Approximate Bayesian computation reveals the factors that influence genetic diversity and population structure of foxsnakes.

Contemporary geographical range and patterns of genetic diversity within species reflect complex interactions between multiple factors acting across spatial and temporal scales, and it is notoriously difficult to disentangle causation. Here, we quantify patterns of genetic diversity and genetic population structure using mitochondrial DNA sequences (101 individuals, cytochrome b) and microsatellites (816 individuals, 12 loci) and use Approximate Bayesian computation methods to test competing models of the demographic history of eastern and western foxsnakes. Our analyses indicate that post-glacial colonization and past population declines, probably caused by the infilling of deciduous forest and cooler temperatures since the mid-Holocene, largely underpin large-scale genetic patterns for foxsnakes. At finer geographical scales, our results point to more recent anthropogenic habitat loss as having accentuated genetic population structure by causing further declines and fragmentation.

Phylogeny of the Colubroidea (Serpentes): new evidence from mitochondrial and nuclear genes.

The Colubroidea contains over 85% of all the extant species of snakes and is recognized as monophyletic based on morphological and molecular data. Using DNA sequences (cyt b, c-mos) from 100 species we inferred the phylogeny of colubroids with special reference to the largest family, the Colubridae. Tree inference was obtained using Bayesian, likelihood, and parsimony methods. All analyses produced five major groups, the Pareatidae, Viperidae, Homalopsidae, the Elapidae, and the Colubridae. The specific content of the latter two groups has been altered to accommodate evolutionary history and to yield a more stable taxonomy. We propose an updated classification based on the reallocation of species as indicated by our inferred phylogeny.

Gene conversions may obscure actin gene family relationships.

Phylogenetic hypotheses of muscle actin evolution are significantly different when a sea urchin is used as a representative echinoderm than when a sea star is used. While sea urchin muscle actins support an echinoderm-chordate sister relationship, sea star sequences suggest that echinoderm muscle actins are convergent with chordate muscle actins. Our results suggest that gene conversion in the sea star muscle actin may be responsible for these discordant results.

New directions in biogeography?

The deduction of biogeographic process from the study of its history is complicated by the fact that history is a singular thing. This singularity allows no estimation of the degree of determinism surrounding the realization of biogeographic processes, and consequently we know almost nothing about the generality of such deductions. Here we discuss a new approach, called 'experimental biogeography', that exploits computers to model faunal build-up repeatedly against a fixed vicariant background over ecological and evolutionary time scales. This new approach enables a biogeographer to be omniscient - to know both vicariant history and actual phylogeny. Moreover, history can be replayed repeatedly to accumulate a sample of multiple phylogenies and to estimate probability density functions for biogeographic variables. Roles of stochastic, historical and ecological processes in adaptive radiations can also be assessed. Experimental biogeography allows examination of the reliability of various methods of recovering historical patterns.

The phylogeny of xantusiid lizards: the concern for analysis in the search for a best estimate of phylogeny.

In the onrush of molecular-based phylogenetic hypotheses, previous morphological-based phylogenies are being ignored, discarded, or even treated with disdain. Coupled with this implicit superiority of molecular data is the sometimes tendency to construct a phylogeny from the molecular data with less than analytical rigor. This paper examines the phylogenetic relationships within the lizard family Xantusiidae employing both molecular and morphological data. The analysis focuses on four analytical points of the molecular data and on the phylogenetics synthesis of the two data sets. We conclude that the phylogeny of xantusiid lizards is not yet a robust hypothesis.