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Aim: Understanding the biotic and abiotic mechanisms underlying the generation and maintenance of biogeographic transitions represent long‐standing topics in evolutionary biology. The Isthmus of Kra (IOK) divides Sundaland and Indochina and constitutes a poorly characterized terrestrial biogeographic transition. Here we looked at population genetic structure of three species that are distributed across the IOK to gain insights into the drivers that have shaped this transition and regional diversification patterns. Location: Tropical east Asia: Sundaland and Indochina. Taxa: Callosciurus caniceps, Tamiops mcclellandii, and Dremomys rufigenis‐ornatus species complex (Mammalia: Rodentia: Sciuridae). Methods: We generated complete mitogenomes and sequences of 11 nuclear intron fragments from 61 and 67 museum specimen samples, respectively. We assessed population structure by constructing Maximum Likelihood mitogenome phylogenies (IQTREE2), and nuclear marker haplowebs and conspecificity matrices (HaplowebMaker and CoMa). We estimated divergence dates through Bayesian phylogenetic inference (BEAST2) and put these results in the context of climatic and geological history. Results: High levels of mitochondrial and nuclear divergence were identified across the IOK in all three squirrels. Lineage turnover was consistent with the two major mammal species distribution transitions near the Kangar‐Pattani Line and at the juncture between the Thai‐Malay peninsula and the mainland. Divergence of mitochondrial lineages across Kra was estimated in the late Pliocene/ early Pleistocene for all three taxa. Older Miocene/Pliocene divergences were estimated within Indochina in D. rufigenis‐ornatus and T. mcclellandii, which were paraphyletic. Main Conclusions: Sundaic and Indochinese populations have possibly diverged in allopatric habitat refugia in or around mountains during periods of increased aridity and evergreen forest contraction. Ecological differences and/or topography might have influenced genetic differentiation during periods of rainforest expansion. Alternative hypotheses remain to be tested with more informative nuclear markers and additional geographic sampling. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We studied the taxonomy and biogeography of Mazama bricenii, a brocket deer classified as Vulnerable by the IUCN, drawing on qualitative and quantitative morphology and sequences of the mitochondrial cytochrome-b gene. We used Ecological Niche Modeling (ENM) to evaluate the hypothesis that M. bricenii of the Venezuelan Cordillera de Mérida (CM) might have become isolated from populations of its putative sister species, Mazama rufina, in the Colombian Cordillera Oriental (CO). This hypothesis assumes that warm, dry climatic conditions in the Táchira Depression were unsuitable for the species. Our analyses did not reveal morphological differences between specimens geographically attributable to M. bricenii and M. rufina, and phylogenetic analyses of molecular data recovered M. bricenii nested within the diversity of M. rufina. These results indicate that M. bricenii should be regarded as a junior synonym of M. rufina. ENM analyses revealed the existence of suitable climatic conditions for M. rufina in the Táchira Depression during the last glacial maximum and even at present, suggesting that gene flow between populations in the CO and CM may have occurred until at least the beginning of the current interglacial period and may continue today. Because this pattern might characterize other mammals currently considered endemic to the CM, we examined which of these species match two criteria that we propose herein to estimate if they can be regarded as endemic to the CM with confidence: (1) that morphological or molecular evidence exists indicating that the putative endemic taxon is distinctive from congeneric populations in the CO; and (2) that the putative endemic taxon is restricted to either cloud forest or páramo, or both. Only Aepeomys reigi, Cryptotis meridensis, and Nasuella meridensis matched both criteria; hence, additional research is necessary to assess the true taxonomic status and distribution of the remaining species thought to be CM endemics. [ABSTRACT FROM AUTHOR]

The critically endangered Central American River Turtle (Dermatemys mawii) is the only remaining member of the Dermatemydidae family, yet little is known about its population structuring. In a previous study of mitochondrial (mt) DNA in the species, three main lineages were described. One lineage (Central) was dominant across most of the range, while two other lineages were restricted to Papaloapan (PAP; isolated by the Isthmus of Tehuantepec and the Sierra de Santa Marta) or the south-eastern part of the range (1D). Here we provide data from seven polymorphic microsatellite loci and the R35 intron to re-evaluate these findings using DNA from the nuclear genome. Based on a slightly expanded data set of a total of 253 samples from the same localities, we find that mtDNA and nuclear DNA markers yield a highly congruent picture of the evolutionary history and population structuring of D. mawii. While resolution provided by the R35 intron (sequenced for a subset of the samples) was very limited, the microsatellite data revealed pronounced population structuring. Within the Grijalva-Usumacinta drainage basin, however, many populations separated by more than 300 kilometers showed signals of high gene flow. Across the entire range, neither mitochondrial nor nuclear DNA show a significant isolation-by-distance pattern, but both genomes highlight that the D. mawii population in the Papaloapan basin is genetically distinctive. Further, both marker systems detect unique genomic signals in four individuals with mtDNA clade 1D sampled on the southeast edge of the Grijalva-Usumacinta basin. These individuals may represent a separate cryptic taxon that is likely impacted by recent admixture. [ABSTRACT FROM AUTHOR]

