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Chaetodipus nelsoni occurs on rocky substrates across the Mexican Altiplano. We investigated phylogeographic diversity within the species using morphologic, karyotypic, and molecular data. Data from nuclear (AFLP) and mitochondrial DNA support three distinct genetic groups with minimal substructuring coincident with biogeographic barriers previously identified in the Chihuahuan Desert and drainage basins of the Altiplano. We examined the morphological and karyotypic data in light of the molecular data. The results support recognition of three species within the currently accepted widespread C. nelsoni : 1) C. nelsoni restricted to a distribution centered on the El Salado River Basin; 2) elevation of C. n. collis to species, with two subspecies: one centered on Trans-Pecos Texas, the other on the Mapimí Basin (new subspecies); and 3) recognition of a new species, C. durangae , centered on the Nazas Basin and upper Río Mezquital drainage. [ABSTRACT FROM AUTHOR]

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range-wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil-calibrated and rate-calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide-ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well-supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co-distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid-adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 949-967. [ABSTRACT FROM AUTHOR]

Aim The Mohave ground squirrel ( Xerospermophilus mohavensis) is one of a few endemic species of the Mojave Desert of south-western North America. We describe phylogeographic patterns within this species and its sister taxon ( Xerospermophilus tereticaudus) and test hypotheses concerning their biogeographical history using genetic signatures of stable versus expanding populations. We compare these patterns with those of other Mojave species to evaluate the role of vicariance in producing phylogeographic structure during the assembly of the Mojave Desert biota. Location The Mojave Desert and adjacent desert regions of south-western North America. Methods Complete cytochrome b gene sequences of X. mohavensis (46 individuals representing 11 localities) and X. tereticaudus (38 individuals representing 14 localities) were analysed using Bayesian methods to infer phylogenetic relationships. Genetic signals of stable or expanding populations were examined based on the distribution of recent mutations and pairwise differences, as well as with a coalescent-based approach. Results The two species are reciprocally monophyletic and may have diverged in response to the late Pliocene–early Pleistocene uplift of the Transverse Ranges and Mojave block. Little phylogeographic structure is evident within X. mohavensis, but there is a signature of northern expansion from a presumably full-pluvial refugium in the Mojave River basin. Four geographic subgroups are evident within X. tereticaudus, and there is a signature of northern expansion from a presumably full-pluvial refugium in the Sonoran coastal plains. Roughly congruent phylogeographic patterns are found within five arid-adapted taxa, indicating a strong element of vicariance during the assembly of the generally transitional Mojave Desert biota. Main conclusions We present a preliminary model for the historical assembly of the Mojave Desert biota that indicates a strong vicariant element producing autochthonous lineages (including X. mohavensis) that diverged during the major geological and climatic events of the last 5 Myr. Phylogeographic partitioning within the Mojave Desert underscores the necessity of immediate conservation measures for this unique and fragile arid ecosystem that is locked between two large metropolitan population centres and is the target of continued adverse environmental impact. [ABSTRACT FROM AUTHOR]

The genetic consequences of climate-driven range fluctuation during the Pleistocene have been well studied for temperate species, but cold-adapted (e.g., alpine, arctic) species that may have responded uniquely to past climatic events have received less attention. In particular, we have no a priori expectation for long-term evolutionary consequences of elevation shifts into and out of sky islands by species adapted to alpine habitats. Here, we examined the influence of elevation shifts on genetic differentiation and historical demography in an alpine specialist, the American pika ( Ochotona princeps). Pika populations are divided into five genetic lineages that evolved in association with separate mountain systems, rather than lineages that reflect individual sky islands. This suggests a role for glacial-period elevation shifts in promoting gene flow among high-elevation populations and maintaining regional cohesion of genetic lineages. We detected a signature of recent demographic decline in all lineages, consistent with the expectation that Holocene climate warming has driven range retraction in southern lineages, but unexpected for northern populations that presumably represent postglacial expansion. An ecological niche model of past and future pika distributions highlights the influence of climate on species range and indicates that the distribution of genetic diversity may change dramatically with continued climate warming. [ABSTRACT FROM AUTHOR]

Evaluates the role of Late Miocene to Pleistocene geological history in the evolution of a distinct Baja California Peninsular Desert biota. Analyses of phylogeographic population structure across a suite of animal species; Comparative examination of phylogroup distributions; Evidence for the occurrence of vicariance events.

We review the expanding role of molecular genetics in the emergence of a vibrant and vital integrative biogeography. The enormous growth over the past several decades in the number and variety of molecular-based phylogenetic and population genetics studies has become the core information used by biogeographers to reconstruct the causal connections between historical evolutionary and ecological attributes of taxa and biotas, and the landscapes and seascapes that contain them. A proliferation of different approaches, sequences, and genomes have provided for the integration of a 'biogeography of the Late Neogene' with other Earth and biological sciences under the rubrics of phylogeography, landscape genetics, and phylochronology. Approaches designed explicitly to take advantage of unique properties of molecular genetic information have led to the re-emergence of dispersal as an analytically tractable process that historical biogeographers can now use, along with vicariance, to reconstruct the geographical context of diversification. Concomitant with the expanding amount of information available, molecular data sets often provide for estimates of lineage divergence dates, and analytical tools for doing so continue to improve. The comparability of molecular-based estimates of phylogenetic and population genetic histories across non-related taxa has stimulated deployment of new methods to test for spatial and temporal congruence across co-distributed taxa and ecosystems, and thus increased rigour in hypothesis-testing. We illustrate how a molecular genetics framework has provided robust and novel reconstructions of historical biogeographical pattern and process in three different systems, and finish with some thoughts on the role a molecular genetic-based biogeography will play in predicting alternative futures of biodiversity. [ABSTRACT FROM AUTHOR]