Late Pleistocene Altitudinal Segregation and Demography Define Future Climate Change Distribution of the Peromyscus mexicanus Species Group: Conservation Implications.

Mountains harbor a significant number of the World's biodiversity, both on tropical and temperate regions. Notably, one crucial gap in conservation is the consideration of historical and contemporary patterns influencing differential distribution in small mammal mountain species and how climate change will affect their distribution and survival. The mice Peromyscus mexicanus species group is distributed across mountains in Guatemala-Chiapas and Central America, which experienced significant effects of glacial and interglacial cycles. We determined phylogeographic and demographic patterns of lowlands and highlands mountain lineages, revealing that the radiation of modern P. mexicanus lineages occurred during the Pleistocene (ca. 2.6 mya) along Nuclear Central America. In concert with climatic cycles and the distribution of habitats, lowland and highland lineages showed recent population size increase and decrease, respectively. We also estimated the current and future distribution ranges for six lineages, finding marked area size increase for two lineages for which vegetation type and distribution would facilitate migrating towards higher elevations. Contrastingly, three lineages showed range size decrease; their ecological requirements make them highly susceptible to future habitat loss. Our findings are clear evidence of the negative impacts of future climate change, while our ability to manage and conserve these vulnerable ecosystems and mountain species is contingent on our understanding of the implications of climate change on the distribution, ecology, and genetics of wildlife populations.

Novel genomic resources contribute to the systematics of threatened arboreal deer mice of the genus Habromys Hooper & Musser, 1964 (Cricetidae, Neotominae) within a neotomine-peromyscine phylogeny.

The Crested-tailed deer mouse, Habromyslophurus, 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 Holochilussciureus. 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.

First description of the mitochondrial genomes of the Central American brocket deer Mazama temama (Kerr, 1792) and the Yucatán Peninsula brocket deer Odocoileus pandora Merriam, 1901.

BACKGROUND: The Central American (Mazama temama) and the Yucatán Peninsula brocket deer (Odocoileus pandora) are deer species with cryptic habits, and little is known about their biology. Odocoileus pandora is listed as Vulnerable on the 2015 IUCN Red List of Threatened Species, while M. temama is considered Data Deficient; however, it currently faces a decreasing population trend. METHODS AND RESULTS: We assembled the complete mitochondrial genome for two M. temama specimens and one complete and one partial for O. pandora from Illumina 150 bp paired-end reads. The mitogenomes of M. temama and O. pandora have a length of 16,479-16,480 and 16,419 bp, respectively, AT-biased; they consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region, most of them follow a transcription direction in the heavy strand of the molecule. The mitochondrial genome of O. pandora shows some particularities compared to other deer species, like a shorter control region of 987-990 bp and a cytochrome b gene with a length of 1,143 bp. Our phylogenetic analyses confirm the close affinity of M. temama to South American M. americana and the nested position of the genus Odocoileus, including O. pandora, into the genus Mazama. CONCLUSIONS: Here, we described for the first time the complete mitochondrial genome for these two species. While our study provides additional information about the taxonomic status of the northern neotropical brocket deer, further research is needed to solve the complicated taxonomy of neotropical deer.

First mitochondrial genome of the Amazonian marsh rat Holochilus sciureus Wagner 1842 (Rodentia, Cricetidae, Sigmodontinae).

The Amazonian marsh rat, Holochilus sciureus, is a member of the subfamily Sigmodontinae, the second-largest subfamily of muroid rodents, with 410 species and ca. 84 genera in 12 tribes. This semiaquatic rodent is distributed in South America and is of great economic and epidemiological importance. In this study, we obtained the first mitochondrial genome of the genus Holochilus obtained from a tissue sample associated with a museum voucher specimen. The generated mitogenome sequence of H. sciureus is 16,358 bp length. It comprises a control region and a conserved set of 37 genes encoding for 2 rRNA genes, 22 tRNA genes and 13 protein-coding genes. We conducted a phylogenetic analysis that included H. sciureus and the only five other published mitochondrial genomes of this poorly studied subfamily of rodents.

Defining intraspecific conservation units in the endemic Cuban Rock Iguanas (Cyclura nubila nubila).

Defining conservation units is an important step in species management and requires interpretation of the genetic diversity and ecological function of the taxon being considered. We used the endemic Cuban Rock Iguanas (Cyclura nubila nubila) as a model to highlight this challenge and examined patterns of its intraspecific genetic diversity across Cuba. We evaluated nuclear (microsatellite loci) and mitochondrial diversity across eight populations from the island and its off-shore cays, and applied the population genetics results for assignment of Management Unit (MU) status and Evolutionary Significant Units (ESUs) based on phylogeographic and time of divergence information. We identified at least six distinct Cuban Rock Iguana MUs, encompassing demographically isolated and genetically differentiated populations across Cuba, most with low effective population size, declining populations, and with high risk of inbreeding and genetic drift. Hence, each MU should be considered of urgent conservation priority. Given the key ecological seed dispersal role of C. n. nubila, the disappearance of any MU could trigger the loss of local ecological functional diversity and major negative impacts on their ecosystems. Two divergent ESUs were also identified, exhibiting an historical east-west geographic separation on Cuba. Based on a Caribbean phylogeographic assessment, our findings strengthen the conclusion that all geographically and evolutionarily differentiated Cyclura species and subspecies across the archipelago warrant ESU distinction.

Comparison of genomic diversity and structure of sable antelope (Hippotragus niger) in zoos, conservation centers, and private ranches in North America.

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.

Parthenogenesis in a captive Asian water dragon (Physignathus cocincinus) identified with novel microsatellites.

Reptiles show varying degrees of facultative parthenogenesis. Here we use genetic methods to determine that an isolated, captive female Asian water dragon produced at least nine offspring via parthenogenesis. We identified microsatellites for the species from shotgun genomic sequences, selected and optimized primer sets, and tested all of the offspring for a set of seven microsatellites that were heterozygous in the mother. We verified that the seven loci showed high levels of polymorphism in four wild Asian water dragons from Vietnam. In all cases, the offspring (unhatched, but developed eggs, or hatched young) had only a single allele at each locus, and contained only alleles present in the mother's genotype (i.e., were homozygous or hemizygous). The probability that our findings resulted from the female mating with one or more males is extremely small, indicating that the offspring were derived from a single female gamete (either alone or via duplication and/or fusion) and implicating parthenogenesis. This is the first documented case of parthenogenesis in the Squamate family Agamidae.

Evolutionary diversification and speciation in rodents of the Mexican lowlands: the Peromyscus melanophrys species group.

Despite some studies of the species groups within the genus Peromyscus have been performed, both evolutionary relationships among species within groups and group composition have remained controversial. In this study, we address phylogenetic relationships among species in the Peromyscus melanophrys group (P. melanophrys, P. perfulvus, and P. mekisturus), using a molecular phylogenetic analysis. This analysis is the first to include the poorly known P. mekisturus. We conducted maximum likelihood and Bayesian inference analyses with the ND3, tRNA-Arginine, ND4L, and partial ND4 mitochondrial genes, and the GHR nuclear gene. We consistently recovered a P. melanophrys group that is monophyletic with respect to the set of outgroups. Also, we recovered two distinct clades within P. perfulvus and two within P. melanophrys, one of which contain P. mekisturus among other P. melanophrys, all with geographic consistency. According to our divergence time estimates, the P. melanophrys group diverged during the Pliocene and the main diversification events within the group occurred at the end of the Pliocene and through the Pleistocene.