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Tree squirrels (Sciurinae, Sciurini) represent a diverse radiation that successfully colonized Europe, Asia and the Americas during the Miocene-Pliocene, but information on their evolutionary history remains unclear. In the Neotropics, they have been shown to exhibit the highest rate of diversification amongst all arboreal squirrels, with strikingly high species accumulation rates in the past 3 My. In this study, we investigated the tempo and mode of diversification of tree squirrels using a mitogenome dataset that includes 43 Sciurini species. Our results corroborate the date of origin of the tribe Sciurini around 14 Mya (13.4-15.5) but suggest that their ancestral area was most likely in North America. This is in contrast to previous findings that suggested that the ancestors of this tribe occupied Eurasia. We estimated that cladogenetic events leading to the Eurasian lineages occurred twice at 10.5 and 9.7 Mya. Current North American genera originated in a temporal window from 6.2 to 2.3 Mya, and the origin of the Neotropical radiation was estimated to have occurred around 6 Mya in northwestern South America in the Pacific dominion. Remarkably, our results indicate that tree squirrels entered South America at an earlier date than previously estimated. This could have happened either through a land corridor connecting the Caribbean islands or through the Panamanian land bridge. Most cladogenetic events in Eurasia and North America appear to have occurred either late in the Miocene or in the Pleistocene, while the majority of Neotropical cladogenetic events occurred along the Pliocene—right after the South American invasion. We found a fairly constant speciation rate for tree squirrels (averaging 0.29), which contrasts with the peak of lineage accumulation observed in the Pliocene. The absence of fluctuations in the diversification rate may be the result of several extinction events that were responsible for equalizing the number of lineages maintained over time. Finally, we conclude that the South American invasion was not as recent as previously inferred, but the diversification there was indeed very fast.

Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth’s biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3% of our metagenomic data of a total 81.8 million unique, merged reads cannot be taxonomically identified due to the absence of genomic references in public databases. Of the remaining 7.7%, most of the data (93.0%) derive from Bacteria and Archaea, whereas only 0–5.8% are from Metazoa and 0–6.9% from Viridiplantae, in part due to unbalanced taxa representation in the reference data. The plant DNA record at ordinal level agrees well with local pollen data but resolves less diversity. Our animal DNA record reveals the presence of 41 native taxa (16 orders) including Afrotheria, Carnivora, and Ruminantia at Bwindi during the past 2200 years. Overall, we observe no decline in taxonomic richness with increasing age suggesting that several-thousand-year-old information on past biodiversity can be retrieved from tropical sediments. However, comprehensive genomic surveys of tropical biota need prioritization for sedimentary DNA to be a viable methodology for future tropical biodiversity studies.

A surprising amount of hidden phylogenetic diversity exists in the small to medium size, drab colored squirrels of the genus Sundasciurus. This genus is endemic to Sundaland and the Philippines, where it is widespread. An earlier revision of this genus found that the high elevation ‘populations’ of the widespread, lowland slender squirrel (S. tenuis) were different species. Previous phylogenies based on mitochondrial cytochrome b sequences also suggested that the widespread, lowland Low’s squirrel (S. lowii) and the narrow endemic Fraternal squirrel (S. fraterculus) are not reciprocally monophyletic. Additionally, deep divergences have been identified between lineages within Low’s squirrel that date to the early Pliocene. Here we focus on evaluating the relationships and differences within and between populations of these two nominal species using whole mitochondrial genome sequences, nuclear intron sequences, and morphology. We reassess the taxonomy of this group, revalidate the species status of Robinson’s squirrel (Sundasciurus robinsoni Bonhote, 1903) support the species level recognition of the Natuna squirrel (Sundasciurus natunensis Thomas, 1895) and identify three other lineages that require further study. We estimate times of divergence and integrate geologic history to find that most of the divergences are pre-Pleistocene, and thus predate the Pleistocene flooding of Sundaland. Biogeographic, and ecological factors may have played a more important role than climatic factors in generating these patterns. While divergence in allopatry seems to be the main process driving speciation in lowland Sundaland squirrels (Sundasciurus), ecomorphological and behavioral adaptations in this clade suggest an important role of niche divergence., AH was supported by an Ernst Mayr Travel grant and AMNH Collection Study Grant during museum data collection. This research received support from the SYNTHESYS Project financed by European Community Research Infrastructure Action under the FP7 “Capacities” Program. AH was also supported by a Spanish Ministry of Economy contract CGL2014-58793-P. The Spanish Ministry of Science and Innovation grant CGL2017-86068-P to JL supported this study. MH was supported by discretionary research funding from Humboldt State University.

The endangered San Joaquin kit fox (SJKF; Vulpes macrotis mutica) is strongly linked ecologically to xeric areas with high abundance of kangaroo rats. Endemic to the San Joaquin Desert of central California, the elusive nature of SJKF, coupled with steady habitat loss and lack of comprehensive surveys, has precluded efforts to quantify the species’ population size and distribution, especially in the central and northern parts of its range. Because the Ciervo-Panoche Natural Area contains the largest area of high-quality habitat in this central/northern region, we conducted systematic transect surveys for SJKF scats with professionally trained dog-handler teams throughout the area during 2009–2011. We collected almost 600 scats over 473 km of transects, documenting the freshness and location of each scat. Using molecular methods, we identified 93 SJKF individuals (56 males and 37 females) from 332 samples. Half of the individuals carried a mtDNA haplotype with a 16 bp deletion that had not been previously detected in other areas surveyed. Four individuals were recaptured in 2010 and five in 2011, including one female that was captured every year. We documented a unique mtDNA haplotype and more individuals across a wider area of the Ciervo-Panoche Natural Area than expected. Population analyses revealed two distinct subpopulations, with low connectivity between foxes in the Panoche Valley that are separated by hills with unsuitable habitat from those on the adjacent valley floor next to a major Interstate highway (I-5). While individuals detected within 6 km of each other were closely related, overall relatedness within each subpopulation approached zero. Genetic population models indicated a conservative population estimate of 90 kit foxes in total, with 60–90 individuals in the Panoche Valley and 17–27 individuals in the I-5 area. These results will help to inform management of the SJKF and identify areas that may be important to maintaining connectivity between populations.

Virginia has seen dramatic increases in reported cases of Lyme disease and Rocky Mountain spotted fever, but basic knowledge on the community ecology of these tick-borne diseases is poor. We examined the tick burdens of 5 small-mammal species in northwest Virginia from October 2011 to December 2012. We live-trapped individuals, quantified the tick burdens, assessed the burden structure, and tested a subset of the ticks for tick-borne pathogens. We found the tick burdens to be composed predominantly of Ixodes scapularis (Black-Legged Tick), and Ixodes sp. ticks, with Amblyomma americanum (Lone Star Tick) and Dermacentor variabilis (American Dog Tick) also present at lower densities. We detected Borrelia burgdorferi (prevalence 15%), Rickettsia spp. (4%), Anaplasma phagocytophilum (4%), and Hepatozoon spp. (1%). Black-Legged Ticks, a species which has shown range expansion in recent decades, tested positive for B. burgdorferi (17%) and for multiple pathogens in individual ticks. For better predictions of tick-borne disease risk across the Mid-Atlantic region, we recommend tracking changes in tick communities by continuous monitoring of tick burdens, densities of questing ticks, and prevalence of tick-borne pathogens.

