We use analyses of phylogeographic population structure across a suite of 12 mammalian, avian, amphibian, and reptilian species and species-groups to assess the role of Late Miocene to Pleistocene geological history in the evolution of a distinct Baja California Peninsular Desert biota. Comparative examination of phylogroup distributions provides support for previously hypothesized vicariant events produced by: a middle Pleistocene midpeninsular seaway, a late Pliocene northward transgression of the Sea of Corté z, and a Pliocene seaway across the southern peninsular Isthmus of La Paz. Most of this phylogeographic architecture is cryptically embedded within widespread taxonomic species and speciesgroups, such that the unique evolutionary history of the Peninsular Desert has been obscured and ignored. The Peninsular Desert can no longer be considered a subset of the Sonoran Desert-it is a separate regional desert with its own unique evolutionary history, ecological arena, and conservation value.

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 ( For low-elevation temperate species, historical global cooling is generally a driver of range retraction and habitat fragmentation, and isolation by barriers associated with glacial periods has contributed to intra-and interspecific genetic structuring in many taxa (Taberlet et

No abstract

Reevaluation of Quaternary sites of fossil pika (Ochotona) lends no support for the inference that Nearctic pikas were not restricted to rocky habitat. The saxicolous nature of all widespread, isolated populations of extant Nearctic pikas and their closest Palearctic sister taxa support consideration of O. princeps, and perhaps all Nearctic Quaternary Ochotona , as indicators of cool, mesic, rocky situations. As indicators of rocky microhabitat, fossil remains of O. princeps do not require that the entire region was cool and mesic, but only that suitable rocky microhabitat existed in the vicinity. Use of fossil pika dung alone as indicative of pikas in the immediate community is suspect, as the small, round, and buoyant pellets may be transported downslope by hydraulic flushing of talus habitat. Current local elevational lower limits (E) of appropriate habitat for paleoecological reconstruction at extralimital fossil sites are predicted by the equation: E(m) = 14087 - (56.6)°N - (82.9)°W.

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.

Phylogeographic relationships among 26 populations from throughout the geographic range of the Peromyscus eremicus species group are described based on sequence data for a 699-bp fragment of the mitochondrial DNA COIII gene. Distance, maximum-likelihood, and maximum-parsimony analyses of phylogenetic trees generated under four separate character-weighting strategies and representing five alternative biogeographic hypotheses revealed the existence of a cryptic species (Peromyscus fraterculus, previously included under P. eremicus) on the Baja California Peninsula and adjacent southwestern California and two distinct forms of P. eremicus, one from the Mojave, Sonoran, and northwestern Chihuahuan regional deserts (West) and one from the remainder of the Chihuahuan Desert (East). Distinctiveness of P. fraterculus is supported by previous morphometric and allozyme analyses, including comparisons with neighboring P. eremicus and parapatric P. eva, with which P. fraterculus shares a sister taxon relationship. Divergence of the eva ؉ fraterculus, West ؉ East eremicus, and P. merriami haplotype lineages likely occurred in the late Neogene (3 Ma), in response to northern extension of the Sea of Corté z and elevation of the Sierra Madre Occidental; divergence of eva from fraterculus is concordant with the existence of a trans-Peninsular seaway during the Pleistocene (1 Ma); and divergence of West from East eremicus occurred during the Pleistocene pluvial-interpluvial cycles, but well before the Wisconsinan glacial interval. The sequence of divergence within the eremicus species group and causal association of geological events of the Neogene and Holocene provide a working hypothesis against which phylogeographic patterns among other arid-adapted species of the warm regional deserts of North America may be compared. © 2000 Academic Press Key Words: biogeography; phylogeography; systematics; North American deserts; mitochondrial DNA; rodents; Peromyscus eremicus; Peromyscus eva; Peromyscus merriami; Peromyscus fraterculus. INTRODUCTIONKnowledge of the diversification and distribution of taxa and biotas through time is fundamentally based on our understanding of the geographic distribution of and relationships among evolutionary lineages. For example, debate over the prevalence of vicariance versus dispersal will reflect the extent to which similarity among populations fails to obscure historical divergence among evolutionary lineages. Reconstructions of biogeographic history will necessarily be wrong if paraphyletic or polyphyletic lineages are erroneously interpreted to be monophyletic.We might expect basic biogeographic patterns in the North American mammal fauna to be relatively well characterized, given a century of intensive systematic and biogeographic investigations that began with the creation of the United States Biological Survey in the late 1800s (Hoffmeister and Sterling, 1994). Instead, molecular-based studies repeatedly reveal cryptic evolutionary lineages embedded within long-recognized species of North Americ...

Aim We studied the history of colonization, diversification and introgression among major phylogroups in the American pika, Ochotona princeps (Lagomorpha), using comparative and statistical phylogeographic methods. Our goal was to understand how Pleistocene climatic fluctuations have shaped the distribution of diversity at mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) loci in this alpine specialist.Location North America's Intermountain West.Methods We accumulated mtDNA sequence data (c. 560-1700 bp) from 232 pikas representing 64 localities, and sequenced two nuclear introns (mast cell growth factor, c. 550 bp, n = 148; protein kinase C iota, c. 660 bp, n = 139) from a subset of individuals. To determine the distribution of major mtDNA lineages, we conducted a phylogenetic analysis on the mtDNA sequence data, and we calculated divergence times among the lineages using a Bayesian Markov chain Monte Carlo approach. Relationships among nuclear alleles were explored with minimum spanning networks. Finally, we conducted coalescent simulations of alternative models of population history to test for congruence between nDNA and mtDNA responses to Pleistocene glacial cycles.Results We found that: (1) all individuals could be assigned to one of five allopatric mtDNA lineages; (2) lineages are associated with separate mountain provinces; (3) lineages originated from at least two rounds of differentiation; (4) nDNA and mtDNA markers exhibited overall phylogeographic congruence; and (5) introgression among phylogroups has occurred at nuclear loci since their initial isolation.Main conclusions Pika populations associated with different mountain systems have followed separate but not completely independent evolutionary trajectories through multiple glacial cycles. Range expansion associated with climate cooling (i.e. glaciations) promoted genetic admixture among populations within mountain ranges. It also permitted periodic contact and introgression between phylogroups associated with different mountain systems, the record of which is retained at nDNA but not mtDNA loci. Evidence for different histories at nuclear and mtDNA loci (i.e. periodic introgression versus deep isolation, respectively) emphasizes the importance of multilocus perspectives for reconstructing complete population histories.

No abstract