Diversification and gene flow in nascent lineages of island and mainland North American tree squirrels (Tamiasciurus).

Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data, we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and Tamiasciurus hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the Late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mitochondrial DNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the Late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the last glacial maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow. Sequence data have been archived in GenBank­accession numbers: KF882736­KF885216.

Phylogenetic relationships of the mockingbirds and thrashers (Aves: Mimidae).

The mockingbirds, thrashers and allied birds in the family Mimidae are broadly distributed across the Americas. Many aspects of their phylogenetic history are well established, but there has been no previous phylogenetic study that included all species in this radiation. Our reconstructions based on mitochondrial and nuclear DNA sequence markers show that an early bifurcation separated the Mimidae into two clades, the first of which includes North and Middle American taxa (Melanotis, Melanoptila, Dumetella) plus a small radiation that likely occurred largely within the West Indies (Ramphocinclus, Allenia, Margarops, Cinclocerthia). The second and larger radiation includes the Toxostoma thrasher clade, along with the monotypic Sage Thrasher (Oreoscoptes) and the phenotypically diverse and broadly distributed Mimus mockingbirds. This mockingbird group is biogeographically notable for including several lineages that colonized and diverged on isolated islands, including the Socorro Mockingbird (Mimus graysoni, formerly Mimodes) and the diverse and historically important Galapagos mockingbirds (formerly Nesomimus). Our reconstructions support a sister relationship between the Galapagos mockingbird lineage and the Bahama Mockingbird (M. gundlachi) of the West Indies, rather than the Long-tailed Mockingbird (M. longicaudatus) or other species presently found on the South American mainland. Relationships within the genus Toxostoma conflict with traditional arrangements but support a tree based on a preivous mtDNA study. For instance, the southern Mexican endemic Ocellated Thrasher (T. ocellatum) is not an isolated sister species of the Curve-billed thrasher (T. curvirostre).

The origin and diversification of Galapagos mockingbirds.

Evolutionary radiations of colonists on archipelagos provide valuable insight into mechanisms and modes of speciation. The apparent diversification of Galapagos mockingbirds (Nesomimus) provoked Darwin's initial conception of adaptive radiation, but the monophyly of this historically important exemplar has not been evaluated with molecular data. Additionally, as with most Galapagos organisms, we have a poor understanding of the temporal pattern of diversification of the mockingbirds following colonization(s) from source populations. Here we present a molecular phylogeny of Galapagos and other mockingbird populations based on mitochondrial sequence data. Monophyly of Galapagos mockingbirds was supported, suggesting a single colonization of the archipelago followed by diversification. Our analyses also indicate that Nesomimus is nested within the traditional genus Mimus, making the latter paraphyletic, and that the closest living relatives of Galapagos mockingbirds appear to be those currently found in North America, northern South America, and the Caribbean, rather than the geographically nearest species in continental Ecuador. Thus, propensity for over-water dispersal may have played a more important role than geographic proximity in the colonization of Galapagos by mockingbirds. Within Galapagos, four distinct mitochondrial DNA clades were identified. These four clades differ from current taxonomy in several important respects. In particular, mockingbirds in the eastern islands of the archipelago (Española, San Cristóbal, and Genovesa) have very similar mitochondrial DNA sequences, despite belonging to three different nominal species, and mockingbirds from Isabela, in the west of the archipelago, are more phylogenetically divergent than previously recognized. Consistent with current taxonomy is the phylogenetic distinctiveness of the Floreana mockingbird (N. trifasciatus) and close relationships among most mockingbirds from the central and northern region of the archipelago (currently considered conspecific populations of N. parvulus). Overall, phylogeographic patterns are consistent with a model of wind-based dispersal within Galapagos, with colonization of more northerly islands by birds from more southern populations, but not the reverse. Further radiation in Galapagos would require coexistence of multiple species on individual islands, but this may be prevented by relatively limited morphological divergence among mockingbirds and by lack of sufficient habitat diversity in the archipelago to support more than one omnivorous mimid.

Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest.

To investigate the evolutionary and biogeographical history of Peromyscus keeni and P. maniculatus within the coastal forest ecosystem of the Pacific Northwest of North America, we sampled 128 individuals from 43 localities from southeastern Alaska through Oregon. We analysed mitochondrial DNA variation using DNA sequence data from the mitochondrial cytochrome-b (cyt-b) gene and control region, and we found two distinct clades consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt-b and 0.0396 for the control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. We also examined the historical demography of the two clades using stepwise and exponential expansion models, both of which indicated recent rapid population growth. Furthermore, using the program migrate we found evidence of migration from populations north of the Fraser River (British Columbia) to the south in both clades. This study demonstrates the utility of these model-based demographic methods in illuminating the evolutionary and biogegographic history of natural systems.