RESUMEN
Meller's mongoose (Rhynchogale melleri) is a member of the family Herpestidae (Mammalia: Carnivora) and the sole species in the genus Rhynchogale. It is primarily found in savannas and open woodlands of eastern sub-Saharan Africa. Here, we report the first complete mitochondrial genome for a female Meller's mongoose collected in Tanzania, generated using a genome-skimming approach. The mitogenome had a final length of 16,644 bp and a total of 37 annotated genes. Phylogenetic analysis validated the placement of this species in the herpestid subfamily Herpestinae. Ultimately, the outcomes of this research offer a genetic foundation for future studies of Meller's mongoose.
RESUMEN
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.
RESUMEN
The golden jackal (Canis aureus) is a canid species found across southern Eurasia. Several subspecies of this animal have been genetically studied in regions such as Europe, the Middle East, and India. However, one subspecies that lacks current research is the Indochinese jackal (Canis aureus cruesemanni), which is primarily found in Southeast Asia. Using a genome skimming approach, we assembled the first complete mitochondrial genome for an Indochinese jackal from Thailand. To expand the number of available Canis aureus mitogenomes, we also assembled and sequenced the first complete mitochondrial genome of a golden jackal from Turkey, representing the C. a. moreotica subspecies. The mitogenomes contained 37 annotated genes and are 16,729 bps (C. a. cruesemanni) and 16,669 bps (C. a. moreotica) in length. Phylogenetic analysis with 26 additional canid mitogenomes and analyses of a cytochrome b gene-only data set together support the Indochinese jackal as a distinct and early-branching lineage among golden jackals, thereby supporting its recognition as a possible subspecies. These analyses also demonstrate that the golden jackal from Turkey is likely not a distinct lineage due to close genetic relationships with golden jackals from India and Israel.
Asunto(s)
Genoma Mitocondrial , Chacales , Animales , Europa (Continente) , Chacales/clasificación , Chacales/genética , Filogenia , Turquía , Femenino , Masculino , Tailandia , Citocromos b/genéticaRESUMEN
The Saharan striped polecat (Ictonyx libycus) is endemic to Africa, inhabiting the edges of the Saharan Desert. Little is known about the biology or genetic status of this member of the weasel family (Mustelidae). We present the first complete mitochondrial genome of the Saharan striped polecat, assembled from data generated using a genome skimming approach. The assembled mitogenome is 16,549 bps in length and consists of 37 genes including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, an origin of replication, and a control region. Phylogenetic analysis confirmed the placement of the Saharan striped polecat within the subfamily Ictonychinae.
RESUMEN
The woodrats or packrats of the genus Neotoma have been the subject of a wide array of research including paleoecology, physiology, morphological evolution, systematics, speciation, and hybridization. In recent years, much work has been done to elucidate evolutionary relationships within and between closely related species of the genus; in particular the addition of newly collected specimens from critical geographic regions has provided new opportunities for taxonomic assessment. Given these new data and their potential, parsimony (PARS), maximum likelihood (ML), and Bayesian inference (BI) analyses were conducted on DNA sequences obtained from nine individual genes (four mitochondrial loci: 12S, 16S, CoII, and Cytb; five nuclear loci: AdhI2, BfibI7, En2, Mlr, and Myh6) to estimate the phylogenetic relationships among 23 species of Neotoma. Results of these analyses depicted a wide array of phylogenetic relationships among taxa; with substantial nodal support recovered in both the ML and PARS analyses at some mid-level and terminal positions. Several individual genes, particularly 12S, AdhI2, BfibI7, CoII, and Cytb, provided support at several basal positions; however, phylogenetic resolution was limited in the other genes. A final BI analysis where the nine genes were concatenated into a single data set produced several supported clades that corresponded to previously recognized species groups (floridana, micropus, mexicana, and lepida) and the subgenus Homodontomys. Levels of genetic divergence for within-species comparisons (estimated from the Cytb data set) ranged from 0.88% (N. magister) to 6.82% (N. fuscipes); for between sister species comparisons ranged from 4.68% (N. devia and N. lepida) to 12.70% (N. angustapalata and N. nelsoni); and for members within closely related clades ranged from 8.70% (N. bryanti and N. lepida) to 12.57% (N. goldmani and N. magister). Evaluations of generic, subgeneric, and species group boundaries were explored using phylogenetic principles on the DNA sequence data presented herein, as well as morphological findings from previous studies. Results obtained suggest that the most conservative taxonomic interpretation involves the abandonment of subgeneric delineations and relies on the recognition of eight species groups (cinerea, floridana, fuscipes, lepida, mexicana, micropus, phenax, and stephensi) as the backbone of the woodrat classification.