The small red brocket deer Mazama bororo is one of the most endangered deer in the Neotropics. The great morphological similarities with three other sympatric brocket deer species, coupled with the fact that they inhabit densely forested habitats complicate detection and prevent the use of traditional methodologies for accurate identification of species. The ability to determine the presence of this endangered species in an area is crucial for estimating its distribution range, and is critical for establishing conservation management strategies. Here we describe a fast and reliable noninvasive genetic method for species identification of Mazama species from faeces. We designed a primer set that amplifies a short 224-bp fragment of the cytochrome b and demonstrate its effectiveness in successful amplification of DNA isolated from both tissue and faecal samples. This fragment contains a BSTNI/ ECORII digestion site that is unique to the endangered M. bororo. The digested polymerase chain reaction products yielded a 160-bp fragment that is clearly visible in a 2% agarose gel. Two other diagnostic sites were identified to differentiate the other three sympatric species, SspI (M. gouazoubira) and AflIII ( M. americana, and M. nana). [ABSTRACT FROM AUTHOR]

Raccoons occur on a number of islands in the Bahamas and the Lesser Antilles in the West Indies. Zooarcheological studies have long suggested that these animals are not native to the West Indies. Originally, Caribbean populations were described as endemic insular species Procyon maynardi (Bahamas), P. minor (Guadeloupe), and P. gloveralleni (Barbados), a classification that was recognized throughout much of the 20th century. More recently, studies of qualitative morphology and a review of historical publications and documents have been used to bolster arguments that these populations of raccoons are not unique species worthy of special conservation attention, but invasive populations of the North American raccoon (P. lotor) introduced in recent centuries. Raccoons in the Bahamas and the French Antilles appear to be spreading onto other islands with human assistance, but the population on Barbados is now apparently extinct. We present evidence from the mitochondrial control region, including sequence data from the extinct population on Barbados generated using ancient DNA protocols, indicating that all 3 major insular populations of West Indian raccoons are conspecific with P. lotor and probably originated via recent translocations from eastern North America. Like nonnative populations of raccoons that have been established elsewhere (e.g., in Alaska, Japan, and Europe), the raccoons of the West Indies deserve no special taxonomic recognition or conservation status. They may be destructive to native wildlife on West Indian islands where they have been introduced, particularly if their spread to and across other islands continues. [ABSTRACT FROM AUTHOR]

The ornate shrew ( Sorex ornatus) is restricted to the vanishing wetlands of California, USA and Baja California, Mexico. Several subspecies of ornate shrews are considered ‘mammal species of special concern’ in California by the Department of Fish and Game, and one ( Sorex ornatus relictus) has recently been listed as endangered. Populations of shrews around Buena Vista Lake have been diminished or extirpated due to habitat deterioration and human development. In order to study the patterns of genetic variation in isolated populations of Buena Vista Lake shrews, we developed 10 polymorphic microsatellite loci. There were 6–27 alleles per locus, and the loci had heterozygosity values that ranged from 20 to 80%. In addition, we screened 20 different populations of S. ornatus, eight species within two subfamilies of shrews (Soricinae and Crocidurinae), as well as in a mole (Talpidae, Neurotrichus gibbsii), to determine if these loci could be informative in other species as well. [ABSTRACT FROM AUTHOR]

Reproductive microbiomes contribute to reproductive health and success in humans. Yet data on reproductive microbiomes, and links to fertility, are absent for most animal species. Characterizing these links is pertinent to endangered species, such as black-footed ferrets (Mustela nigripes), whose populations show reproductive dysfunction and rely on ex-situ conservation husbandry. To understand microbial contributions to animal reproductive success, we used 16S rRNA amplicon sequencing to characterize male (prepuce) and female (vaginal) microbiomes of 59 black-footed ferrets at two ex-situ facilities and in the wild. We analyzed variation in microbiome structure according to markers of fertility such as numbers of viable and non-viable offspring (females) and sperm concentration (males). Ferret vaginal microbiomes showed lower inter-individual variation compared to prepuce microbiomes. In both sexes, wild ferrets harbored potential soil bacteria, perhaps reflecting their fossorial behavior and exposure to natural soil microbiomes. Vaginal microbiomes of ex-situ females that produced non-viable litters had greater phylogenetic diversity and distinct composition compared to other females. In males, sperm concentration correlated with varying abundances of bacterial taxa (e.g., Lactobacillus), mirroring results in humans and highlighting intriguing dynamics. Characterizing reproductive microbiomes across host species is foundational for understanding microbial biomarkers of reproductive success and for augmenting conservation husbandry. Genital microbiomes of black-footed ferrets are associated with reproductive outcomes, such as non-viable offspring and sperm quality, and differ between wild and ex-situ environments. [ABSTRACT FROM AUTHOR]