The crested rat, Lophiomys imhausi, is the only mammal known to sequester plant toxins. Found in eastern Africa, this large rodent is thought to defend against predation by coating specialized hairs along its sides with cardenolide toxins from the poison arrow tree, Acokanthera schimperi. To better understand the ecology of this unusual poisonous mammal, we used camera traps, livetrapping, and captive behavioral observations, to study L. imhausi in central Kenya. Although crested rats were rarely detected with camera traps, 25 individuals were caught in live traps, with estimated densities of up to 15 rats/km(2) at one of nine trapping sites. Trapping records and behavioral observations suggest that L. imhausi live in male–female pairs, with juveniles that might exhibit delayed dispersal. We observed chewing of A. schimperi and/or anointing in 10 of 22 individuals, confirming the previous poison sequestration observation. We monitored crested rat activity using cameras and found that chewing on A. schimperi and cardenolide exposure had no effect on feeding, movement, or total activity. One crested rat also fed on milkweed (Gomphocarpus physocarpus; Gentaniales: Apocynaceae), but did not anoint with this cardenolide containing plant. This observation, combined with L. imhausi’s selective use of A. schimperi, suggests the potential for use of alternative poison sources. This research provides novel insight into the ecology of L. imhausi, while also suggesting that more field observations, feeding trials, and chemical analyses are needed to understand their behavior and physiology. Furthermore, their complex social interactions, slow life history, and fragmented populations suggest that L. imhausi could be at risk of decline.

Janzen's influential "mountain passes are higher in the tropics" hypothesis predicts restricted gene flow and genetic isolation among populations spanning elevational gradients in the tropics. Few studies have tested this prediction, and studies that focus on population genetic structure in Southeast Asia are particularly underrepresented in the literature. Here, we test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited dispersal across their broad elevational range which spans ~2,300 m on two peaks in Kinabalu National Park (KNP) in Borneo: Mt Tambuyukon (MT) and Mt Kinabalu (MK). We sampled 83 individuals across elevations on both peaks and performed population genomics analyses on mitogenomes and single nucleotide polymorphisms from 4,106 ultraconserved element loci. We detected weak genetic structure and infer gene flow both across elevations and between peaks. We found higher genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of historical processes and limited upslope gene flow on MT. Importantly, our results serve as a foundational estimate of genetic diversity and population structure from which to track potential future effects of climate change on mountain treeshrews in KNP, an important conservation stronghold for the mountain treeshrew and other montane species.

Key insights into the evolutionary history of recently extinct or critically endangered species can be obtained through analysis of genomic data collected using high-throughput sequencing and ancient DNA from museum specimens, particularly where specimens are rare. For instance, the evolutionary history of the critically endangered Puebla deer mouse, Peromyscus mekisturus, remains unclear due to discordance between morphological and molecular phylogenetic analyses. However, previous molecular analyses were based on PCR and Sanger sequencing of only a few mitochondrial genes. Here, we used ancient DNA from historical museum specimens followed by target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and whole mitochondrial genomes to test the validity of the previous phylogenetic placement of P. mekisturus. Based on UCEs and mitogenomes, our results revealed that P. mekisturus forms a well-supported distinct lineage outside the clade containing all other members of the Peromyscus melanophrys group. Additionally, the mitogenome phylogeny further supports the placement of P. mekisturus as the sister species of the genus Reithrodontomys. This conflicts with the previous mtDNA phylogenetic reconstruction, in which P. mekisturus was nested within the species P. melanophrys. Our study demonstrates that high-throughput sequencing of ancient DNA, appropriately controlling for contamination and degradation, can provide a robust resolution of the evolutionary history and taxonomic status of species for which few or no modern genetic samples exist. In light of our results and pending further analysis with denser taxon sampling and the addition of morphological data, a re-evaluation of the taxonomy and conservation management plans of P. mekisturus is needed to ensure that the evolutionary distinctiveness of this species is recognized in future conservation efforts.

High-throughput sequencing methods have facilitated obtaining large amounts of data from degraded DNA, thus resulting in a dramatic increase in destructive sampling requests to museums. Because the tissues taken from museum specimens as sources of DNA are destroyed during analysis, consideration of the costs and benefits of loss of valuable specimen material relative to knowledge gained is required for any project utilizing destructive sampling. Variation exists in the preservation of DNA in historical specimens due to specimen age and type of museum preparation, among other factors. Thus, it is important to assess DNA yield and quality from different sources of museum specimens when considering the needs of a particular molecular project. We compared DNA derived from several common sources of museum specimens including bone, claw, skin, and soft tissue adherent to skeletal preparations. To account for differences in preparation type and therefore specimen preservation, we tested the performance of samples representing 3 taxonomic groups: mephitids, rodents, and marsupials. We also compared yields from 2 commonly used DNA extraction techniques. DNA quality was assessed by comparing average fragment size, concentration, and copy number of template DNA (for mitochondrial and nuclear markers) in genomic DNA extracts, as well as mitochondrial genome sequence coverage resulting from shotgun sequencing. We show that DNA quality derived from historic museum samples differs depending on specimen and sample type; however, all samples yielded high mitochondrial copy number except the skin and nail from the tanned specimen. Overall, claw samples produced the greatest number of high-quality sequencing reads with the least amount of bacterial contamination. We also found that high DNA concentrations did not necessarily result in high percentages of on-target reads; in fact, the samples that yielded the highest DNA quantities also had the highest amount of exogenous bacterial DNA. Our results indicate that most historical tissue types can be suitable for next-generation sequencing approaches, therefore providing multiple options for natural history collection staff and researchers when considering destructive sampling requests.

