The effect of natural selection on phylogeny reconstruction algorithms

Abstract. We study the effect of natural selection on the performance of phylogeny reconstruction algorithms using Avida, a software platform that maintains a population of digital organisms (self-replicating computer programs) that evolve subject to natural selection, mutation, and drift. We compare the performance of neighbor-joining and maximum parsimony algorithms on these Avida populations to the performance of the same algorithms on randomly generated data that evolve subject only to mutation and drift. Our results show that natural selection has several specific effects on the sequences of the resulting populations, and that these effects lead to improved performance for neighbor-joining and maximum parsimony in some settings. We then show that the effects of natural selection can be partially achieved by using a non-uniform probability distribution for the location of mutations in randomly generated genomes.

Comparative genomics in the triticeae

International audienceThe genomes of grasses are very different in terms of size, ploidy level and chromosome number. Among them, the Triticeae species (wheat, barley, rye) have some of the largest and complex genomes. Comparative mapping studies between rice, maize, sorghum, barley and wheat have pioneered the field of plant comparative genomics a decade ago. They showed that the linear order (colinearity) of genetic markers and genes is very well conserved opening the way to accelerated map-based cloning and defining rice as a model for grasses. More recently, the availability of BAC libraries and large sets of genomic sequences including the completion of the rice genome have permitted micro-colinearity studies that revealed rearrangements between the grass genomes and provided some insights into mechanisms that have shaped their genome during evolution. This review summarizes a decade of comparative genomics Studies In grasses with a special emphasis on the wheat and barley genomes