Datasets for evolutionary comparative genomics

Abstract

Many decisions about genome sequencing projects are directed by perceived gaps in the tree of life, or towards model organisms. With the goal of a better understanding of biology through the lens of evolution, however, there are additional genomes that are worth sequencing. One such rationale for whole-genome sequencing is discussed here, along with other important strategies for understanding the phenotypic divergence of species.

Figure 1

A standard rooted phylogenetic tree of eutherian mammals [5]. It indicates the branches where the aquatic species, seals, whales, and manatees, evolved together with their closest relatives that do (in bold) or do not (plain text) have complete genome sequencing projects. Some relationships are indicated in non-binary nodes where the branching order is not clear.

Figure 2

The evolution of cichlid fish. (a) A phylogenetic tree adapted with permission from [7] indicates the origin of Lake Malawi and Lake Victoria cichlids from a single lineage of Lake Tanganyika cichlids; the bracket indicates the Lake Tanganyika and riverine cichlids. MYA, millions of years ago; numbers of species are indicated in parentheses; all species shown are cichlids. (b) A single lineage from the diverse cichlid species of Lake Tanganyika (left) recapitulates a diverse group of cichlid species in Lake Malawi (right) from a single lineage. Many of the Lake Malawi cichlids evolved to fill similar niches to more distantly related species in Lake Tanganyika, and species in similar niches have a surprisingly similar appearance (reproduced from [8] with permission from Roberto Osti).

Figure 3

The relationship of polar bears to other bears. (a) A rooted phylogenetic tree adapted from [11]. Polar bears are thought to have diverged from brown bears from the ABC Islands in Canada after these brown bears had diverged from other brown bears. Black bears and other bear species are more distantly related to both polar bears and brown bears. The pictures show (b) a brown bear (not from the ABC islands) (Ursus arctos) and (c) a polar bear (Ursus maritimus). Original bear images courtesy of Peter Haase, Carl Lund and Michael Petersen (Copenhagen Zoo).