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known as evolution-development (“evo-devo”) addresses how the evolving genomes of diverse taxa are epigenetically modified and otherwise regulated during ontogeny to yield particular organismal phenotypes, including complex adaptations (Carroll et al., 2004; Avise and Ayala, 2007). The evo-devo paradigm will continue to motivate scientific interest and generate vast research opportunities for the foreseeable future.

Here, I discuss three other areas of opportunity for molecular genetics in evolutionary biology, specifically in the realms of phylogenetics and conservation. For each of these three topics in a discipline that I call “biodiversity genetics,” I first summarize conventional wisdom, but then I intend to be provocative by raising scientific proposals that currently are far from mainstream but nevertheless have the potential to invigorate and perhaps even reshape the biodiversity sciences.



Legions of biologists are currently gathering extensive molecular genetic data as part of a grand collective effort to reconstruct, once and for all, the history of life on Earth (Cracraft and Donoghue, 2004). Guiding this endeavor is the powerful conceptual metaphor of a phylogenetic tree, popularized by Ernst Haeckel in 1866. Within the next decade or two, major branches and numerous twigs in the Tree of Life will be reconstructed (nearly as accurately as may ever become possible given the finite size of genomes and the relative ease by which DNA sequence data can now be gathered). The Tree of Life project will have completed its initial descriptive mission when it enters a more mature phase in which the gains in phylogenetic understanding about species’ relationships, per unit of sequencing effort, will gradually diminish.

In the meantime, goals of the exuberant young Tree of Life initiative are to estimate not only branch topologies but also the evolutionary dates of various internal nodes (Hedges and Kumar, in press). Molecular “clocks” will play a key role. Rates of DNA sequence evolution are known to be highly variable across lineages and loci (Li, 1997), but experience indicates that when clocks are carefully calibrated and the dates they imply are compiled across dozens or even hundreds of unlinked loci, approximate origination times can be recovered for particular clades (Kumar and Hedges, 1998; Kumar, 2005). The calibrations normally require secure temporal reference points from independent evidence, e.g., from paleontology or biogeography. Thus, estimating absolute dates as well as branch topologies in phylogenetic trees is inherently an integrative endeavor that should engage many of the biodiversity sciences.

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