The repatterning of eukaryotic genomes by random genetic drift

Abstract

Recent observations on rates of mutation, recombination, and random genetic drift highlight the dramatic ways in which fundamental evolutionary processes vary across the divide between unicellular microbes and multicellular eukaryotes. Moreover, population-genetic theory suggests that the range of variation in these parameters is sufficient to explain the evolutionary diversification of many aspects of genome size and gene structure found among phylogenetic lineages. Most notably, large eukaryotic organisms that experience elevated magnitudes of random genetic drift are susceptible to the passive accumulation of mutationally hazardous DNA that would otherwise be eliminated by efficient selection. Substantial evidence also suggests that variation in the population-genetic environment influences patterns of protein evolution, with the emergence of certain kinds of amino-acid substitutions and protein-protein complexes only being possible in populations with relatively small effective sizes. These observations imply that the ultimate origins of many of the major genomic and proteomic disparities between prokaryotes and eukaryotes and among eukaryotic lineages have been molded as much by intrinsic variation in the genetic and cellular features of species as by external ecological forces.

Figure 1

A compilation of estimates of the average amount of recombination per unit of physical distance in eukaryotic genomes, derived from 137 meiotic genetic maps. The diagonal lines have slopes of −1.

Figure 2

The scaling of genome content with genome size across ~150 eukaryotes. The full data set is available from the authors upon request. Note that the pool of intronic DNA can contain mobile elements and/or pseudogenes. Abbreviation: LTR, long terminal repeat.

Figure 3

The distribution of protein-complex types into three broad taxonomic assemblages. Relative frequencies of the three main classes of protein structures were obtained from data deposited in 3D Complex.org v2.0 (53, 54), based primarily on taxa for which at least 20 records were available. Sample sizes are 3,545, 628, and 4,125 for eubacteria, unicellular eukaryotes, and vertebrates, respectively.