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Castañeda-Rico S, Parker LD, Sánchez E, Rivas-Trasvina S, Hawkins MTR, Edwards CW, Maldonado JE. 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. Zookeys 2023; 1179:157-168. [PMID: 37731536 PMCID: PMC10507443 DOI: 10.3897/zookeys.1179.108759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Abstract
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.
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Affiliation(s)
- Susette Castañeda-Rico
- Smithsonian-Mason School of Conservation, Front Royal, VA, USASmithsonian-Mason School of ConservationFront RoyalUnited States of America
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USACenter for Conservation Genomics, Smithsonian National Zoo and Conservation Biology InstituteWashingtonUnited States of America
- Department of Biology, George Mason University, Fairfax, VA, USAGeorge Mason UniversityFairfaxUnited States of America
| | - Lillian D. Parker
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USACenter for Conservation Genomics, Smithsonian National Zoo and Conservation Biology InstituteWashingtonUnited States of America
- Department of Anthropology, University of Oklahoma, Norman, OK, USAUniversity of OklahomaNormanUnited States of America
| | - Evelyn Sánchez
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USACenter for Conservation Genomics, Smithsonian National Zoo and Conservation Biology InstituteWashingtonUnited States of America
| | - Sheccid Rivas-Trasvina
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USACenter for Conservation Genomics, Smithsonian National Zoo and Conservation Biology InstituteWashingtonUnited States of America
| | - Melissa T. R. Hawkins
- Department of Vertebrate Zoology, Division of Mammals, National Museum of Natural History, Washington DC, USADepartment of Vertebrate Zoology, Division of Mammals, National Museum of Natural HistoryWashingtonUnited States of America
| | - Cody W. Edwards
- Smithsonian-Mason School of Conservation, Front Royal, VA, USASmithsonian-Mason School of ConservationFront RoyalUnited States of America
- Department of Biology, George Mason University, Fairfax, VA, USAGeorge Mason UniversityFairfaxUnited States of America
| | - Jesús E. Maldonado
- Smithsonian-Mason School of Conservation, Front Royal, VA, USASmithsonian-Mason School of ConservationFront RoyalUnited States of America
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USACenter for Conservation Genomics, Smithsonian National Zoo and Conservation Biology InstituteWashingtonUnited States of America
- Department of Biology, George Mason University, Fairfax, VA, USAGeorge Mason UniversityFairfaxUnited States of America
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Colunga-Salas P, Marines-Macías T, Hernández-Canchola G, Barbosa S, Ramírez C, Searle JB, León-Paniagua L. Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat. MAMMAL RES 2023. [DOI: 10.1007/s13364-022-00667-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Abstract
Genomic tools are now commonly used to assess the genetic diversity and genetic structure of species and populations, and they provide the ability to describe and address the negative effects of population declines and fragmentation. However, such studies are lacking for arboreal mammals despite their contribution to various ecosystem services, especially in uncommon and critically endangered ecosystems such as cloud forests. The aim of this work was to evaluate and compare the genetic diversity and population structure of two endemic arboreal mice from Mexican cloud forests that are associated with areas with different levels of impacts from human activities. We performed genotyping-by-sequencing in 47 Habromys schmidlyi and 17 Reithrodontomys wagneri individuals to evaluate genetic diversity and differentiation. In both species, the genetic diversity was low compared to other cricetid species, and we observed different population structure patterns, potentially linked to the different ecological associations. We detected two genetic groups in H. schmidlyi, that is a territorial species present in areas of low incline, while a single genetic group was found in R. wagneri, which forms family groups in areas with steep slopes. Overall, these results highlight how species’ genetic diversity can be differentially impacted depending on differential ecological associations within the same ecosystem. This information is essential for the development of the adequate conservation and management of these species.
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Contreras-Medina R, Santiago-Alvarado M, Espinosa D, Rivas G, Luna-Vega I. Distributional patterns and conservation of the genus Habromys (Rodentia: Cricetidae) in Mesoamerica. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2022. [DOI: 10.1080/01650521.2022.2085071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Raúl Contreras-Medina
- Escuela de Ciencias, Universidad Autónoma “Benito Juárez” de Oaxaca (UABJO), Av. Universidad s/n, Oaxaca, Mexico
| | - Margarita Santiago-Alvarado
- Unidad Multidisciplinaria de Investigación Experimental Zaragoza, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - David Espinosa
- Unidad Multidisciplinaria de Investigación Experimental Zaragoza, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Gerardo Rivas
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Isolda Luna-Vega
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
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Zaragoza-Quintana EP, Rodríguez-Santiago NV, Hernández-Betancourt S, León-Paniagua L, MacSwiney MCG. Microhabitat and diet composition of the Yucatán vesper mouse, Otonyctomys hatti, in southeastern Mexico. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00139-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Espindola S, Cuarón AD, Gaggiotti OE, Vázquez-Domínguez E. High genetic structure of the Cozumel Harvest mice, a critically endangered island endemic: conservation implications. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0625-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Castañeda-Rico S, León-Paniagua L, Vázquez-Domínguez E, Navarro-Sigüenza AG. Evolutionary diversification and speciation in rodents of the Mexican lowlands: the Peromyscus melanophrys species group. Mol Phylogenet Evol 2013; 70:454-63. [PMID: 24140979 DOI: 10.1016/j.ympev.2013.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 10/26/2022]
Abstract
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.
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Affiliation(s)
- Susette Castañeda-Rico
- Museo de Zoología "Alfonso L. Herrera", Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P. 70-399, Ciudad Universitaria, México, DF 04510, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510, Coyoacán, México, DF 04510, Mexico.
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Vázquez-Domínguez E, Suárez-Atilano M, Booth W, González-Baca C, Cuarón AD. Genetic evidence of a recent successful colonization of introduced species on islands: Boa constrictor imperator on Cozumel Island. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0217-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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