Made available in DSpace on 2018-11-26T17:44:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-01-01 Programa de Desarrollo de las Ciencias Basicas (PEDECIBA, Uruguay) Agencia Nacional de Investigacion e Innovacion (ANII, Uruguay) Smithsonian Conservation Biology Institute Center for Conservation Genomics (Washington, DC, USA) Smithsonian Institution National Geographic Society Wildlife Conservation Society The maned wolf Chrysocyon brachyurus is the largest South American canid and categorized as Near Threatened on the IUCN Red List. The major threat to conservation efforts is the drastic reduction of suitable habitat for the species. A large portion of its range has been converted into farm and ranch lands as well as urban areas. To better understand the impact that these anthropogenic activities are having over the remaining populations across their current distribution range, we evaluated patterns of genetic variability and differentiation between them. We also compared these results with those obtained from captive maned wolves in order to make proper ex situ recommendations. We cross-amplified 12 microsatellite loci in maned wolf samples collected throughout their range (from Argentina, Brazil, Uruguay and Bolivia) and from captive stocks (from captive breeding centers and zoos in Brazil, Argentina and the USA). We found that wild populations retain moderate levels of genetic variability compared with other microsatellite studies on wild canids, and our structure analysis revealed 2 genetic clusters in wild samples, one of which included samples exclusively from Bolivia. This cluster could represent a different management unit with conservation priority. The captive stock population showed higher levels of genetic variability, with the ones from Brazil being the most genetically diverse stock. The USA stock showed strong genetic differences with all other groups. This is the first study to examine the patterns of genetic diversity of both wild and captive populations of maned wolves. These results should be incorporated into further population viability assessments and in the Maned Wolf Species Survival Plan. IIBCE, Dept Biodiversidad & Genet, Genet Conservac, Montevideo 11600, Uruguay Univ Republ UdelaR, Fac Ciencias, Secc Genet Evolut, Montevideo 11400, Uruguay Smithsonian Inst, Natl Museum Nat Hist, Dept Vertebrate Zool, Washington, DC 20013 USA Univ Estadual Paulista, Dept Zootecnia, Nucleo Pesquisa & Conservacao Cervideos, BR-14884900 Jaboticabal, SP, Brazil Minist Ambiente & Desarrollo Sustentable, RA-1004 Buenos Aires, DF, Argentina Smithsonian Conservat Biol Inst, Natl Zool Pk, Ctr Conservat Gen, Washington, DC 20008 USA Univ Estadual Paulista, Dept Zootecnia, Nucleo Pesquisa & Conservacao Cervideos, BR-14884900 Jaboticabal, SP, Brazil Agencia Nacional de Investigacion e Innovacion (ANII, Uruguay): FCE_3_2011_1_6619

The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation.

Genes of the major histocompatibility complex (MHC) play a primary role in resistance to infectious disease and have been implicated in mate choice and recognition of close relatives. We describe genetic diversity at three MHC class II genes in urban and non-urban populations of San Joaquin kit fox (Vulpes macrotis mutica), an endangered canid endemic to California’s San Joaquin Valley. We used multi-tagged pyrosequencing synthesis to characterize genetic diversity in 96 kit foxes at three MHC class II genes, DQA1, DQB1, and DRB1. Using rigorous bioinformatics methods to limit sequencing artifacts, we identified 11 DQA alleles, 13 DQB alleles, and 29 DRB alleles, which translated into 1, 7, and 28 unique antigen-binding sites for the respective genes. The high polymorphism did not correlate with sequencing depth or sample location but was found across individuals and indicated polygenic loci for DQB (two gene copies) and DRB (three copies). A phylogeny based on all known carnivore MHC alleles resolved two major clades, one with alleles from DQA and one with alleles from DQB and DRB, regardless of the taxa. Based on Tajima’s D, we found evidence of negative selection in DQA (D = −1.90) and positive selection in DRB (D = 2.36). We analyzed 48 urban kit foxes that were living in the city of Bakersfield and 48 non-urban foxes living in the nearby LoKern and Carrizo plain areas. We found similar levels of MHC allelic diversity in the urban and non-urban populations. However, many of the common DRB alleles found in the non-urban population were absent in the urban population. This could result from a founder effect or different selective pressures on the two populations. The levels of MHC diversity in the SJKF are similar to or higher than MHC diversity of more wide-spread canid species, although this subspecies has been isolated in the San Joaquin Valley for millennia and has low mtDNA haplotype diversity. Our study provides baseline data on three MHC genes that can contribute to future studies of disease resistance and mate choice in the endangered San Joaquin kit fox.

Population monitoring is critical to effective conservation, but forest living taxa can be difficult to directly observe. This has been true of African forest elephants (Loxodonta cyclotis), for which we have limited information regarding population size and social behavior despite their threatened conservation status. In this study, we estimated demographic parameters using genetic capture-recapture of forest elephants in the southern Industrial Corridor of the Gamba Complex of Protected Areas in southwestern Gabon, which is considered a global stronghold for forest elephants. Additionally, we examined social networks, predicting that we would find matrilineal structure seen in both savanna and forest elephants. Given 95% confidence intervals, we estimate population size in the sampled area to be between 754 and 1,502 individuals and our best density estimate ranges from 0.47 to 0.80 elephants per km2. When extrapolated across the entire Industrial Corridor, this estimate suggests an elephant population size of 3,033 to 6,043 based on abundance or 1,684 to 2,832 based on density, approximately 40–80% smaller than previously suggested. Our social network analysis revealed approximately half of network components included females with different mitochondrial haplotypes suggesting a wider range of variation in forest elephant sociality than previously thought. This study emphasizes the threatened status of forest elephants and demonstrates the need to further refine baseline estimates of population size and knowledge on social behavior in this taxon, both of which will aid in determining how population dynamics in this keystone species may be changing through time in relation to increasing conservation threats.

Karuppannan KV, Aifat NR, Mohamed KA, Ahmad-Tahir NFD, Nordin FM, Yaakop S, Maldonado JE, Md-Zain BM. 2019. Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences. Biodiversitas 20: 2494-2502. Asian elephant (Elephas maximus) is an important large mammal in Peninsular Malaysia and is completely protected by the Wildlife Conservation Act 2010 (Act 716). The conservation of this species requires strong information-based research, such as genetic evaluations. The aim of this study was to compare mitochondrial control region variation among selected elephants from the Taman Negara National Parks (TNNP) population with other selected populations in Peninsular Malaysia. DNA materials were extracted from fecal samples and amplified using partial mitochondrial D-loop region. Total 13 haplotypes with haplotype diversity (Hd) of 0.7524 were observed. A total of 34 base pair (bp) segregation sites were formed in 547 bp sequences. Both phylogenetic trees showed that a few individual elephants from the TNNP formed a clade together with individuals from other populations. The remaining individual elephants from TNNP formed a monophyletic clade supported by a high bootstrap value. Low genetic distance was detected among the tested populations, which proved that both individuals from the TNNP and other selected populations have similar genetic patterns. High gene flow among tested populations would impact on fitness and long-term resilience of the populations. This highly significant outcome provides strong baseline data for Department of Wildlife and National Parks (DWNP) in monitoring elephant populations in order to reduce number of human-elephant conflicts which indirectly minimize translocating conflict elephants to TNNP.

