Comparative genomics of Bifidobacterium species isolated from marmosets and humans.

The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced.

The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates.

With the large collections of gene and genome sequences, there is a need to generate curated comparative genomic databases that enable interpretation of results in an evolutionary context. Such resources can facilitate an understanding of the co-evolution of genes in the context of a genome mapped onto a phylogeny, of a protein structure, and of interactions within a pathway. A phylogenetically indexed gene family database, the adaptive evolution database (TAED), is presented that organizes gene families and their evolutionary histories in a species tree context.

A unified model of autopolyploid establishment and evolution.

The prevalence of polyploidy among flowering plants is surprising given the hurdles impeding the establishment and persistence of novel polyploid lineages. In the absence of strong assortative mating, reproductive assurance, or large intrinsic fitness advantages, new polyploid lineages face almost certain extinction through minority cytotype exclusion. Consequently, much work has focused on a search for adaptive advantages associated with polyploidy such as increased competitive ability, enhanced ecological tolerances, and increased resistance to pathogens.

Neopolyploidy and diversification in Heuchera grossulariifolia.

Newly formed polyploid lineages must contend with several obstacles to avoid extinction, including minority cytotype exclusion, competition, and inbreeding depression. If polyploidization results in immediate divergence of phenotypic characters these hurdles may be reduced and establishment made more likely. In addition, if polyploidization alters the phenotypic and genotypic associations between traits, that is, the P and G matrices, polyploids may be able to explore novel evolutionary paths, facilitating their divergence and successful establishment.

Neopolyploidy and pathogen resistance.

Despite the well-documented historical importance of polyploidy, the mechanisms responsible for the establishment and evolutionary success of novel polyploid lineages remain unresolved. One possibility, which has not been previously evaluated theoretically, is that novel polyploid lineages are initially more resistant to pathogens than the diploid progenitor species. Here, we explore this possibility by developing and analysing mathematical models of interactions between newly formed polyploid lineages and their pathogens.

Antagonistic coevolution mediated by phenotypic differences between quantitative traits.

Many well-studied coevolutionary interactions between predators and prey or hosts and parasites are mediated by quantitative traits. In some interactions, such as those between cuckoos and their hosts, interactions are mediated by the degree of phenotype matching among species, and a significant body of theory has been developed to predict the coevolutionary dynamics and outcomes of such interactions. In a large number of other cases, however, interactions are mediated by the extent to which the phenotype of one species exceeds that of the other.