Cody W. Edwards

MOLECULAR PHYLOGENETICS OF THE NEOTOMA ALBIGULA SPECIES GROUP: FURTHER EVIDENCE OF A PARAPHYLETIC ASSEMBLAGE

Abstract Phylogenetic relationships among 8 subspecies of Neotoma albigula and sister species from the United States and Mexico were examined using DNA sequence data from the mitochondrial DNA cytochrome-b gene. Parsimony, likelihood, and neighbor-joining analyses revealed a strong dichotomy between populations of N. albigula from Texas and eastern Mexico (eastern form) and those from New Mexico, Arizona, and northwestern Mexico (western form). These analyses indicate presence of 2 cryptic species within this taxon that are paraphyletic under current taxonomy. A sister-group relationship was found between N. albigula from Texas and eastern Mexico and N. micropus, whereas populations of N. albigula from New Mexico, Arizona, and northwestern Mexico formed a sister-group relationship with N. floridana. That latter group in turn formed a sister-taxon relationship to the Texas–eastern Mexico N. albigula and N. micropus clade. The Rio Grande and Rio Conchos seem to have been the major barriers restricting gene flow between ancestral populations of a N. floridana–like woodrat. Populations of N. floridana were further isolated geographically by reduction of suitable habitat brought about by changing climatic patterns that allowed formation of xeric plant communities soon after the end of the Late Wisconsin.

Molecular systematics of the genus Neotoma

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.

MOLECULAR SYSTEMATICS AND HISTORICAL PHYLOBIOGEOGRAPHY OF THE NEOTOMA MEXICANA SPECIES GROUP

Abstract Phylogenetic relationships among 15 individuals representing 6 subspecies of Neotoma mexicana from the United States and Mexico were examined using DNA sequences from the mitochondrial DNA cytochrome b gene. Parsimony, likelihood, and genetic distance analyses revealed a dichotomy between populations of N. mexicana from the United States and northern Mexico and those from south of the Trans-Volcanic belt in southern Mexico. A 2nd dichotomy existed between wood rats in the Sierra Madre del Sur in southwestern Mexico and those south of the Isthmus of Tehuantepec. Further, populations of N. mexicana from the United States and those from Mexico possessed relatively high levels of sequence divergence indicating substantial genetic differentiation between these 2 groups. These data indicate that the 3 taxa probably represent sibling species and that consideration should be given to the elevation of the southern and southwestern Mexico forms to specific status. Additionally, paleontological material from Pleistocene wood rat middens in New Mexico and Mexico provided evidence for the effects of climatic changes on this group of wood rats and the means for assessing the phylobiogeography of the N. mexicana species group.

Multilocus molecular phylogenetic analysis of the montane Craugastor podiciferus species complex (Anura: Craugastoridae) in Isthmian Central America

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.

PHYLOGENETIC RELATIONSHIPS OF NEOTOMINE–PEROMYSCINE RODENTS: BASED ON DNA SEQUENCES FROM THE MITOCHONDRIAL CYTOCHROME-b GENE

Abstract DNA sequences obtained from the mitochondrial cytochrome-b gene were used to evaluate phylogenetic relationships among 15 genera of putative neotomine–peromyscine rodents. Tree topologies obtained from maximum likelihood and Bayesian analyses revealed 4 primary clades that, in general, conform to the 4 tribes proposed by Carleton (1980). The Peromyscini (Megadontomys, Ochrotomys, Osgoodomys, Peromyscus, and Reithrodontomys) was sister to the Neotomini (Hodomys, Neotoma, Onychomys, and Xenomys). These 2 clades were then joined by the Baiomyini (Baiomys and Scotinomys) and Tylomyini (Nyctomys, Ototylomys, and Tylomys). The most apparent departure from previously proposed arrangements involved the placement of Onychomys in the Neotomini instead of the Peromyscini.

Coyote colonization of northern Virginia and admixture with Great Lakes wolves

Abstract Ecological invasions of generalist species often are facilitated by anthropogenic disturbance. Coyotes (Canis latrans) have benefitted from anthropogenic changes to North American ecosystems and have experienced a dramatic range expansion since the early 19th century. The region east of the Mississippi River has been colonized via 2 routes that have converged in the mid-Atlantic region during the past few decades. Coyotes using the northern route of expansion show molecular evidence of admixture with the Great Lakes wolf (GLW). We used noninvasive molecular techniques to detect the geographic origins of the recent coyote colonization of northern Virginia as a representative of the mid-Atlantic region and to detect signatures of admixture with GLWs. Of 455 individual canid scats screened, we sequenced a variable 282-base pair fragment of the mitochondrial control region from 126 coyote scats, assigned individual identities to samples using 6 microsatellite loci, and conducted phylogeographic analyses by comparing our sequences to previously published haplotypes. In 39 individuals identified in our scat surveys we detected 7 mitochondrial DNA haplotypes, all of which have been previously reported in diverse surrounding geographic localities. Phylogeographic analyses indicate multiple sources of colonization of northern Virginia. One common haplotype detected in northern Virginia is of wolf origin, indicating the presence of admixed coyotes and GLWs from the north.

