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Comment on "The Origins of Genome Complexity" Vincent Daubin and Nancy A. Moran Science 306, 978 (2004); DOI: 10.1126/science.1098469

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TECHNICAL COMMENT
Comment on ‘‘The Origins of Genome Complexity’’
Lynch and Conery (1) argued that genome
complexity reflects a history ofgenetic drift caused by small genetic population size (Ne), which in turn enables the spread of mildly deleterious selfish elements and duplications. Under this argument, large organisms, which tend to have small Ne, also exhibit larger (complex) genomes, and the small size of bacterial genomes reflects their position at the extreme large end of the range for Ne. Genome size can vary among bacteria byat least an order of magnitude, but the fraction of noncoding DNA is consistently low (È15%). Consequently, larger bacterial genomes are expected to result from more selection, because they maintain more functional DNA. Indeed, large genome size in bacteria commonly has been considered an adaptation to changing environments (2–6). Furthermore, small Ne in symbiotic bacteria appears to result inreduced genomes through gene loss (7, 8). Thus, the relation between Ne and genome size in bacteria is, if anything, expected to be the opposite of that proposed by Lynch and Conery (1). The claimed relationship between Ne and genome size is based on inferring Neu (where u is the mutation rate per nucleotide) from estimates of polymorphism using sequence divergences among isolates (1). Thisapproach, however, has several drawbacks, which are especially severe in bacteria. One concern is the assumption of similar mutation rates across bacteria, which is required if estimates of Neu are interpreted as directly reflecting variation in Ne. Lynch and Conery (1) justify this assumption by citing a survey (9) that included only a single bacterial strain; other evidence indicates that bacteriallineages vary substantially in mutation rates (10)—as would be expected, because their genomes differ markedly in content of genes known to impact mutation. Thus, polymorphism levels reflect mutational input as well as Ne. Even more problematic is the assumption that taxonomic names correspond to cohesive species, which is implicit in the use by Lynch and Conery (1) of polymorphism data to estimate...