California's Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine‐scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco‐evolutionary processes enable the coexistence of terrestrial carnivores–and their microbiomes–in island environments. [ABSTRACT FROM AUTHOR]

Environmental variation can influence the reproductive success of species managed under human care and in the wild, yet the mechanisms underlying this phenomenon remain largely mysterious. Molecular mechanisms such as epigenetic modifiers are important in mediating the timing and progression of reproduction in humans and model organisms, but few studies have linked epigenetic variation to reproductive fitness in wildlife. Here, we investigated epigenetic variation in black‐footed ferrets (Mustela nigripes), an endangered North American mammal reliant on ex situ management for survival and persistence in the wild. Despite similar levels of genetic diversity in human‐managed and wild‐born populations, individuals in ex situ facilities exhibit reproductive problems, such as poor sperm quality. Differences across these settings suggest that an environmentally driven decline in reproductive capacity may be occurring in this species. We examined the role of DNA methylation, one well‐studied epigenetic modifier, in this emergent condition. We leveraged blood, testes, and semen samples from male black‐footed ferrets bred in ex situ facilities and found tissue‐type specificity in DNA methylation across the genome, although 1360 Gene Ontology terms associated with male average litter size shared functions across tissues. We then constructed gene networks of differentially methylated genomic sites associated with three different reproductive phenotypes to explore the putative biological impact of variation in DNA methylation. Sperm gene networks associated with average litter size and sperm count were functionally enriched for candidate genes involved in reproduction, development, and its regulation through transcriptional repression. We propose that DNA methylation plays an important role in regulating these reproductive phenotypes, thereby impacting the fertility of male ex situ individuals. Our results provide information into how DNA methylation may function in the alteration of reproductive pathways and phenotypes in artificial environments. These findings provide early insights to conservation hurdles faced in the protection of this rare species. [ABSTRACT FROM AUTHOR]

North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management of RV is accomplished through vaccination targeting mesocarnivore reservoir populations, such as the raccoon (Procyon lotor) in Eastern North America. Raccoons are a common generalist species, and populations may reach high densities in developed areas, which can result in contact with humans and pets with potential exposures to the raccoon variant of RV throughout the eastern United States. Understanding the spatial movement of RV by raccoon populations is important for monitoring and refining strategies supporting the landscape‐level control and local elimination of this lethal zoonosis. We developed a high‐throughput genotyping panel for raccoons based on hundreds of microhaplotypes to identify population structure and genetic diversity relevant to rabies management programs. Throughout the eastern United States, we identified hierarchical population genetic structure with clusters that were connected through isolation‐by‐distance. We also illustrate that this genotyping approach can be used to support real‐time management priorities by identifying the geographic origin of a rabid raccoon that was collected in an area of the United States that had been raccoon RV‐free for 8 years. The results from this study and the utility of the microhaplotype panel and genotyping method will provide managers with information on raccoon ecology that can be incorporated into future management decisions. [ABSTRACT FROM AUTHOR]

The Crested-tailed deer mouse, Habromys lophurus, is one of seven arboreal species within the genus Habromys. Species of this genus are monotypic, relatively rare, and occur in low densities. Their geographical distribution is highly fragmented due to being restricted to montane cloud forest in Mesoamerica and they are of conservation concern. All Habromys species are endemic to Mexico, except H. lophurus, which is also distributed in Guatemala and El Salvador. In this study, we obtained and characterized the first mitogenome and several thousand nuclear ultraconserved elements (UCEs) of H. lophurus to determine its phylogenetic position within neotomine-peromyscine mice. Its mitogenome sequence (16,509 bp) is only the second complete mitogenome obtained for this poorly known genus. We also obtained the first nuclear genomic data for H. lophurus, including 3,654 UCE loci, as well as a partial mitogenome of H. simulatus (6,349 bp), and 2,186 UCE for the outgroup Holochilus sciureus. Phylogenetic analyses that included our newly generated genomic data coupled with previously published data from other neotomine-peromyscine mice confirm the placement of H. lophurus, H. simulatus, and H. ixtlani within a highly supported clade. The Habromys clade was nested within a clade that also contains members of the genus Peromyscus and provides further support for the hypothesis of the paraphyly of Peromyscus. These genomic resources will contribute to future phylogenomic studies that aim to further elucidate the evolutionary history of this rare and critically endangered genus of rodents. [ABSTRACT FROM AUTHOR]

The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species. [ABSTRACT FROM AUTHOR]

We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and noninvasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research. [ABSTRACT FROM AUTHOR]