We investigated the patterns of genetic diversity and structure of African forest elephants in a human‐modified landscape in the Gamba complex of protected areas (GCPA), a tropical wilderness area along the southwest coast of Gabon. We collected 298 elephant fecal samples from four sites (Sette Cama, Gamba area, Vera Plains, and Mayonami), along approximately 80 km of coastline from north to south. We used microsatellites and mitochondrial DNA (mtDNA) to successfully genotype 295 of the 298 fecal samples, and identified 213 individuals. Using sex markers, we identified 84 males and 118 females; we could not determine the sex of the remaining 11 individuals. We also characterized the sex, group size, and social status of crop‐raiding elephants and did not find characteristics distinguishing them from nonraiders. Overall, our mtDNA and microsatellite markers revealed that elephants in the research area maintain high levels of genetic variation and low levels of subdivision. Gene flow appears to be mostly mediated by male dispersal away from natal herds. Our structure analysis revealed two highly admixed genetic clusters, attributable to high connectivity among the protected areas. However, forest areas within the GCPA have become increasingly fragmented by human‐induced habitat modification. We detected a pattern of isolation by distance, accentuated by the presence of the town of Gamba between Sette‐Cama and Mayonami. We found a high degree of connectivity among sampling locations within the GCPA. This supports the importance of establishing agricultural best practices to reduce habitat loss that may sever gene exchange and to maintain connectivity, as well as to avoid human–elephant conflict that can result in retaliatory killing of elephants in this area. This study emphasizes the importance of conducting baseline monitoring of demographic data, genetic diversity, and structure to enable future comparisons to assess the long‐term impact of human‐induced habitat fragmentation.

Characterizing Toll-like receptors across taxa can lead to an increasingly accurate documentation of the evolutionary processes acting within this receptor class, as well as a greater understanding of the diseases associated with these receptors. This study examines 2 sequenced portions of the Toll-like receptor 5 (TLRS5) protein coding gene in 2 imperiled canid species: the Near Threatened maned wolf Chrysocyon brachyurus and the Critically Endangered red wolf Canis rufus, to characterize genetic variation and investigate the presence of single nucleotide polymorphisms (SNPs) previously associated with canine inflammatory bowel disease (IBD). Both maned and red wolves suffer from inflammatory bowel disease, threatening the sustainability of their crucial ex situ populations. Here we report novel polymorphic positions found in maned and red wolf TLR5, differences in variation with regard to nucleotide polymorphisms and resulting amino acid variation among maned wolves, red wolves, gray wolves and domestic dogs. Domestic dog SNPs associated with IBD were not found to be polymorphic in maned wolves and red wolves. Samples of both focal species and gray wolves lack the protective alleles present in many dog breeds, suggesting a potential genetic predisposition for IBD in these 2 wild canid species and a possible development of these protective alleles post domestication. This potential predisposition informs ex situ management practices and treatment for IBD.

Coatis (Procyonidae; Nasua) are considered the only truly social meso-carnivore mammals in Neotropical forests. In Mexico, white-nosed coatis (Nasua narica) are suspected to have undergone population reduction due to habitat loss and fragmentation and led to a lack of genetic adaptability and genetic isolation throughout its range. We examined patterns of genetic diversity and connectivity of five populations of Nasua narica distributed throughout Mexico (n = 60) by sequencing an ≈ 800 bp fragment of the mitochondrial cytochrome-b gene and also by screening 12 microsatellite loci. We found moderate to high levels of genetic variability for both genetic markers. We recorded twenty-two different cytochrome-b haplotypes throughout the 5 sampled areas and found that each of the sampled population of white-nosed coatis in Mexico harbors unique haplotypes and only three haplotypes were shared among two different populations that were closer geographically. All populations had high haplotype diversity (h) (0.968 ± 0.008 (SD)) but lower levels of nucleotide diversity (π) of 0.007 ± 0.001 (SD). All microsatellite loci were polymorphic in all of the populations and the mean number of alleles per locus was 5.033 ± 1.545 (SD) with expected (HE) and observed (HO) heterozygosity values of 0.774 and 0.664, respectively. However, low Wright F statistic values suggest the existence of a reduced heterozygosity (FST = 0.203, FIS = 0.134 and FIT = 0.310). Significant differences between the five populations confirmed isolation by distance, which suggests genetic structure among five subpopulations.

Understanding how human activities have influenced the foraging ecology of wildlife is important as our planet faces ongoing and impending habitat and climatic change. We review the canine surrogacy approach (CSA)—a tool for comparing human, dog, and other canid diets in the past—and apply CSA to investigate possible ancient human resource provisioning in an endangered canid, the California Channel Islands fox (Urocyon littoralis). We conducted stable isotope analysis of bone collagen samples from ancient and modern island foxes (n = 214) and mainland gray foxes (Urocyon cinereoargenteus, n = 24). We compare these data to isotope values of ancient humans and dogs, and synthesize 29 Accelerator Mass Spectrometry (AMS) radiocarbon dates that fine-tune the chronology of island foxes. AMS dates confirm that island foxes likely arrived during the early Holocene (>7300 cal BP) on the northern islands in the archipelago and during the middle Holocene (>5500 cal BP) on the southern islands. We found no evidence that island foxes were consistently using anthropogenic resources (e.g., food obtained by scavenging around human habitation sites or direct provisioning by Native Americans), except for a few individuals on San Nicolas Island and possibly on San Clemente and Santa Rosa islands. Decreases in U. littoralis carbon and nitrogen isotope values between prehistoric times and the 19th century on San Nicolas Island suggest that changes in human land use from Native American hunter-gatherer occupations to historical ranching had a strong influence on fox diet. Island foxes exhibit considerable dietary variation through time and between islands and have adapted to a wide variety of climatic and cultural changes over the last 7300 years. This generalist foraging strategy suggests that endemic island foxes may be resilient to future changes in resource availability.

Ectoparasites frequently vector pathogens from often unknown pathogen reservoirs to both human and animal populations. Simultaneous identification of the ectoparasite species, the wildlife host that provided their most recent blood meal(s), and their pathogen load would greatly facilitate the understanding of the complex transmission dynamics of vector-borne diseases. Currently, these identifications are principally performed using multiple polymerase chain reaction (PCR) assays. We developed an assay (EctoBaits) based on in-solution capture paired with high-throughput sequencing to simultaneously identify ectoparasites, host blood meals and pathogens. We validated our in-solution capture results using double-blind PCR assays, morphology and collection data. The EctoBaits assay effectively and efficiently identifies ectoparasites, blood meals, and pathogens in a single capture experiment, allowing for high-resolution taxonomic identification while preserving the DNA sample for future analyses.

Sex determination among wild Asian elephant (Elephas maximus) populations in Taman Negara National Parks (TNPP), Peninsular Malaysia were very crucial by using ecological techniques such as biodiversity inventories or dung count survey. With advance molecular sexing technique, the sex ratio among wild E. maximus in study area can be determined. As a first move, we conduct this particular experiment by using two Y-specific and one X-specific molecular sexing primers on 63 wild Asian elephant faecal samples together with 10 positive controls from known elephant individuals in National Elephant Conservation Centre (NECC) Kuala Gandah, Pahang, Peninsular Malaysia. DNA extraction were done by using Qiagen kits and we carried out multiplex PCR and visualized those PCR products on agarose gel before proceed with fragment analysis. Fragment analyses with 3 peaks were confirmed for male while female showed the expected 1 peak. The outcome showed, 31 samples were from female elephants while remaining 32 samples from male. This is very significant and strong outcome which proofs that molecular sexing markers can be used in non-invasive samples as well and be a good baseline data to study Asian elephant social organization in TNPP, Peninsular Malaysia.

