The ancestors of the archosaurs, a major branch of the diapsid reptiles, originated more than 240 MYA near the dawn of the Triassic Period. We used maximum likelihood phylogenetic ancestral reconstruction methods and explored different models of evolution for inferring the amino acid sequence of a putative ancestral archosaur visual pigment. Three different types of maximum likelihood models we...

We give a formal study of the relationships between the transition cost parameters and the generalized maximum parsimonious reconstructions of unknown (ancestral) binary character states {0,1} over a phylogenetic tree. As a main result, we show there are two thresholds λ¹n and λ⁰n , generally confounded, associated to each node n of the phylogenetic tree and such that there exists a maximum par...

Chimpanzees, but very few other animals, figure prominently in (recent) attempts to reconstruct the evolution of uniquely human traits. In particular, the chimpanzee is used (i) to identify traits unique to humans, and thus in need of reconstruction; (ii) to initialize the reconstruction, by taking its state to reflect the state of the last common ancestor of humans and chimpanzees; (iii) as a ...

Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tre...

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse pl...

This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate...

Comparative genomics, evolutionary biology, and cancer researches require tools to elucidate the evolutionary trajectories and reconstruct the ancestral genomes. Various methods have been developed to infer the genome content and gene ordering of ancestral genomes by using such genomic structural variants. There are mainly two kinds of computational approaches in the ancestral genome reconstruc...