Asiatic black bears (Ursus thibetanus) have a widespread distribution in mountain landscapes, and are considered vulnerable globally, but are low-priority species for conservation in Nepal. Habitat fragmentation, illegal hunting, and human-bear conflict are the major threats to Asiatic black bears across their global range. Having an adequate level of genetic variation in a population helps with adapting to rapidly changing environments, and thus is important for the long-term health of bear populations. Accordingly, we conducted non-invasive surveys of bear populations in the Annapurna Conservation Area (ACA) to elucidate genetic diversity, genetic structure, and the phylogenetic relationship of Asiatic black bears from this region of Nepal to other subspecies. To assess levels of genetic diversity and population genetic structure, we genotyped eight microsatellite loci using 147 samples, identifying 60 individuals in an area of approximately 525 km2. We found that the Asiatic black bear population in the ACA has maintained high levels of genetic diversity (HE = 0.76) as compared to other bear populations from range countries. We did not detect a signature of population substructure among sampling localities and this suggests that animals are moving freely across the landscape within the ACA. We also detected a moderate population size that may increase with the availability of suitable habitat in the ACA, so bear-related conflict should be addressed to ensure the long-term viability of this expanding bear populations. Primers specific to bears were designed to amplify a 675 bp fragment of the mitochondrial control region from the collected samples. Three haplotypes were observed from the entire conservation area. The complete mitochondrial genome (16,771 bp), the first obtained from wild populations of the Himalayan black bear (U. t. laniger), was also sequenced to resolve the phylogenetic relationships of closely related subspecies of Asiatic black bears. The resulting phylogeny indicated that Himalayan black bear populations in Nepal are evolutionary distinct from other known subspecies of Asiatic black bears. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Eptesicus Rafinesque, 1820 is widely distributed in the Old and New World (26 species), and Histiotus Gervais, 1856 is a South American endemic (11 species). Molecular phylogenies have recovered Eptesicus (sensu lato) as polyphyletic, with New World Eptesicus and the sister genus Histiotus in a paraphyletic American clade sister to Old World Eptesicus. Based on these phylogenetic reconstructions, authors have treated Histiotus as either a subgenus of Eptesicus or restricted Eptesicus to the New World species, treating Histiotus as a full genus, and using the name Cnephaeus Kaup, 1829 at the generic rank to comprise Old World Eptesicus. Based on recently published molecular studies, and on novel qualitative and quantitative morphological comparisons of representatives of Histiotus and New and Old World Eptesicus, we provide evidence for restricting the name Eptesicus to the species E. fuscus (Palisot de Beauvois, 1796) and E. guadeloupensis Genoways & Baker, 1975, allocating the remaining New World species under a new genus, keeping Histiotus as a full genus, and raising Cnephaeus to generic rank to comprise all Old World taxa currently under Eptesicus. This arrangement resolves the paraphyly of New World Eptesicus, and promotes taxonomic stability for Histiotus, which is a well-established genus of easily recognizable Neotropical bats and treated separate from Eptesicus by most authorities. [ABSTRACT FROM AUTHOR]

Patterns of rarity, endemism, and vulnerability are known for four species of yellow-eared bats of the genus Vampyressa: V. melissa, V. voragine, V. elisabethae, and V. sinchi, the last two described based on skull and external morphology. We extracted DNA from the holotypes of V. elisabethae and V. sinchi using strict ancient DNA protocols and sequenced the complete cytochrome-b gene of the mtDNA to investigate the phylogenetic relationships within the genus and employed species-delimitation tests to evaluate the validity of all the currently named species of Vampyressa. The resulting tree topology and our species-delimitation analyses corroborate the validity of V. elisabethae and V. voragine, but places V. sinchi in V. melissa. Based on these results and phenotypic variation, we recognize five valid species in Vampyressa and treat sinchi as a subspecies of a polytypic V. melissa; for which we provide a rediagnosis. Our results show that V. elisabethae is as highly divergent genetically as it is morphologically, and suggest that V. thyone, one of the two species of Vampyressa known to have wide distributions, is a species complex requiring further investigation. [ABSTRACT FROM AUTHOR]

Notiosorex is the only genus of shrews in North America with particular adaptations for arid habitats such as deserts. Five species currently are recognized in the genus, one of which, Notiosorex evotis , lives in deciduous rain forest from northern Sinaloa to the state of Jalisco in México. Notiosorex evotis originally was described as a subspecies of N. crawfordi ; however, it was recently proposed as a valid species based on a discriminant function analysis of craniodental characters. Morphological differentiation between N. evotis populations and sympatric occurrences with N. crawfordi in northern Sinaloa have been recognized. Here, we used a phylogenetic analysis of a mitochondrial gene (Cytb ; 1,140 bp) and the nuclear beta fibrinogen intron 7 (β-fib I7 ; 385 bp), as well as cranial geometric morphometrics, to assess the taxonomic status of N. evotis. We found sequences of N. evotis forming two main subclades: one that includes the populations of the state of Sinaloa, the other including populations of Nayarit and Jalisco. The boundaries between the two groups seem to be related to the ecotonal cline between the Pacific Lowlands province and the Trans-Mexican Volcanic Belt province, which acts as a geographical barrier. The discriminant function analysis revealed clear differences in skull shape between the three species of Notiosorex to the northwest of its distribution. Considering these multiple lines of evidence from our data set, we confirm that N. evotis is a monotypic species. Our results suggest that geometric morphometrics can be used successfully to identify sibling species by shape, especially in groups where determination by craniodental measurements is not possible. [ABSTRACT FROM AUTHOR]