PATTERNS OF KARYOTYPIC MEGAEVOLUTION IN REITHRODONTOMYS : EVIDENCE FROM A CYTOCHROME- b PHYLOGENETIC HYPOTHESIS

Abstract Phylogenetic relationships among 7 species of Reithrodontomys were examined using the complete mitochondrial cytochrome-b gene. DNA-sequence data were analyzed using parsimony (weighted and unweighted) and genetic distance methods. In all analyses, R. sumichrasti, R. megalotis, and R. zacatecae formed a monophyletic clade. Likewise, R. montanus and R. raviventris were depicted as sister taxa in all analyses. Our study supports recognition of R. zacatecae as a species distinct from R. megalotis and recognition of R. raviventris as distinct from R. montanus. Patterns of chromosomal evolution were examined using differential staining as resolved by 3 DNA probes and fluorescent in situ hybridization. Using the phylogeny based on DNA sequences, we concluded that there has been extensive chromosomal repatterning (in most cases karyotypic megaevolution) in the evolution of R. zacatecae, R. megalotis, R. sumichrasti, R. montanus, R. raviventris, and R. humulis.

MOLECULAR PHYLOGENETICS OF THE NEOTOMA FLORIDANA SPECIES GROUP

Abstract Phylogenetic relationships among 4 subspecies of Neotoma floridana and sister species from the United States and Mexico were examined using DNA sequence data from the mitochondrial DNA cytochrome b gene. Parsimony, likelihood, and neighbor-joining analyses support the recognition of N. f. magister as a distinct species (N. magister). Populations of eastern woodrats from the southern and western United States also possessed relatively high levels of sequence divergence (5.3%), which may be indicative of ongoing divergence between these populations. These findings support conclusions from previous studies and add clarity to the biogeographic processes influencing evolution and diversification of this group of rodents.

Systematics of the Neotoma mexicana species group (Mammalia: Rodentia: Cricetidae) in Mesoamerica: new molecular evidence on the status and relationships of N. ferruginea Tomes, 1862

Abstract Analyses of the mitochondrial cytochrome-b gene were used to determine levels of genetic differentiation and patterns of relationship among members of the Neotoma mexicana (Mexican woodrat) species group in Mesoamerica. Three well-supported clades were obtained that conform to the species N. ferruginea Tomes, 1862, N. mexicana Baird, 1855, and N. picta Goldman, 1904. Neotoma ferruginea is the senior name for the clade that contains samples from southern Mexico and Nuclear Central America previously identified as N. isthmica Goldman, 1904, or as subspecies of N. mexicana (chamula Goldman, 1909; vulcani Sanborn, 1935). The phylogeographic pattern observed within the N. mexicana species group resembles that reported for other vertebrates co-distributed in mountains to the west (Trans-Mexican Neovolcanic Belt, Oaxacan sierras) and east (highlands of Chiapas, Mexico, and Nuclear Central America) of the Isthmus of Tehuantepec. Resumen Análisis filogenéticos del gen mitocondrial Citocromo b se utilizaron para determinar los niveles de diferenciación genética y los patrones de relaciones entre miembros del grupo de especies de Neotoma mexicana en Mesoamerica. Se obtuvieron tres clados bien soportandos que están conformados por las especies Neotoma ferruginea Tomes, 1862; N. mexicana Baird, 1855; y N. picta Goldman, 1904. Neotoma ferruginea es el nombre más antiguo para el clado que contiene muestras del sur de México y Centro América Nuclear que previamente fueron identificadas como N. isthmica Goldman, 1904, y una subespecie de N. mexicana (chamula Goldman, 1909; vulcani Sanborn, 1935). El patrón filogeográfico observado entre el grupo de especies de N. mexicana se asemeja al reportado para otros vertebrados co-distribuidos en las montañas del Oeste (Eje neovolcánico transversal, Sierras de Oaxaca) y el Este (tierras altas de Chiapas, México y Centro América Nuclear) del Itsmo de Tehuantepec.

Cryptic diversity in Black rats Rattus rattus of the Galápagos Islands, Ecuador

Abstract 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.