BACKGROUND AND AIMS Angiosperms with simple vessel perforations have evolved many times independently of species having scalariform perforations, but detailed studies to understand why these transitions in wood evolution have happened are lacking. We focus on the striking difference in wood anatomy between two closely related genera of Adoxaceae, Viburnum and Sambucus, and link the anatomical d...

Using parsimony to reconstruct ancestral character states on a phylogenetic tree has become a popular method for testing ecological and evolutionary hypotheses. Despite its popularity, the assumptions and uncertainties of reconstructing the ancestral states of a single character have received less attention than the much less challenging endeavor of reconstructing phylogenetic trees from many c...

We tested the hypothesis that early Pliocene Australopithecus anamensis was ancestral to A. afarensis by conducting a phylogenetic analysis of four temporally successive fossil samples assigned to these species (from earliest to latest: Kanapoi, Allia Bay, Laetoli, Hadar) using polarized character-state data from 20 morphological characters of the dentition and jaws. If the hypothesis that A. a...

We present an efficient and flexible method for computing likelihoods for phenotypic traits on a phylogeny. The method does not resort to Monte Carlo computation but instead blends Felsenstein's discrete character pruning algorithm with methods for numerical quadrature. It is not limited to Gaussian models and adapts readily to model uncertainty in the observed trait values. We demonstrate the ...

Island systems have long been useful models for understanding lineage diversification in a geographic context, especially pertaining to the importance of dispersal in the origin of new clades. Here we use a well-resolved phylogeny of the flowering plant genus Cyrtandra (Gesneriaceae) from the Pacific Islands to compare four methods of inferring ancestral geographic ranges in islands: two develo...

Despite the extensive diversity of bacteria and their importance to fundamental functioning terrestrial ecosystems, distribution patterns are still not fully known. To fill gap further understand biogeographic in bacteria, we investigated phylogeographic structure underlying drivers diversification among populations cyanobacterium Microcoleus spp. The phylogenetic history was reconstructed usin...

Resurrecting ancestral proteins in the laboratory can be a powerful tool in studies of protein structure and function as they can offer a rare glimpse into the evolutionary history of molecular function (Malcolm et al., 1990; Adey et al., 1994; Chandrasekharan et al., 1996; Dean and Golding, 1997; Bishop et al., 2000; Chang and Donoghue, 2000; Sun et al., 2002; Zhang and Rosenberg, 2002; Thornt...

UNLABELLED A population of human immunodeficiency virus (HIV) within a host often descends from a single transmitted/founder virus. The high mutation rate of HIV, coupled with long delays between infection and diagnosis, make isolating and characterizing this strain a challenge. In theory, ancestral reconstruction could be used to recover this strain from sequences sampled in chronic infection;...

Detailed biogeographic studies of pantropical clades are still relatively few, and those conducted to date typically use parsimony or event-based methods to reconstruct ancestral areas. In this study, a recently developed likelihood method for reconstructing ancestral areas (the dispersal-extinction cladogenesis [DEC] model) is applied to the angiosperm family Simaroubaceae, a geographically wi...