The golden jackal (Canis aureus) is one of the most common and widely distributed carnivores in India but phylogeographic studies on the species have been limited across its range. Recent studies have observed absence of mitochondrial (mt) DNA diversity in European populations while some North African populations of golden jackal were found to carry gray wolf (Canis lupus lupaster) mtDNA lineages. In the present study, we sequenced 440 basepairs (bp) of control region (CR) and 412 bp of cytochrome b (cyt b) gene of mtDNA from 62 golden jackals sampled from India (n = 55), Israel (n = 2) and Bulgaria (n = 5), to obtain a total of eighteen haplotypes, comprising sixteen from India and one each from Israel and Bulgaria. Except for three previously described haplotypes represented by one cyt b and one CR haplotype both from India, and one CR haplotype from Bulgaria, all haplotypes identified in this study are new. Genetic diversity was high in golden jackals compared to that reported for other canids in India. Unlike the paraphyletic status of African conspecifics with the gray wolf, the Indian (and other Eurasian) golden jackal clustered in a distinct but shallow monophyletic clade, displaying no evidence of admixture with sympatric and related gray wolf and domestic dog clades in the region. Phylogeographic analyses indicated no clear pattern of genetic structuring of the golden jackal haplotypes and the median joining network revealed a star-shaped polytomy indicative of recent expansion of the species from India. Indian haplotypes were observed to be interior and thus ancestral compared to haplotypes from Europe and Israel, which were peripheral and hence more derived. Molecular tests for demographic expansion confirmed a recent event of expansion of golden jackals in the Indian subcontinent, which can be traced back ~ 37,000 years ago during the late Pleistocene. Our results suggest that golden jackals have had a potentially longer evolutionary history in India than in other parts of the world, although further sampling from Africa, the Middle East and south-east Asia is needed to test this hypothesis. [ABSTRACT FROM AUTHOR]

The genus Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Twenty-eight Neotropical species are currently recognized. In this study, we evaluate molecular and morphological variation in the M. keaysi complex, a high elevation clade of Neotropical myotine bats characterized by complex taxonomy and high morphological variation. A phylogeny inferred with cytochrome- b sequences recovered two clades composed of samples traditionally assigned to M. keaysi , with 9% of genetic divergence between them. These clades were also suggested as putative distinct species by molecular species delimitation methods. Qualitative and quantitative morphological analyses indicated a phenotypic discontinuity between specimens from central Andes (including the holotype of M. keaysi) and western lowlands of Ecuador, showing strong congruence between molecular and morphological approaches. We therefore describe a new species for the Tumbes-Choco-Magdalena region, documenting their external and cranial diagnostic characters by comparing them with other Neotropical species. In addition, we provide an emended diagnosis for our new concept of M. keaysi. [ABSTRACT FROM AUTHOR]

Subsidization of predator populations increases predation pressure on prey species, which is exacerbated when natural resources are scarce. Estimating the frequency of predation by subsidized predators on vulnerable species, especially low‐density, long‐lived species such as the federally threatened Mojave desert tortoise (Gopherus agassizii), allows landscape managers to evaluate the need for actions like reducing subsidies, discouraging predation by taste aversion, or predator removal. Most studies of Mojave desert tortoise predation have relied on morphological analysis to identify hard parts in predator scat. Here, we developed and validated a qPCR assay to test for the presence of Mojave desert tortoise in DNA extracted from scat and pellets. We used the assay to detect tortoise DNA in scat and pellets collected in a conservation easement adjacent to Boulder City, Nevada, from three Mojave desert tortoise predators: coyotes (Canis latrans), desert kit foxes (Vulpes macrotis arsipus), and common ravens (Corvus corax)—all of which consume anthropogenic resources. We compared the results of our qPCR assay to results from morphological analysis of the same samples and found that the qPCR method is much more sensitive at detecting the presence of tortoise remains. Although neither method can determine whether consumption was the result of predation or scavenging, nor how many individual tortoises were consumed, our findings indicate that conservation managers may benefit from focusing efforts on reducing subsidies that attract and support predators and on reducing tortoise mortality from predation. [ABSTRACT FROM AUTHOR]

Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in‐solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat‐derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field‐collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low‐quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples. [ABSTRACT FROM AUTHOR]