Las ratas cambalacheras del género Neotoma han sido estudiadas en varios tipos de investigaciones incluyendo paleoecología, fisiología, evolución morfológica, sistemática, especiación e hibridación. Recientemente, se han realizado numerosos estudios para elucidar las relaciones evolutivas dentro del género y entre especies cercanamente relacionadas al mismo; en particular la inclusión de nuevos especímenes provenientes de regiones geográficas críticas han brindado nuevas oportunidades para evaluaciones taxonómicas. A partir de estos nuevos datos se realizaron análisis de parsimonia (PARS), Máxima Verosimilitud (MV), e Inferencia Bayesiana (IB) en secuencias de ADN provenientes de nueve genes individuales (cuatro loci mitocondriales: 12S, 16S, CoII, y Cytb; cinco loci nucleares: Adh-I2, Bfib-I7, En2, Mlr, and Myh6) para determinar la relación filogenética de 23 especies de Neotoma. Los resultados de estos análisis presentan una amplia gama de relaciones filogenéticas entre taxa con un soporte nodal importante en los análisis de MV y PARS en algunas posiciones terminales de nivel medio. Varios genes individuales, en particular 12S, Adh-I2, Bfib-I7, CoII, and Cytb, ofrecieron soporte en varias posiciones basales; sin embargo, la resolución filogenética fue reducida en los demás genes. El último análisis de IB, en donde nueve genes se concatenaron en un solo conjunto de datos, produjo soporte en varios clados que correspondieron a especies de grupos previamente reconocidos (floridana, micropus, mexicana, y lepida) y el sub-género Homodontomys. Los niveles de divergencia genética para comparaciones intraespecíficas fluctuaron entre 0.88% (N. magister) y 6.82% (N. fuscipes); para especies hermanas (4.68%N. devia y N. lepida hasta 12.70%N. angustapalata y N. nelsoni); y para los miembros de clados cercanos (8.70%N. bryanti y N. lepida hasta 12.57%N. goldmani y N. magister). Las evaluaciones de los limites genéricos, subgenéricos y de grupos de especies fueron explorados usando principios filogenéticos en las secuencias de ADN de este trabajo, y también se basaron en las conclusiones morfológicas de estudios previos. Los resultados obtenidos sugieren que la interpretación taxonómica más conservadora incluye el abandono de las delineaciones subgenéricas y se depende en el reconocimiento de ocho grupos de especies (cinerea, floridana, fuscipes, lepida, mexicana, micropus, phenax, y stephensi) como el pilar central de la clasificación de las ratas cambalacheras.
RESUMEN
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.
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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.
RESUMEN
Human activity has facilitated the introduction of a number of alien mammal species to the Galápagos Archipelago. Understanding the phylogeographic history and population genetics of invasive species on the Archipelago is an important step in predicting future spread and designing effective management strategies. In this study, we describe the invasion pathway of Rattus rattus across the Galápagos using microsatellite data, coupled with historical knowledge. Microsatellite genotypes were generated for 581 R. rattus sampled from 15 islands in the archipelago. The genetic data suggest that there are at least three genetic lineages of R. rattus present on the Galápagos Islands. The spatial distributions of these lineages correspond to the main centers of human settlement in the archipelago. There was limited admixture among these three lineages, and these finding coupled with low rates of gene flow among island populations suggests that interisland movement of R. rattus is rare. The low migration among islands recorded for the species will have a positive impact on future eradication efforts.
