Species distributions reflect the suite of resources and range of environmental conditions required by a species. Distributions of many species change seasonally, however, in response to changes in resource availability and environmental conditions, many of which are projected to shift in response to climate change. We sought to identify environmental and anthropogenic factors associated with seasonal changes in the distribution of vertebrates that inhabit the Madrean Archipelago in southern Arizona, which is important for identifying mechanisms through which climate change may affect these species. From July 2012 to February 2015 (966 days), we used remote cameras to survey 200 sites across 16 mountain ranges for a total of 69,434 trap days and used dynamic occupancy models to determine how landscape features, vegetation composition, and anthropogenic factors influenced the distributions and seasonal rates of local colonization and extinction of 13 vertebrates. For these 13 species, we recorded 37,888 detections, with gray foxes, skunks, and squirrels detected most frequently. Bobcats, cottontails, gray foxes, skunks, squirrels, javelina, puma, and coatimundis were all detected across the entire range of elevations surveyed, from 935 to 2395 m. Black bears and wild turkeys were never detected below 1270 m, Sonoran opossums never detected above 1980 m, and coyotes and ringtails never detected above 2020 m. Composition and structure of vegetation in the understory, midstory, and overstory influenced initial occupancy of several species, including skunks, coatimundis, Sonoran opossums, and cottontails. Season, either directly or as an interaction with the estimated amount of solar radiation reaching a site, influenced local extinction rates of all 13 target species and local colonization rates of 9 of 13 species. Elevation influenced local colonization rates of black bears and coatimundis positively, and coyotes, Sonoran opossums, and cottontails negatively, and local extinction rates of skunks negatively and coyotes and black bears positively. These patterns indicate that the distributions of many species in this region change seasonally, likely as a mechanism to meet dietary, behavioral, or physiological needs in response to shifts in environmental conditions and resource availability. Therefore, species that depend on seasonal resources may be at higher risk of distributional shifts or range contractions if the distribution and phenology of these resources change in response to changes in climate.

Estimates from radiocarbon-dated packrat middens indicate that the high elevation woodland communities of the Madrean Sky Islands were continuous as recently as 8,000 to 12,000 years ago. A number of population studies on a diverse collection of taxa have investigated the extent to which the Madrean Sky Island system has limited gene flow among mountain ranges. The results of several of these studies indicate that population divergences may be more ancient than the Holocene. Yarrow’s spiny lizards, Sceloporus jarrovii, were sampled from eight sites representing seven mountain ranges. The populations of S. jarrovii are host to the malarial parasite, Plasmodium chiricahuae. DNA sequences from the lizards and their malarial parasites were used to reconstruct the evolutionary relationships and estimate the ages of the populations for both host and parasite. The findings of these analyses indicate that the sky island populations of S. jarrovii have been isolated for hundreds of thousands of years and did not experience gene flow during the last woodland expansion. In contrast, the results indicate that the malarial infection occurred more recently, possibly during the Holocene woodland expansion. In addition, the prevalence of the malarial infection was compared to multiple attributes of the lizards. This analysis revealed a negative relationship between the genetic diversity of the lizard populations and the prevalence of infection. Furthermore, lizard populations with lower prevalence of infection have a lower frequency of multiclonal infections.

Because American black bears (Ursus americanus) are an important game species in Arizona and are endangered in México, an understanding of the population structure, gene flow, and connectivity are important for effective management. Black bears inhabit coniferous and broadleaf deciduous woodlands in southern Arizona and northern México, usually in sky islands (sky islands are mountains that rise from the desert and are isolated from each other). Because a single sky island is too small to support a viable bear population, black bears move through desert lowlands to reach other sky islands. My objective was to assess genetic structure, connectivity, and conservation implications for sky island black bears in southern Arizona and northern México. I addresses 4 components of bear ecology and genetics: a literature review of genetic information available for black bears in North America; the use of 2 mitochondrial DNA genes (Control Region and ATP synthase protein 8) to study the phylogenetic relationship of black bears from the sky islands of southern Arizona and northern México relative to all North America; the use of 10 microsatellite loci to detect the current genetic structure of black bears in the sky islands in Arizona and northern México; and the use of noninvasive samples collected from the field to determine bear density and population size for black bear in Sierra San Luis, Sonora, México. These studies provide information that can be used by biologists, land managers, and others to assist in the conservation of black bears and their habitat.

