phylogenetics

Morphological characters are indispensable in phylogenetic analyses for understanding the pattern, process, and tempo of evolution. If …

Diversity of the mammalian olfactory receptor (OR) repertoire has been globally reshaped by niche specialization. However, little is …

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. …

How ecological opportunity relates to diversification is a central question in evolutionary biology. However, there are few empirical …

• A wide range of factors (developmental, physiological, ecological) with unpredictable inter- actions control variation in leaf form. …

Although the natural history of the Caribbean is better understood now than ever before, a general biogeographic explanation for the …

Despite recent genome-based advances in understanding Plasmodium molecular evolution and its relationship to disease mechanisms and potential drug development, the phylogenetics of the group is currently limited to single-gene analyses. Here we develop and analyze a set of >100 putative orthologous genes derived from genome comparisons. We aimed to minimize systematic errors that arise when reconstructing the Plasmodium phylogeny with a genome-scale data set by evaluating the congruence of different genes, optimality criteria, and models of sequence evolution with previous studies encompassing fewer characters and more species. Saturation in substitutions and bias in base frequencies at third-codon positions characterized most Plasmodium genes. Molecular evolution models that partitioned rates of change by codon position were best at accounting for these sequence characteristics, as were analyses of amino acid alignments. These methods also ameliorated, but did not entirely avoid, the impact of reduced taxon sampling on phylogeny. The use of these models and expanded taxon sampling are necessary to maximize detection of multiple substitutions, overcome compositional biases, and, ultimately, resolve with confidence the phylogeny of Plasmodium.

Two assumptions have framed previous systematic and biogeographic studies of the family Natalidae: that it comprises a few widespread species, and that extant lineages originated in Mexico and/or Central America. This study analyzes new sequence data from the mitochondrial cytochrome b and the nuclear Rag2, to clarify species boundaries and infer relationships among extant taxa. Fixed differences in cytochrome b coincide with published morphological characters, and show that the family includes at least eight species. One newly recognized species is known to live from a single locality in Jamaica, suggesting immediate conservation measures and underscoring the urgency of taxonomic revision. Among the three genera, Chilonatalus and Natalus form a clade, to the exclusion of Nyctiellus. This phylogeny and the geographic distribution of natalids, both extant and extinct, are hardly compatible with a Middle American origin for the group. Instead, extant natalids appear to have originated in the West Indies. The threat of Caribbean hurricanes early in their evolutionary history might account for the specialized cave roosting that characterizes all natalids, even continental species.

Vicariance and dispersal are the main hypotheses used to explain the distribution and diversification of taxa on both continents and …