the ensuing clutches by genotyping groups of eggs and larvae at 5 microsatellite loci and subtracting the known maternal alleles, thereby identifying male-contributed alleles. Seventy-five percent of the clutches presented multiple paternity, with a mode of 2 fathers siring the clutch. Males associated with the females on the host always sired some offspring. In 1 case, a male was the sire of clutches derived from 2 females, indicating both polygyny and polyandry may occur for this species. These results, combined with those of several other recent studies, suggest that multiple paternity might be frequent for ixodid ticks.

While testing genetic sexing techniques in Ovenbirds (Seiurus aurocapilla), we found a genetic polymorphism in the ATP5A1 gene in 38% of individuals. The Z′ allele included changes in both intronic and exonic portions of the sequenced region, but there was no evidence that this changed the resulting ATP synthase product. Males that had one or more copies of this allele had higher relative body mass (mass corrected for size) than other genotypes. This allele was unrelated to stable isotope signatures, and so was not a useful predictor of latitude within the eastern portion of the Ovenbird breeding range. Future studies are needed to determine whether this polymorphism may be a useful geographic marker. This study is the first to link polymorphisms in the sex-linked ATP5A1 gene with fitness effects.

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.