TL;DR: Analysis of DNA sequences from the mitochondrial cytochrome-b gene of 44 species of deer mice used to develop a molecular phylogeny for Peromyscus depicted strong support for a clade placing Habromys, Megadontomys, Neotomodon, OsgoodomYS, and Podomys within Peromycus.
Abstract: One hundred DNA sequences from the mitochondrial cytochrome-b gene of 44 species of deer mice (Peromyscus (sensu stricto), 1 of Habromys, 1 of Isthmomys, 2 of Megadontomys, and the monotypic genera Neotomodon, Osgoodomys, and Podomys were used to develop a molecular phylogeny for Peromyscus. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were conducted to evaluate alternative hypotheses concerning taxonomic arrangements (sensu stricto versus sensu lato) of the genus. In all analyses, monophyletic clades were obtained that corresponded to species groups proposed by previous authors; however, relationships among species groups generally were poorly resolved. The concept of the genus Peromyscus based on molecular data differed significantly from the most current taxonomic arrangement. Maximum-likelihood and Bayesian trees depicted strong support for a clade placing Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys within Peromyscus. If Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are regarded as genera, then several species groups within Peromyscus (sensu stricto) should be elevated to generic rank. Isthmomys was associated with the genus Reithrodontomys; in turn this clade was sister to Baiomys, indicating a distant relationship of Isthmomys to Peromyscus. A formal taxonomic revision awaits synthesis of additional sequence data from nuclear markers together with inclusion of available allozymic and karyotypic data.
TL;DR: Species-level phylogenetic relationships among the seven described Habromys species using 1331 aligned bases from the mitochondrial ND3 and ND4 regions suggest that H. simulatus and H. lophurus are each composed by two different taxa.
TL;DR: To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, this work detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, OsgoodomYS, and Podomys are retained as genera, subsumed as subgenera, or subsuming as species groups within PeromYScus.
Abstract: The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.
TL;DR: A new species of Habromys, H. delicatulus, is described from an isolated patch of cloud forest situated on a northern exposure of the Cordillera Neovolcanica, Estado de Mexico, which is the smallest so far known in the genus.
Abstract: A new species of Habromys, H. delicatulus, is described from an isolated patch of cloud forest situated on a northern exposure of the Cordillera Neovolcanica, Estado de Mexico. The species is the smallest so far known in the genus and is further characterized by its delicate cranial features. Morphometric comparisons with the five other species-group taxa currently allocated to the genus recommend the elevation of ixtlani Goodwin, 1964, as a species distinct from Habromys lepturus (Merriam, 1898). Habromys lophurus (Merriam, 1908), known from highlands east of the Isthmus of Tehuantepec, appears to be the sister taxon to the former pair, each restricted to separate Oaxacan ranges west of the Isthmus. Habromys chinanteco (Robertson & Musser, 1976) is retained as a species, but its possible status as a junior synonym under H. simulatus (Osgood, 1904) warrants continued investigation with improved samples. The montane distribution of Habromys in naturally discontinuous humid-forest associations of northern Mesoamerica is considered in the context of diversity patterns summarized for other small terrestrial mammals confined to such forests.
TL;DR: This work analysed the distributional patterns of six terrestrial vertebrate taxa from the Oaxacan Highlands through a cladistic biogeographical approach, in order to test their naturalness as a biotic unit.
Abstract: Aim We analysed the distributional patterns of six terrestrial vertebrate taxa from the Oaxacan Highlands (Sierra Mazateca, Nudo de Zempoaltepetl and Sierra de Juarez) through a cladistic biogeographical approach, in order to test their naturalness as a biotic unit. Location The Oaxacan Highlands, Mexico. Methods The cladistic biogeographical analysis was based on the area cladograms of the Pseudoeurycea bellii species group (Amphibia: Plethodontidae), the genus Chlorospingus (Aves: Thraupidae), the genera Microtus, Reithrodontomys and Habromys, and the Peromyscus aztecus species group (Mammalia: Rodentia). We obtained paralogy-free subtrees, from which the components were coded in a data matrix for parsimony analysis. The data matrix was analysed with Nona through