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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., (© The Author(s) 2023. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

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., Competing Interests: The authors have declared that no competing interests exist.

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.

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.

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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]

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]

Modern non-invasive genetic technologies are useful in studies of rare and difficult-to-observe species. An examination of endangered African wild dog (Lycaon pictus) faecal DNA revealed that 11.4% of samples were assigned incorrectly to an individual. Sampling mistakes in the field are not normally considered in non-invasive genetic assessments, but can be a significant source of error. To ensure meticulous data interpretation, non-invasive genetic studies should track and report sampling inaccuracies. [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]

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]