Most Neotropical lowland forest taxa occur exclusively on one side of the Andes despite the availability of appropriate habitat on both sides. Almost all molecular phylogenies and phylogenetic analyses of species assemblages (i.e. area cladograms) have supported the hypothesis that Andean uplift during the Late Pliocene created a vicariant barrier affecting lowland lineages in the region. However, a few widespread plant and animal species occurring in lowland forests on both sides of the Andes challenge the generality of this hypothesis. To understand the role of the Andes in the history of such organisms, we reconstructed the phylogeographic history of a widespread Neotropical flycatcher (Mionectes oleagineus) in the context of the other four species in the genus. A molecular phylogeny based on nuclear and mitochondrial sequences unambiguously showed an early basal split between montane and lowland Mionectes. The phylogeographic reconstruction of lowland taxa revealed a complex history, with multiple cases in which geographically proximate populations do not represent sister lineages. Specifically, three populations of M. oleagineus west of the Andes do not comprise a monophyletic clade; instead, each represents an independent lineage with origins east of the Andes. Divergence time estimates suggest that at least two cross-Andean dispersal events post-date Andean uplift.

BackgroundEarth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis.ResultsPhylogenetic analysis revealed deep mtDNA structure with six lineages across the species' range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America.ConclusionWe show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in C. cardinalis. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered simultaneously.

Analyses of craniodental measurement data from 15 wild-collected population samples of the Neotropical muroid rodent genus Zygodontomys reveal consistent patterns of relative variability and correlation that suggest a common latent structure. Eigenanalysis of each sample covariance matrix of logarithms yields a first principal component that accounts for a large fraction of the total variance. Variances of subsequent sample principal components are much smaller, and the results of bootstrap resampling together with asymptotic statistics suggest that characteristic roots of the covariance matrix after the first are seldom distinct. The coefficients of normalized first principal components are strikingly similar from sample to sample: inner products of these vectors reveal an average between-sample correlation of 0.989, and the mean angle of divergence is only about eight degrees. Since first principal component coefficients identify the same contrasts among variables as comparisons of relative variability and correlation, we conclude that a single factor accounts for most of the common latent determination of these sample dispersions. Analyses of variance based on toothwear (a coarse index of age) and sex in the wild-collected samples, and on known age and sex in a captive-bred population, reveal that specimen scores on sample first principal components are age- and sex-dependent; residual sample dispersion, however, is essentially unaffected by age, sex, or age × sex interaction. The sample first principal component therefore reflects the covariance among measured dimensions induced by general growth, and its coefficients are interpretable as exponents of postnatal growth allometry. Path-analytic models that incorporate prior knowledge of the equivalent allometric effects of general growth within these samples can be used to decompose the between-sample variance by factors corresponding to other ontogenetic mechanisms of form change. The genetic or environmental determinants of differences in sample mean phenotypes induced by such mechanisms, however, can be demonstrated only by experiment.

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The emberizid genera Aimophila and Pipilo represent longstanding taxonomic conundrums. Each is comprised of subclades whose members appear to share diagnostic morphological and behavioral characters; however, relationships among sub-clades within each of these genera remain unclear, and numerous authors have suggested that either one or both of these genera may be polyphyletic. We addressed this taxonomic problem by sequencing and analyzing complete mitochondrial cytochrome-b and NADH dehydrogenase subunit 2 genes for all members of Aimophila and Pipilo along with 33 species representing 17 additional emberizid genera. Our maximum likelihood and Bayesian analyses indicate that both Aimophila and Pipilo are polyphyletic. Aimophila is divided into a minimum of three distinct groups. The forms notosticta, ruficeps, and rufescens are part of a well-supported clade that includes all members of Melozone and some members of Pipilo. Aimophila quinquestriata is placed within Amphispiza, and the remaining members of Aimophila are placed within a clade that includes all members of Arremonops and some members of Ammodramus. Within Pipilo, the ''rufous-sided'' and ''brown'' towhee groups do not form sister groups. Rather, the former are most closely related to the tropical genus Atlapetes whereas the latter are placed nearest Melozone and some Aimophila. Our analyses reject traditional taxonomic arrangements for both genera, and we present suggestions for a revised taxonomy for all members of Aimophila and Pipilo. These results provide further evidence of discordance among phylogenetic hypotheses based on morphological and molecular characters for groups of birds with generally conserved morphology.

The latitudinal gradient in species richness is a nearly universal ecological phenomenon. Similarly, conspecific genetic diversity often increases towards the equator -usually explained as the consequence of post-glacial range expansion or due to the shared response of genetic diversity to processes that promote species richness. However, no study has yet examined the relationship between latitude and within-population genetic diversity in exclusively tropical species. We surveyed genetic variation in nine resident bird species co-occurring in tropical lowlands between southern Mexico and western Ecuador, where avian species richness increases with decreasing latitude. Withinpopulation genetic variation was always highest at mid-range latitudes, and not in the most equatorial populations. Differences in demography and gene flow across species' ranges may explain some of our observations; however, much of the pattern may be due simply to geometric constraints. Our findings have implications for conservation planning and for understanding how biodiversity scales from genes to communities.

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Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where genetic structure can be driven by isolation by distance (IBD) and/or isolation by environment (IBE). Here, we used variation in ~1,600 high-quality SNPs derived from paired-end sequencing of double-digest restriction site-associated DNA (ddRAD-Seq) to test hypotheses related to IBD and IBE in the Yucatan jay (Cyanocorax yucatanicus), a tropical bird endemic to the Yucatán Peninsula. This peninsula is characterized by a precipitation and vegetation gradient-from dry to evergreen tropical forests-that is associated with morphological variation in this species. We found a moderate level of nucleotide diversity (π = .008) and little evidence for genetic differentiation among vegetation types. Analyses of neutral and putatively adaptive SNPs (identified by complementary genome-scan approaches) indicate that IBD is the most reliable explanation to account for frequency distribution of the former, while IBE has to be invoked to explain those of the later. These results suggest that selective factors acting along a vegetation gradient can promote local adaptation in the presence of gene flow in a vagile, nonmigratory and geographically restricted species. The putative candidate SNPs identified here are located within or linked to a variety of genes that represent ideal targets for future genomic surveys.