Sloth bears (Melursus ursinus) are endemic to the Indian subcontinent. As a result of continued habitat loss and degradation over the past century, sloth bear populations have been in steady decline and now exist only in isolated or fragmented habitat across the entire range. We investigated the genetic connectivity of the sloth bear meta-population in five tiger reserves in the Satpura-Maikal landscape of central India. We used noninvasively collected fecal and hair samples to obtain genotypic information using a panel of seven polymorphic loci. Out of 194 field collected samples, we identified 55 individuals in this meta-population. We found that this meta-population has moderate genetic variation, and is subdivided into two genetic clusters. Further, we identified five first-generation migrants and signatures of contemporary gene flow. We found evidence of sloth bears in the corridor between the Kanha and Pench Tiger Reserves, and our results suggest that habitat connectivity and corridors play an important role in maintaining gene flow in this meta-population. These corridors face several anthropogenic and infrastructure development threats that have the potential to sever ongoing gene flow, if policies to protect them are not put into action immediately. [ABSTRACT FROM AUTHOR]

The sloth bear (Melursus ursinus) is a threatened species endemic to the Indian subcontinent. To date, no reliable method has been developed for identifying individuals or monitoring their populations. Here we describe a non-invasive genetic monitoring technique for individual identification of sloth bears. After testing 18 microsatellites developed for other carnivore species, including ursids, we optimized a panel of 7 highly polymorphic microsatellite loci that yielded a cumulative Probability of Identity between siblings value of 2.15E-03. We used this panel to identify 55 individual sloth bears from 190 fecal and 4 hair samples collected in tiger reserves in central India. This panel can be used for population genetic studies and population monitoring of sloth bears. [ABSTRACT FROM AUTHOR]

Gene flow is a critical ecological process that must be maintained in order to counteract the detrimental effects of genetic drift in subdivided populations, with conservation benefits ranging from promoting the persistence of small populations to spreading adaptive traits in changing environments. We evaluated historical and contemporary gene flow and effective population sizes of leopards in a landscape in central India using noninvasive sampling. Despite the dramatic changes in land-use patterns in this landscape through recent times, we did not detect any signs that the leopardpopulations have been through a genetic bottleneck, and they appear to have maintained migration-drift equilibrium. We found that historical levels of gene flow (mean mh = 0.07) were significantly higher than contemporary levels (mean mc = 0.03), and populations with large effective population sizes (Satpura and Kanha Tiger Reserves) are the larger exporters of migrants at both timescales. The greatest decline in historical versus contemporary gene flow is between pairs of reserves that are currently not connected by forest corridors (i.e., Melghat-Pench mh - mc = 0.063; and Kanha-Satpura mh - mc = 0.054). We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries, and suggest protection of forest corridors to maintain gene flow in this landscape. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We examined intraspecific relationships in the eastern fox squirrel (Sciurus niger) and the eastern gray squirrel (S. carolinensis) using sequence variation in a portion of the mitochondrial DNA cytochrome-fo gene and part of the D-loop in the control region. These closely related species are codistributed temperate forest obligates that have similar generation time and population ecologies. For both species, we documented high haplotype diversity, low nucleotide variation, and several groups of divergent haplotypes. However, there is a general lack of spatial structure in maternal lineages within each species. For S. carolinensis, we observed a pattern of population genetic structure that suggests the presence of at least 2 distinct refugial populations that evolved in isolation during the Pleistocene (approximately 98.3-266.3 thousand years ago [kya]) and subsequently expanded to the species' current range following the last glacial maximum. For S. niger, the genetic structure was much less pronounced, with fewer strongly diverged haplotypes. This finding suggests that eastern fox squirrels persisted in either a single population in a glacial refugium or as several refugial populations that maintained gene flow throughout the Pleistocene. For both species, there is evidence that scattered populations were present in multiple, small refugia close to the Laurentide Ice Sheet, allowing rapid range expansion following glacial recession. Taken together, our results indicate that S. niger and S. carolinensis underwent multiple episodes of genetic divergence during isolation in glacial refugia, followed by range expansion and contact that resulted in admixture of divergent maternal lineages within each species during interglacials. Examination of our data further indicates that the most recent range expansion in both species occurred within the past 12-20 kya. [ABSTRACT FROM AUTHOR]

Strategies of males in harem-forming mammals may change depending on 2 variables, female group size and consequent ability of the harem male to monopolize copulations, and the relative costs and benefits of tolerating other males. We studied harems of 4-20 females associated with a dominant male in small groups of Artibeus jamaicensis (<14 females), and with dominant and subordinate males in large groups (>14 females). Dominant males displayed defensive behavior toward satellite males when they intruded into the roosting site. Small groups received the highest number of visits by satellite males, and dominant males did not display total defense of females. During the breeding season, females roosted in highly compacted clusters and dominant males were more active in their defensive behavior. Subordinate males were generally tolerated in harem groups and their presence reduced the number of adult male visits. Some young in large harem groups were sired by subordinate males, resulting in a genetic benefit for both dominant and subordinate males. Dominant males had the highest fitness in the large harem groups by sharing paternity with related subordinate males and by rejecting unrelated intruders. [ABSTRACT FROM AUTHOR]