RESUMEN
The Craugastor podiciferus complex is a group of phenotypically polymorphic direct-developing frogs that inhabit the Talamancan highlands of Costa Rica and Panama. The montane distribution of this group creates natural allopatry among members and offers an excellent opportunity to explore geographic models of speciation. Using a multilocus approach, we obtained data from one nuclear (c-myc) and three mitochondrial (12S, 16S, and COI) gene regions from 40 individuals within the C. podiciferus complex. Molecular phylogenetic analyses revealed a basal split that placed samples from western Panama as sister to Costa Rican (CR) samples, corroborating a previous suggestion that the former lineage may represent an undescribed species. Within the CR clades we found six distinct haplogroups whose distributions largely corresponded to geographic features and included instances of sympatry. Divergence estimates were used to develop a preliminary evolutionary timeframe for the diversification of the C. podiciferus complex. Based on collective evidence, we hypothesize that movement of the CR haplogroups has occurred between currently isolated areas of suitable habitat via second order climatic fluctuations during the Pleistocene. The levels of genetic differentiation within the C. podiciferus complex are remarkable given the relatively small geographic area (ca. 8000 km(2)) of occurrence. This diversity emphasizes the need for further study and taxonomic revision to aid in conservation planning for this complex which, like many amphibians, has experienced recent population declines.
Asunto(s)
Anuros/genética , Evolución Molecular , Especiación Genética , Filogenia , Animales , Anuros/clasificación , Teorema de Bayes , Núcleo Celular/genética , Costa Rica , ADN Mitocondrial/genética , Genética de Población , Geografía , Panamá , Análisis de Secuencia de ADNRESUMEN
Recently, sequences from two nuclear genes (exon 6 of the dentin matrix protein 1 gene and intron 7 of the beta-fibrinogen gene) and one mitochondrial gene (cytochrome b gene) were used independently in an attempt to resolve phylogenetic relationships within the neotomine-peromyscine complex. Although these studies provided testable hypotheses regarding this group of rodents, the affinities of certain tribes and genera remain uncertain. To elucidate these relationships, the three data partitions were tested for heterogeneity and then concatenated according to conditional data combination and total evidence approaches. Support was found for five clades, four of which correspond to well recognized tribes (the Neotomini, Peromyscini=Reithrodontomyini, Baiomyini, and Tylomyini). Recommendations are made regarding the recognition of Ochrotomys as a tribe of its own, the Ochrotomyini, paralleling other recent findings. The Peromyscini, Baiomyini, and Ochrotomyini are unresolved in relation to each other, but as a whole are sister to the Neotomini. The Tylomyini is basal to all clades. It appears that combined data from the nuclear and mitochondrial genes (analyzing all three partitions simultaneously) resulted in the best phylogenetic hypothesis regarding the complex.
Asunto(s)
Núcleo Celular/genética , ADN Mitocondrial/genética , Roedores/genética , Animales , Secuencia de Bases , Citocromos b/genética , Proteínas de la Matriz Extracelular/genética , Fibrinógeno/genética , Fosfoproteínas/genética , Filogenia , Roedores/clasificaciónRESUMEN
DNA sequences from the mitochondrial DNA cytochrome-b gene were used to infer the systematic relationships of 13 species of wood rats (genus Neotoma). Parsimony, likelihood, and neighbor-joining analyses produced similar topologies in most cases and produced six systematic conclusions. First, results of previous studies were supported in the recognition of N. floridana magister as distinct species (N. magister). Second, evidence was provided for the recognition of cryptic species within N. albigula (N. albigula and N. leucodon) and N. mexicana (N. mexicana, N. isthmica, and N. picta). Third, the subgenus Neotoma is composed of four species groups (floridana, lepida, mexicana, and micropus). Fourth, support was provided for placement of N. stephensi within the lepida species group. Fifth, support was provided for the recognition of Hodomys as a separate genus, sister to Xenomys. Sixth, support for the elevation of the subgenus Teonoma to generic status is discussed.