Myotis planiceps (flat-headed myotis) was known from only 3 specimens collected from 3 different sites in the states of Coahuila, Nuevo Leon, and Zacatecas, Mexico, since its discovery in 1952. The last specimen was collected in 1970; in 1996, after efforts to recollect samples failed, the species was listed as extinct. However, an expedition in 2004 rediscovered a population of M. planiceps and the species was relisted as endangered. Members of this species have a conspicuously flattened cranium, speculated to be an adaptation for living in crevices; however, little is known about its biology and, to date, little work has been done to clarify its phylogenetic relationships with other members of the genus Myotis . In order to elucidate the placement of M. planiceps within the Myotis phylogeny, we sequenced 1,140 base pairs (bps) of the mitochondrial cytochrome- b gene ( Cytb ) and 1,148 bps of the nuclear Recombination Activating Gene 2 ( rag2 ) from 7 samples collected from 4 different localities in north-central Mexico. We found 4 different haplotypes for Cytb that differed by 0.14% mean sequence divergence and 13 alleles for rag2 within samples of M. planiceps . We performed maximum parsimony, maximum likelihood, and Bayesian analyses to compare these samples with Myotis sequences available on GenBank. All reconstructions placed M. planiceps within a strongly supported clade including several Nearctic Myotis ( M. volans , M. sodalis , M. lucifugus , M. thysanodes , and M. evotis ). M. planiceps forms a paraphyletic relationship with M. volans , despite significant differences in skull morphology between the 2 species. Myotis planiceps (Myotis de cabeza plana) era conocido a partir de solo 3 especimenes recolectados en 3 sitios diferentes en los estados de Coahuila, Nuevo Leon y Zacatecas, Mexico, desde su descubrimiento en 1952. El ultimo ejemplar se colecto en 1970 y la especie fue declarada extinta en 1996, despues de que fallaron los esfuerzos para recolectar mas muestras. Sin embargo, durante una expedicion en 2004 se redescubrio una poblacion de M. planiceps y la especie fue recategorizada bajo Peligro de Extincion. Los miembros de esta especie tienen un craneo visiblemente aplanado, rasgo que se especula seria una adaptacion para vivir en las grietas; sin embargo, se sabe poco sobre su biologia y, hasta la fecha, poco se ha hecho para aclarar sus relaciones filogeneticas con otros miembros del genero Myotis . Con el fin de dilucidar la posicion de M. planiceps dentro de la filogenia de Myotis , secuenciamos 1140 pb del gen mitocondrial citocromo-b ( Cytb ) y 1148 pb del gen nuclear Activador de la Recombinacion 2 ( rag2 ) a partir de 7 muestras recolectadas de 4 localidades diferentes en la region norte-central de Mexico. Encontramos 4 haplotipos diferentes para Cytb que presentaron un promedio de divergencia de secuencia de 0.14%, y 13 alelos del gen rag2 en muestras de M. planiceps . Realizamos analisis de maxima parsimonia, maxima verosimilitud y Bayesiano para comparar estas muestras con otras secuencias de Myotis disponibles en GenBank. Todas las reconstrucciones ubican a M. planiceps dentro de un clado bien soportado que incluye tambien a varios Myotis del Neartico ( M. volans , M. sodalis , M. lucifugus , M. thysanodes , y M. evotis ). M. planiceps forma una relacion parafiletica con M. volans , a pesar de diferencias significativas en la morfologia del craneo entre estas especies.

There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.

Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules.

Actualmente, la relacion filogenetica y estructura poblacional de la musarana de Arizona ( Sorex arizonae ) es poco conocida. No obstante, tener informacion sobre su variabilidad genetica es fundamental debido a que es una especie que se encuentra restringida a pequenos fragmentos de habitat llamados “sky islands”, que se encuentran en las zonas altas de EU y del norte de Mexico. Se determino la estructuracion genetica utilizando 64 individuos de cuatro regiones montanosas de Arizona y Nuevo Mexico: Animas, Huachuca, Santa Rita y Chiricahua, utilizando secuencias de citocromo- b mitocondrial y 12 microsatelites. Los resultados del analisis del citochromo- b revelaron que existe un haplotipo unico para la poblacion de las Animas, mientras que las poblaciones restantes comparten un haplotipo. Ademas cada poblacion tiene un haplotipo unico en frecuencias muy bajas. Los estadisticos de FST indican que aunque la diferenciacion genetica es baja, es significativa entre todas las poblaciones, siendo la mas alta la existente entre las poblaciones de Chiricahua y de Animas. Por otro lado, los analisis de STRUCTURE no revelaron diferenciacion significativa entre las poblaciones de Chiricahua y Animas, pero si se detectaron diferenciacion entre el grupo formado por estas dos poblaciones y entre Huachuca y Santa Rita. Los analisis filogeneticos, utilizando las secuencias de citocromo- b disponibles de todas las musaranas norteamericanas, confirman que las musaranas de Arizona se encuentran relacionadas con S. trowbridgii , ambas comparten un grupo monofiletico que es basal al grupo de las musaranas Nearticas, siendo parte de un grupo monofiletico que es hermano del clado del subgenero Otiosorex . Nuestros resultados sugieren que las poblaciones de S.arizonae tienen un alto nivel de divergencia evolutiva respecto a lo encontrado para otras musaranas norteamericanas. Tambien muestran que existe estructuracion genetica entre

The arrival of a novel predator in an ecosystem necessitates many wildlife-management decisions that should be based on sound demographic data. Canis latrans (Coyote) has experienced a dramatic range expansion across North America since the early 19th century, completing its colonization of the continental US in the mid-Atlantic region over the past 20 years. Their arrival in the suburbs of Washington, DC, has generated much public attention, and demonstrated a need for demographic information about this species. To address the challenges of surveying an elusive animal, we used fecal DNA to describe the population genetics and demographics of a newly colonized Coyote population at Marine Corps Base Quantico (MCBQ) in northern Virginia. We collected 331 scats over a period of 2 years at MCBQ, resulting in identification of 23 unique individual Coyotes and 41 total Coyote captures that were analyzed using spatial capture—recapture models. We found evidence of colonization by multiple genetic lineag...

