Population Genetics Mechanisms on a Genomic Scale
Three papers from UC Davis have appeared on the PLoS journals in the past few days that bring together population genetics and genomic sequencing to address questions of importance to evolutionary biology. Their discussions of divergence in coding versus non-coding, and adaptive versus neutral shifts, are what caught my eye. Collectively, they’re three very densely packed studies, providing a fountain of info that only bioinformatics can process.
First, Alisha Holloway et al. found greater divergence in regions that may control gene expression, in the open access journal PLoS Genetics. They also found genes that had a high propensity for significant and recurrent divergence. Generally, genes with adaptive 3′-UTR or coding-sequcne evolution were found in the cytoplasm or are integral to the membrane. Their molecular functions are predominantly protein binding, nucleic acid binding, and translation related. The most common biological processes are related to response to stimuli, RNA regulation (binding, splicing, degradation), and metabolism.
Begun et al. extend these findings to look at patterns of polymorphism for nucleotides, small insertions, and small deletions along chromosome arms, in PLoS Biology. It’s far too much to explain here, other than to say that genome-wide population analyses are demonstrated to be powerful tools.
Lastly, Holloway and Begun then put their heads together for a paper in PLoS ONE. There, they identify regions with recurrent divergence of gene expression (adaptive selection, presumably) are associated with proteins of unknown functions.
From an evolutionary biology standpoint, these lend support to leaders in the area of evo-devo (e.g. Sean B. Carroll), through their points on selection of non-coding elements. Also, from a biomedical sciences perspective, we have a powerful new tool for predicting genes of interest to human health.
- Holloway AK, Lawniczak MKN, Mezey JG, Begun DJ, Jones CD. Adaptive gene expression divergence inferred from population genomics. PLoS Genet. 2007 Oct 26;3(10):2007-13. doi=10.1371/journal.pgen.0030187
- Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans. PLoS Biol. 2007 Nov 6;5(11):e310. doi=10.1371/journal.pbio.0050310
- Holloway AK, Begun DJ. Rampant Adaptive Evolution in Regions of Proteins with Unknown Function in Drosophila simulans. PLoS ONE. 2007 Oct 31;2(10):e1113. doi/10.1371/journal.pone.0001113
About the Author
Dan Rhoads
Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.
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