The Sierra Madre Occidental and neighboring Madrean Sky Islands span a large and biologically diverse region of northwest Mexico and portions of the southwestern United States. Little is known about the abundance and habitat use of breeding birds in this region of Mexico, but such information is important for guiding conservation and management. We assessed densities and habitat relationships of breeding birds across Sky Island mountain ranges in Mexico and adjacent portions of the Sierra Madre from 2009 to 2012. We estimated densities at multiple spatial scales, assessed variation in densities among all major montane vegetation communities, and identified and estimated the effects of important habitat attributes on local densities. Regional density estimates of 65% of 72 focal species varied significantly among eight montane vegetation communities that ranged from oak savannah and woodland at low elevations to pine and mixed-conifer forest at high elevations. Greater proportions of species occurred at peak densities or were relatively restricted to mixed-conifer forest and montane riparian vegetation likely because of higher levels of structural or floristic diversity in those communities, but those species were typically rare or uncommon in the Sky Islands. Fewer species had peak densities in oak and pine-oak woodland, and species associated with those communities were often more abundant across the region. Habitat models often included the effects of broadleaf deciduous vegetation cover (30% of species), which, together with tree density and fire severity, had positive effects on densities and suggest ways for managers to augment and conserve populations. Such patterns combined with greater threats to high-elevation conifer forest and riparian areas underscore their value for conservation. Significant populations of many breeding bird species, including some that are of concern or were not known to occur regionally or in mountain ranges we surveyed, highlight the importance of conservation efforts in this area of Mexico.

Les espèces de haute altitude (Sky-Islands) sont parmi les taxons les plus sensibles aux changements environnementaux et une meilleure connaissance de ces espèces (répartition, groupes génétiques, histoire d’évolution, etc.) est indispensable afin de définir les unités adaptées pour la conservation. Cette thèse a porté sur l’analyse moléculaire de deux gènes mitochondriaux (Cyt b et ND4) chez le groupe d’espèces Montivipera raddei et un gène mitochondrial (COI) chez l’Ophisops elegans dans les montagnes d’Iran qui sont des centres d’endémisme importants pour les reptiles. En me basant sur les données génétiques, je propose de considérer toutes les montivipère d’Iran comme une seule espèce ; Montivipera raddei comprenant trois sous-espèces ; Montivipera raddei albicornuta (nord du Zagros, Zanjan et nord-ouest de l’Iran jusqu’en Turquie), Montivipera raddei latifii (Alborz), et Montivipera raddei kuhrangica (centre du Zagros). Les temps de divergences obtenus entre les clades de montivipères semblent montrer des changements de la connectivité des populations pendant le Pléistocène qui résulte de l’effet fort des oscillations climatiques durant cette époque, notamment pendant les interglaciaires. Ce travail a aussi révélé une grande diversité génétique au sein des clades iraniens d’ophisops élégant ce qui pose la question de l’existence d’espèces/sous-espèces cryptiques en Iran. Finalement, ce travail a permis de définir des ESU pour les montivipères et l’ophisops élégant et notamment je propose que toutes les populations isolées du groupe d’espèces M. raddei et d’O. elegans montrant des haplotypes propres soient considérées comme des ESU pour la conservation. / High-altitude species (Sky-Islands) are among the most sensitive taxa to environmental changes and a better knowledge of these species (distribution, genetic groups, evolutionary history, etc.) is essential in order to define the adapted units for the conversation. This thesis focused on the molecular analysis of two mitochondrial genes (Cyt b and ND4) in the Montivipera raddei (Radde's Rock Viper) species group and a mitochondrial gene (COI) in Ophisops elegans (Snake-Eyed Lizard) in the mountains of Iran, which are important centers of endemism for reptiles. Based on the genetic data, I propose to consider all the Iranian montivipers as one species; Montivipera raddei comprising three subspecies; Montivipera raddei albicornuta (north of Zagros, Zanjan and northwestern Iran to Turkey), Montivipera raddei latifii (Alborz), and Montivipera raddei kuhrangica (central Zagros). The times of divergence between the clades of montivipers seem to show changes in the connectivity of populations during the Pleistocene, which results from the strong, effect of climatic oscillations during this period, especially during interglacial periods. This work also revealed a great genetic diversity within the Iranian clades of snake-eyed lizard, which raises the question of the existence of cryptic species / subspecies in Iran. Finally, this work made it possible to define ESUs for montivipers and snake-eyed lizards. In particular, I propose that all isolated populations of the M. raddei species group and O. elegans showing specific haplotypes to be considered as ESUs for conservation.