Biodiversity across elevational gradients generally follows patterns, the evolutionary origins of which are debated. We trapped small non-volant mammals across an elevational gradient on Mount (Mt.) Kinabalu (4,101 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We also included visual records and camera trap data from Mt. Tambuyukon. On Mt. Tambuyukon we trapped a total of 299 individuals from 23 species in 6,187 trap nights (4.8% success rate). For Mt. Kinabalu we trapped a total 213 animals from 19 species, in 2,044 trap nights, a 10.4% success rate. We documented the highest diversity in the low elevations for both mountains, unlike previous less complete surveys which supported a mid-elevation diversity bulge on Mt. Kinabalu. Species richness decreased gradually towards the highlands to a more even community with different species (high turnover), less rich but with the highest levels of endemism. These patterns suggest that an interplay of topography and climatic history of the region were drivers of the diversity gradient, in addition to standing climatic and spatial hypothesis.

Mountains offer replicated units with large biotic and abiotic gradients in a reduced spatial scale. This transforms them into well-suited scenarios to evaluate biogeographic theories. Mountain biogeography is a hot topic of research and many theories have been proposed to describe the changes in biodiversity with elevation. Geometric constraints, which predict the highest diversity to occur in mid-elevations, have been a focal part of this discussion. Despite this, there is no general theory to explain these patterns, probably because of the interaction among different predictors with the local effects of historical factors. We characterize the diversity of small non-volant mammals across the elevational gradient on Mount (Mt.) Kinabalu (4,095 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We documented a decrease in species richness with elevation which deviates from expectations of the geometric constraints and suggests that spatial factors (e.g., larger diversity in larger areas) are important. The lowland small mammal community was replaced in higher elevations (from above ~1,900 m) with montane communities consisting mainly of high elevation Borneo endemics. The positive correlation we find between elevation and endemism is concordant with a hypothesis that predicts higher endemism with topographical isolation. This supports lineage history and geographic history could be important drivers of species diversity in this region.

[Aim] The genetics of organisms currently isolated in refugia has received little attention compared to post-glacial expansions. We study the population history and connectivity of a rat endemic to montane habitat in Borneo to better understand the history and potential of populations in interglacial mountain refugia., [Location] Sabah, Borneo, Malaysia., [Methods] We performed a field survey of the summit rat (Rattus baluensis) on two mountains, Mt. Kinabalu and Mt. Tambuyukon, its entire known distribution. We sequenced mitogenomes and 27 introns (19 of which were polymorphic) in 49 individuals from both populations. We analysed their current genetic structure and diversity, and inferred their demographic history with approximate Bayesian computation., [Results] Summit rats were tightly associated with mountain mossy forest and scrubland above 2,000 m, facilitating the prediction of their past and future distributions. The genetic analysis supports a Holocene fragmentation of a larger population into smaller ones that are now isolated in interglacial refugia on mountaintops. These findings are consistent with climatic reconstructions and the retreat of upland forest to higher elevations after the Last Glacial Maximum (LGM), ~21 kya., [Main conclusions] The two isolated populations of summit rats formed through the upland shift of their habitat after the LGM. The current trend of global warming will likely lead to diminishing suitable upland habitat and result in the extinction of the population on Mt. Tambuyukon. The population on Mt. Kinabalu, the higher peak, could persist at higher elevations, highlighting the singular value of high tropical mountains as reservoirs of biodiversity during past and ongoing climate change., Logistical support was provided by Laboratorio de Ecología Molecular, Estación Biológica de Doñana, CSIC (LEM‐EBD). Digital elevation models for maps was obtained from the U.S. The Spanish Ministry of Science and Innovation grants CGL2010‐21524 and CGL2014‐58793‐P supported this work. MCS is supported by the Spanish Ministry of Science and Innovation Predoctoral Fellowship BES‐2011‐049186, and part of his fieldwork was also funded by EEBB‐I‐12‐05317.

Utilización de técnicas genéticas no invasivas para contribuir a la conservación del aguará guazú en un fragmento residual del Cerrado de Brasil El aguará guazú es una especie de cánido sudamericano que se considera clave en el Cerrado. Se realizó un estudio genético de varios individuos de aguará guazú que habitan en un pequeño fragmento del Cerrado de Brasil. Se colectaron 84 muestras fecales durante un año y se incluyeron también dos muestras de tejidos de animales atropellados. Se determinaron la especie, el sexo y los individuos mediante marcadores moleculares. Asimismo, se identificaron 13 individuos mediante la amplificación de loci de microsatélites, de los cuales ocho eran hembras y cinco, machos. El grado de variabilidad genética observado y el elevado número de individuos detectados indican la presencia de una población abierta., The maned wolf is a South American canid considered a keystone species of the Cerrado. We performed a genetic assessment of maned wolves that inhabit a small remnant fragment of the Cerrado in Brazil. We collected 84 fecal samples over a year and also included two tissue samples from road–killed animals. We successfully identified the species, sex, and individuals using molecular markers. Using microsatellite loci analysis we identified 13 different individuals, eight females and five males. The genetic variability level found and the high number of individuals detected indicates the presence of an open population.

Made available in DSpace on 2018-11-26T16:16:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-09-01 PEDECIBA CSIC-UdelaR. from Uruguay Smithsonian Conservation Biology Institute's Center for Conservation and Evolutionary Genetics National Zoo Cleveland Metroparks Zoo's Scott Neotropical Fund American Zoo Association's Maned Wolf Species Survival Plan The maned wolf (Chrysocyon brachyurus) is one of the largest South American canids, and conservation across this charismatic carnivore's large range is presently hampered by a lack of knowledge about possible natural subdivisions which could influence the population's viability. To elucidate the phylogeographic patterns and demographic history of the species, we used 2 mtDNA markers (D-loop and cytochrome b) from 87 individuals collected throughout their range, in Argentina, Bolivia, Brazil, and Uruguay. We found moderate levels of haplotype and nucleotide diversity, and the 14 D-loop haplotypes were closely related. Genetic structure results revealed 4 groups, and when coupled with model inferences from a coalescent analysis, suggested that maned wolves have undergone demographic fluctuations due to changes in climate and habitat during the Pleistocene glaciation period approximately 24 000 years before present (YBP). This genetic signature points to an event that occurred within the timing estimated for the start of the contraction of the Cerrado around 50 000 YBP. Our results reveal a genetic signature of population size expansion followed by contraction during Pleistocene interglaciations, which had similar impacts on other South American mammals. The 4 groups should for now be considered management units, within which future monitoring efforts should be conducted independently. MEC, IIBCE, Dept Biodiversidad & Genet, Genet Conservac, Montevideo 11600, Uruguay Fac Ciencias UdelaR, Secc Genet Evolut, Montevideo 11600, Uruguay Smithsonian Inst, Natl Museum Nat Hist, Dept Vertebrate Zool, Washington, DC 20013 USA Natl Fish & Wildlife Fdn, Sci & Evaluat, Washington, DC 20005 USA Univ Estadual Paulista, Dept Zootecnia, Nucleo Pesquisa & Conservacao Cervideos, BR-14884900 Jaboticabal, SP, Brazil Secretaria Ambiente & Desarrollo Sustentable Naci, Buenos Aires, DF, Argentina Smithsonian Conservat Biol Inst, Ctr Conservat & Evolutionary Genet, Washington, DC 20008 USA Univ Estadual Paulista, Dept Zootecnia, Nucleo Pesquisa & Conservacao Cervideos, BR-14884900 Jaboticabal, SP, Brazil