The elephants of the Knysna region continue to survive, despite fears that there was only a single surviving female. Their range is larger than previously believed, and includes the Afromontane forest and mountain fynbos. The five individuals detected in this study were all females, and share a single mitochondrial DNA control region haplotype with individuals from Addo Elephant National Park. At least two of these elephants appear to be first-order relatives, and the others may be part of a single matrilineal group. The genetic diversity detected is lower than that found in most African savanna populations, but is higher than that found at Addo, where individuals represent the descendents of a severe population size bottleneck. Levels of genetic diversity are more similar to those detected at Kruger National Park, suggesting that the Knysna elephants represent a remnant of the once widespread populations of South Africa. [ABSTRACT FROM AUTHOR]

Mazama temama (Kerr, 1792) is a representative species of the northern Neotropics, but the geographic range limits for this species remain unclear. We report the southernmost record of M. temama from the southwestern Colombian Andes, increasing the previously known range of this species by more than 300 km. We obtained a cytochrome gene sequence (849 bp) which is 95% identical to samples from Mexico. This record raises the need for extensive sampling to obtain more complete information about the distribution of M. temama in northern Colombia. [ABSTRACT FROM AUTHOR]

Rapid advances in genomic tools for use in ecological contexts and non‐model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high‐throughput sequencing on chicken (Gallus gallus domesticus) tissues collected over an 11‐day decomposition study in natural Hawaiian habitats. Second, we determined if field‐collected invasive black rats (Rattus rattus; n = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high‐throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds (n = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats (n = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird (Myadestes obscurus) and three introduced bird species (Lophura leucomelanos, Meleagris gallopavo, Zosterops japonicus) were detected in the rats' diets, with individuals from these species (except L. nycthemera) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation. [ABSTRACT FROM AUTHOR]

Here, we present the initial comparison of the nuclear genomes of the North American raccoon (Procyon lotor) and the kinkajou (Potos flavus) based on draft assemblies. These two species encompass almost 21 Myr of evolutionary history within Procyonidae. Because assemblies greatly impact downstream results, such as gene prediction and annotation, we tested three de novo assembly strategies (implemented in ALLPATHS-LG, MaSuRCA, and Platanus), some of which are optimized for highly heterozygous genomes. We discovered significant variation in contig and scaffold N50 and L50 statistics and genome completeness depending on the de novo assembler used. We compared the performance of these three assembly algorithms in hopes that this study will aid others looking to improve the quality of existing draft genome assemblies even without additional sequence data. We also estimate the demographic histories of raccoons and kinkajous using the Pairwise Sequentially Markovian Coalescent and discuss the variation in population sizes with respect to climatic change during the Pleistocene, as well as aspects of their ecology and taxonomy. Our goal is to achieve a better understanding of the evolutionary history of procyonids and to create robust genomic resources for future studies regarding adaptive divergence and selection. [ABSTRACT FROM AUTHOR]

The Mediterranean region is identified as one of the world's 36 biodiversity hotspots, with the Earth's most biologically rich yet threatened areas. Lebanon is a hub for Eastern Mediterranean Region (EMR) biodiversity with 9116 characterized plant and animal species (4486 fauna and 4630 flora). Using DNA barcoding as a tool has become crucial in the accurate identification of species in multiple contexts. It can also complement species morphological descriptions, which will add to our understanding of the biodiversity and richness of ecosystems and benefit conservation projects for endangered and endemic species. In this study, we create the first reference library of standard DNA markers for mammals and plants in the EMR, with a focus on endemic and endangered species. Plant leaves were collected from different nature reserves in Mount Lebanon, and mammal samples were obtained from taxidermized museum specimens or road kills. We generated the 12S rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the trnL and rbcL barcode sequences of 52 plant species from 24 different families. Twenty-five plant species and two mammal species included in this study were sequenced for the first time using these markers. [ABSTRACT FROM AUTHOR]

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/km2 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

As we enter the sixth mass extinction, many species that are no longer self‐sustaining in their natural habitat will require ex situ management. Zoos have finite resources for ex situ management, and there is a need for holistic conservation programs between the public and private sector. Ex situ populations of sable antelope, Hippotragus niger, have existed in zoos and privately owned ranches in North America since the 1910s. Unknown founder representation and relatedness has made the genetic management of this species challenging within zoos, while populations on privately owned ranches are managed independently and retain minimal‐to‐no pedigree history. Consequences of such challenges include an increased risk of inbreeding and a loss of genetic diversity. Here, we developed and applied a customized targeted sequence capture panel based on 5,000 genomewide single‐nucleotide polymorphisms to investigate the genomic diversity present in these uniquely managed populations. We genotyped 111 sable antelope: 23 from zoos, 43 from a single conservation center, and 45 from ranches. We found significantly higher genetic diversity and significantly lower inbreeding in herds housed in zoos and conservation centers, when compared to those in privately owned ranches, likely due to genetic‐based breeding recommendations implemented in the former populations. Genetic clustering was strong among all three populations, possibly as a result of genetic drift. We propose that the North American ex situ population of sable antelope would benefit from a metapopulation management system, to halt genetic drift, reduce the occurrence of inbreeding, and enable sustainable population sizes to be managed ex situ. [ABSTRACT FROM AUTHOR]

Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa. Results: We obtained complete or partial mitochondrial genomes from 232 historical and modern samples, representing 40 of the 43 currently recognized species of Sciurini. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinct analytical methods—strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least six lineages that represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of mammae indicated that alternative conditions of both characters must have evolved multiple times throughout the evolutionary history of tree squirrels. Conclusions: Complete mitogenomes were obtained from museum specimens as old as 120 years, reinforcing the potential of historical samples for phylogenetic inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help explain the incongruence between phylogenetic results and the classification schemes presented so far. Based on our phylogenetic results we suggest a tentative supraspecific taxonomic arrangement for Sciurini, employing 13 generic names used in previous taxonomic classifications. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive (ex situ) and wild (in situ) populations of threatened species. The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is a species that is being managed ex situ in both public (zoo) and private (ranch) collections in the United States. Our objective was to develop whole genome sequence resources that will serve as a foundation for characterizing the genetic status of ex situ populations of sable antelope relative to populations in the wild. Here we report the draft genome assembly of a male sable antelope, a member of the subfamily Hippotraginae (Bovidae, Cetartiodactyla, Mammalia). The 2.596 Gb draft genome consists of 136,528 contigs with an N50 of 45.5 Kbp and 16,927 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 18,828 protein-coding genes and repetitive sequences encompassing 46.97% of the genome. The discovery of single nucleotide variants (SNVs) was assisted by the re-sequencing of seven additional captive and wild individuals, representing two different subspecies, leading to the identification of 1,987,710 bi-allelic SNVs. Assembly of the mitochondrial genomes revealed that each individual was defined by a unique haplotype and these data were used to infer the mitochondrial gene tree relative to other hippotragine species. The sable antelope genome constitutes a valuable resource for assessing genome-wide diversity and evolutionary potential, thereby facilitating long-term conservation of this charismatic species. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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°S and longitudes 47 and 49°W. We show that the species’ distribution is associated with 37,517 km2 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

[Display omitted] • Recovery of UCE loci and mean length per locus were inversely related to sample age. • Deeper sequencing improved the number of UCE recovered but not mean locus length. • None of our phylogenetic inferences resulted in identical topologies. • We resolved deep relationships in Sciuridae and among deepest branches of Sciurini. • Conflicting relationships remain for the rapid Neotropical tree squirrel radiation. Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences—performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria—resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Several recent studies have tried to unravel the complex evolutionary history of Neotropical cervids. However, the two Mesoamerican brocket deer Mazama pandora and M. t emama have not been included in these studies and their relationship to other Neotropical cervids remains unclear. Here, we present analyses that included concatenated sequences from the mitochondrial genes ND2 , Cytb , and tRNA-Pro-Control region. Our results suggest that both Mesoamerican brocket deer fall within the “red” clade, more closely related to genus Odocoileus and red brocket deer species, such as South American Mazama americana , M. bororo , M. nana , and M. rufina . We estimated that M. temama diverged from other red brocket deer ca. two MYA. Two hypothesis emerge regarding the relationship of the Yucatan brocket deer M. pandora with respect to the other Neotropical deer. The first one, based on analyses of concatenated sequences from all three genes, implies an early split from a larger clade that includes Odocoileus and other red Mazama species, with an estimated divergence time dating back to 2.7 MYA. This would suggest isolation on the Yucatan peninsula, limiting the crossing of this species into South America. The second one, based only on Cytb, places M. pandora more closely related to Odocoileus and with an estimated divergence time of ca. 1.9 MYA. This would suggest that the humid tropical forests of Mexico and Central America could have been the most likely place of origin of members of the red brocket deer clade. Deer colonization into South America occurred after the complete formation of the Panamanian land bridge in the late Pliocene, more than one ancestor of the gray brocket deer clade crossed into South America, as well as a red brocket deer ancestor and Odocoileus dispersed southward. A posterior event probably occurred when divergent ancestors of M. temama and M. pandora respectively moved northward after the split with South American red brocket deer. Our results add to the growing body of evidence calling for an extensive taxonomic revision of this group, and we concur with previous recommendations that the generic taxonomic designation of Mazama should be applied not only to the red brocket deer but also to all of the species currently recognized under the genus Odocoileus . [ABSTRACT FROM AUTHOR]