The purpose of this forum is to introduce notable papers and books published by you and other persons. The work can be new or old, but it should be of wide interest and high quality. A brief comment on the significance of the work should be attached. The current categories of the subjects are (1) adaptation, (2) behavioral evolution, (3) dosage compensation, (4) evo-devo, (5) gene evolution, (6) genomic evolution, (7) molecular phylogeny, (8) natural selection, (9) phenotypic evolution, (10) sensory receptors, (11) sex chromosomes, (12) sex determination, (13) speciation, (14) symbiosis and evolution, and (15) horizontal gene transfer. However, new categories can be added if necessary. Emphasis will be given on the biological work rather than on the mathematical. Any person may post a paper by sending it to one of the editors listed below. We also welcome your comments on posted work, but we moderate all the comments to control spam. This forum is primarily for scientific discussion and to construct a database for good molecular evolution papers.

Friday, April 6, 2012

The Phylogeny and Timing of Mammalian Evolution

Contributed by: Blair Hedges

Until the mid-1990s, our understanding of mammal phylogeny and timescale was largely guided by the fossil record. Those data told us, for example, that all mammals with hoofs, such as horses and elephants, were related, and that most ordinal splits among living placentals occurred after the dinosaurs went extinct 66 million years ago (mya). Molecular sequence evidence altered this view by showing that there are continental-scale groups of mammals (1) and deep, Cretaceous, divergences among orders (2,3). By about 10 years ago, this New View of mammal evolution began to stabilize (4).

Against this backdrop, Bininda-Emonds et al. (5) published a supertree analysis of mammal evolution in 2007 that captured people's attention because it included 99% of the 4500 species (although one-third of the species had no data, so were "interpolated"). It did not challenge the major components of the New View, including deep Cretaceous divergences among orders, but they found a curious spike in diversification during the Eocene (~50 mya) that they dubbed the "delayed rise in mammals." Recently, Meredith et al. (6), assembled the largest sequence data set so far (35,603 base pairs, in 164 taxa) and their results do not agree with those of Bininda-Emonds et al. (5). They used a supermatrix (concatenated genes) analysis, finding differences in both the tree topology and timescale (see illustration). Most notably, they did not find a "delayed rise" or as many deep, intra-ordinal splits ("short fuses").

Some would view these differences merely as "fine-tuning" of New View of mammal evolution. Nonetheless, they relate to mechanisms of diversification and therefore are of general interest. Without picking sides, I raise some questions here for discussion. Is a timed supermatrix analysis better than a timed supertree analysis? How many species can be "interpolated" in a study before the interpolation affects the results? What proportion of total lineages (e.g., species) is needed in a study before patterns of diversification can be accurately studied?

Abstract (Meredith et al., 2011): Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

1. Springer, M.S., et al. 1997. Endemic African mammals shake the phylogenetic tree. Nature 388:61-63.
2. Hedges, S.B., et al. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229.
3. Kumar, S. and S.B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
4. Murphy, W.J., et al. 2001. Molecular phylogenetics and the origins of placental mammals. Nature, 2001. 409(6820):614-618.
5. Bininda-Emonds, O.R.P., et al. 2007. The delayed rise of present-day mammals. Nature 446(7135):507-512.

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