Made available in DSpace on 2018-11-26T17:41:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-10-01 Projeto de Conservacao e Utilizacao Sustentavel da Diversidade Biologica Brasileira Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Agencia Nacional de Investigacion y Inovacion Programa de Desarrollo de las Ciencias Basicas Comision Sectorial de Investigacion Cientifica (Uruguay) The small red brocket deer Mazama bororo is endemic to the Brazilian Atlantic Forest, a biome that has been greatly fragmented and altered by human activities. This elusive species is morphologically similar to the red brocket deer Mazama americana and the Brazilian dwarf brocket deer Mazama nana, and genetic typing is necessary for reliable identification. To determine the geographical range of M. bororo more accurately, we conducted non-invasive genetic sampling using scat detection dogs trained to locate deer faeces. We surveyed 46 protected areas located within the species' potential distribution and collected a total of 555 scat samples in 30 of the protected areas. Using a polymerase chain reaction-restriction fragment length polymorphism approach, we genotyped 497 scat samples (89%) and detected M. bororo in seven localities in three Brazilian states. The results support a range extension of the small red brocket deer to latitudes 23 and 28 degrees S and longitudes 47 and 49 degrees W. We show that the species' distribution is associated with 37,517 km(2) of the Ombrophilous Dense Forest in the Brazilian Atlantic Forest, and this conclusion is supported by species distribution modelling. The small red brocket deer is the largest endemic species in Brazil and may have the smallest geographical distribution of any Neotropical deer species. This species occupies fragmented landscapes and is threatened by human encroachment, poaching, and predation by dogs, and based on our findings we recommend policy intervention for conservation planning of the Ombrophilous Dense Forest. Univ Estadual Paulista, Dept Zootecnia, Nucl Pesquisa Conservacao Cervideos, Via Acesso Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, SP, Brazil Univ Fed Integracao Latino Amer, Curitiba, Parana, Brazil Univ Fed Pernambuco, Ctr Acad Vitoria, Vitoria Santo Antao, Vitoria Santo Antao, PE, Brazil Natl Zool Pk, Smithsonian Conservat Biol Inst, Ctr Conservat Genom, Washington, DC USA Minist Educ & Cultura, Inst Invest Biol Clemente Estable, Dept Biodiversidad & Genet, Genet Conservac, Montevideo, Uruguay Smithsonian Inst, Natl Museum Nat Hist, Dept Vertebrate Zool, Washington, DC 20560 USA Univ Republ Oriental Uruguay, Fac Ciencias, Secc Genet Evolut, Montevideo, Uruguay Univ Estadual Paulista, Dept Zootecnia, Nucl Pesquisa Conservacao Cervideos, Via Acesso Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, SP, Brazil

The taxonomy of American deer has been established almost entirely on the basis of morphological data and without the use of explicit phylogenetic methods; hence, phylogenetic analyses including data for all of the currently recognized species, even if based on a single gene, might improve current understanding of their taxonomy. We tested the monophyly of the morphology-defined genera and species of New World deer (Odocoileini) with phylogenetic analyses of mitochondrial DNA sequences. This is the first such test conducted using extensive geographic and taxonomic sampling. Our results do not support the monophyly of Mazama, Odocoileus, Pudu, M. americana, M. nemorivaga, Od. hemionus, and Od. virginianus. Mazama contains species that belong to other genera. We found a novel sister-taxon relationship between “Mazama” pandora and a clade formed by Od. hemionus columbianus and Od. h. sitkensis, and transfer pandora to Odocoileus. The clade formed by Od. h. columbianus and Od. h. sitkensis may represent a valid species, whereas the remaining subspecies of Od. hemionus appear closer to Od. virginianus. Pudu (Pudu) puda was not found sister to Pudu (Pudella) mephistophiles. If confirmed, this result will prompt the recognition of the monotypic Pudella as a distinct genus. We provide evidence for the existence of an undescribed species now confused with Mazama americana, and identify other instances of cryptic, taxonomically unrecognized species-level diversity among populations here regarded as Mazama temama, “Mazama” nemorivaga, and Hippocamelus antisensis. Noteworthy records that substantially extend the known distributions of M. temama and “M.” gouazoubira are provided, and we unveil a surprising ambiguity regarding the distribution of “M.” nemorivaga, as it is described in the literature. The study of deer of the tribe Odocoileini has been hampered by the paucity of information regarding voucher specimens and the provenance of sequences deposited in GenBank. We pinpoint priorities for future systematic research on the tribe Odocoileini.

The black bear Ursus americanus is one of the largest terrestrial carnivores that has a wide distribution in northeastern Mexico, the only country in which black bears are listed as endangered. We used 10 nuclear microsatellite loci to evaluate black bear genetic variability in 6 disjointed populations from northeastern Mexico. Non-invasive genetic techniques were applied to fecal and hair samples. Using a panel of 10 polymorphic microsatellites we identified 64 indi- viduals. Black bears showed low to moderate levels of genetic diversity in all sampled populations (mean ± SD expected heterozygosity, He = 0.63 ± 0.628). Pairwise comparisons between all 6 pop- ulations (φST = 0.315, p < 0.05) detected significant genetic differentiation between the western Coahuila and the northeastern Nuevo Leon regions, suggesting that black bears have low levels of gene flow between these 2 regions. Microsatellites revealed significant structure within the complex of disjoint areas in the region. The inbreeding coefficient was also significant (φIS = 0.143). The largest proportion of genetic variation (82.7%) was found between individuals within populations. Distance and anthropogenic activities may serve to limit gene exchange among pop- ulations which form at least 3 distinct genetic clusters; these may respond differently to environ- mental changes and should be considered distinct management units.

Herein, we compare functional muscle properties among convergent forms of large, obligate avian scavengers. We performed quantitative analyses of all the muscle masses and cross-sectional areas (CSA) of the wings and hindlimbs of five species from two families, Cathartidae (New World vultures; Cathartes aura and Vultur gryphus) and Accipitridae (Old World vultures and raptors; Gyps africanus, Aquila rapax, and Buteo lineatus). These species comprise two paraphyletic functional groups, raptors (Aquila and Buteo) and vultures (Gyps, Cathartes, and Vultur). Our ordination analyses based on all of the muscles of the wings, hindlimbs, and wing and hindlimb muscles combined produced patterns that appeared to be more related to phylogeny, with a hint of a functional signal in wing muscle CSA. However, when wing muscles were grouped according to their functional roles (upstroke, downstroke, and wing stabilization), the percentages of mass and CSA allocated to the upstroke and stabilizing muscles were 1.4–5% greater in the vultures than in the raptors. Conversely, when hindlimb muscles were grouped according to their roles in grasping and terrestrial locomotion, the percentages of mass and CSA allocated to grasping muscles were 5.9–14% greater in the raptors. Our results provide a baseline for future lines of inquiry aimed at understanding how muscle mass and CSA are affected differentially across locomotor modules, possibly in response to differential demands on wing and hindlimb function experienced by these disparate accipitriform clades.

