Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata: Scincidae).

The rapid increase in the ability to generate molecular data, and the focus on model-based methods for tree reconstruction have greatly advanced the use of phylogenetics in many fields. The recent flurry of new analytical techniques has focused almost solely on tree reconstruction, whereas alignment issues have received far less attention. In this paper, we use a diverse sampling of gene regions from lizards of the genus Mabuya to compare the impact, on phylogeny estimation, of new maximum likelihood alignment algorithms with more widely used methods.

Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata: Scincidae).

Skinks are the largest family of lizards and are found worldwide in a diversity of habitats. One of the larger and more poorly studied groups of skinks includes members of the subfamily Scincinae distributed in sub-Saharan Africa. Sub-Saharan African scincines are one of the many groups of lizards that show limb reduction and loss, and the genus Scelotes offers an excellent opportunity to look at limb loss in a phylogenetic context.