Environmental DNA (eDNA) has been used to record the presence of many different organisms in several different aquatic and terrestrial environments. Although eDNA has been demonstrated as a useful tool for the detection of invasive and/or cryptic and declining species, this approach is subject to the same considerations that limit the interpretation of results from traditional survey techniques (e.g. imperfect detection). The wood turtle is a cryptic semi-aquatic species that is declining across its range and, like so many chelonian species, is in-need of a rapid and effective method for monitoring distribution and abundance. To meet this need, we used an eDNA approach to sample for wood turtle presence in northern Virginia streams. At the same time, we used repeat visual encounter surveys in an occupancy-modelling framework to validate our eDNA results and reveal the relationship of detection and occupancy for both methods. We sampled 37 stream reaches of varying size within and beyond the known distribution of the wood turtle across northern Virginia. Wood turtle occupancy probability was 0.54 (0.31, 0.76) and while detection probability for wood turtle occupancy was high (0.88; 0.58, 0.98), our detection of turtle abundance was markedly lower (0.28; 0.21, 0.37). We detected eDNA at 76% of sites confirmed occupied by VES and at an additional three sites where turtles were not detected but were known to occur. Environmental DNA occupancy probability was 0.55 (0.29, 0.78); directly comparable to the VES occupancy estimate. Higher probabilities of detecting wood turtle eDNA were associated with higher turtle densities, an increasing number of days since the last rainfall, lower water temperatures, and lower relative discharges. Our results suggest that eDNA technology holds promise for sampling aquatic chelonians in some systems, even when discharge is high and biomass is relatively low, when the approach is validated and sampling error is quantified.

We describe a fast and reliable genetic method for sexing Neotropical canids by high resolution melting analysis of amplicons obtained by real time polymerase chain reaction. We used a primer set that amplifies a 195 bp fragment of the ZFX and ZFY genes to determine the sex of pampas fox (Pseudalopex gymnocercus), crab eating fox (Cerdocyon thous), maned wolf (Chrysocyon brachyurus), and domestic dog (Canis familiaris). This new method is useful, fast and reliable for sexing of noninvasively obtained samples with low DNA quality and quantity. This protocol could be easily modified to sex non-invasive samples of other canid species.

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.

Prehensile-tailed porcupines (Coendou prehensilis), like other rodents, lack external sexual traits, making it difficult to non-invasively determine their gender. By exploiting genetic differences between the X and the Y chromosome, we developed a simple genetic test to determine the gender of Coendous from shed quills. We Sanger sequenced a short portion (195 bp) of the zinc finger protein gene of known male (XY) Coendous to identify positions that are polymorphic between the X and Y chromosomes at this locus. By directly sequencing this fragment, we were able to correctly determine (confirmed via anatomical sexing) the gender of male and female Coendous by the presences or absence of polymorphisms in the resulting chromatograms. This assay is simple, quick and is applicable to other porcupine species. Zoo Biol. 32:463–466, 2013. © 2013 Wiley Periodicals Inc.

The jungle cat (Felis chaus), a small-sized felid, is distributed across Southeast and South Asia to Egypt in Africa. In India, it is one of the most common small cat species but no reliable methods are available to monitor its population status. We describe a non-invasive genetic monitoring technique using fecal samples for individual identification and sex determination of jungle cats. We evaluated 21 feline microsatellites and optimized a panel of 11 highly polymorphic microsatellite loci that yield a cumulative Probability of Identity between siblings value of 5.51×10−6. We used this panel to identify 110 individuals from 118 jungle cat scats collected from tiger reserves in Central India. We identified 22 males and 35 females by amplifying a fragment of the Amelogenin protein gene. This panel will be helpful to study genetic structure, gene flow, relatedness, sex ratio, and population estimation in jungle cats.

Fil: Cardoni, Daniel Augusto. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencia Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina

We investigated the spatial genetic structure of the tiger meta-population in the Satpura–Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura–Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura–Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India.

Background The African wild dog (Lycaon pictus) is an endangered African canid threatened by severe habitat fragmentation, human-wildlife conflict, and infectious disease. A highly specialized carnivore, it is distinguished by its social structure, dental morphology, absence of dewclaws, and colorful pelage. Results We sequenced the genomes of two individuals from populations representing two distinct ecological histories (Laikipia County, Kenya and KwaZulu-Natal Province, South Africa). We reconstructed population demographic histories for the two individuals and scanned the genomes for evidence of selection. Conclusions We show that the African wild dog has undergone at least two effective population size reductions in the last 1,000,000 years. We found evidence of Lycaon individual-specific regions of low diversity, suggestive of inbreeding or population-specific selection. Further research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole. We documented positive selection on the Lycaon mitochondrial genome. Finally, we identified several candidate genes (ASIP, MITF, MLPH, PMEL) that may play a role in the characteristic Lycaon pelage. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3368-9) contains supplementary material, which is available to authorized users.

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.

Aim Habitat loss and fragmentation can influence the genetic structure of biological populations. Large terrestrial predators can often avoid genetic subdivision due to fragmentation because they have high rates of dispersal-mediated gene flow. Leopards (Panthera pardus) are found in a variety of habitats and are the most widely distributed of the large and middle-sized felids. We investigated the genetic diversity and population substructure of leopards (P.p fusca) in a fragmented meta-population comprised of four populations from five protected areas and inter-connecting corridors spread over an area of 45,000 km2 in central India. Location Kanha, Pench, Satpura and Melghat Tiger Reserves, and interconnecting corridors in the Satpura-Maikal Landscape of Central India. Methods We collected faecal samples and used genetic methods to identify individuals, estimate the genetic variation and evaluate the patterns of genetic substructuring within this meta-population of leopards. Results We identified 217 individual leopards using a panel of seven microsatellite loci. Leopards showed high levels of genetic diversity in all sampled populations. Spatial and non-spatial Bayesian analysis revealed at least two admixed genetic populations with indications of ongoing genetic subdivision. Genetic differentiation between populations was not explained by geographic distance. We identified nine individuals as migrants, most of which were assigned to reserves connected by corridors. Main conclusions Our study demonstrates that the leopard, an adaptable and vagile species, can become genetically differentiated with increased habitat fragmentation. Contrary to our hypothesis of panmixia, our results indicate that although leopards in this landscape are admixed, there is genetic substructuring at both the landscape and the fine-scale level. We conclude that this is due to habitat fragmentation and corridors are of immense value in maintaining genetic connectivity in this landscape.