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All rights reserved. doi:10.1016/j.tim.2006.02.010 Genome Analysis The Neolithic revolution of bacterial genomes Alex Mira, Ravindra Pushker and Francisco Rodrı´guez-Valera Evolutionary Genomics Group, Division of Microbiology, Universidad Miguel Hernandez, San Juan 03550, Alicante, Spain Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. Certain genomic characteristics of prokaryotes can be used to study the impact of ancient human activities on microorganisms. By analyzing DNA sequence similarity features of transposable elements, dramatic genomic changes have been identified in bacteria that are associated with large and stable human communities, agriculture and animal domestication: three features unequivocally linked to the Neolithic revolution. It is hypothesized that bacteria specialized in human-associ- ated niches underwent an intense transformation after the social and demographic changes that took place with the first Neolithic settlements. These genomic changes are absent in related species that are not specialized in humans. The Neolithic revolution Before the Neolithic period, human survival was linked to the hunter-gatherer culture and populations were small and scattered [1]. Approximately 10 000 years ago, however, the advent of agriculture and animal husbandry brought the largest social revolution in the history of humankind [2]. Food resources were more abundant and constant, and the human species increased its population size at an extraordinary annual growth rate of 0.1% [3]. From the point of view of bacterial pathogens, humans suddenly became attractive hosts; they concentrated large populations on limited areas, which maximized the chance for transmission between longer-lived carriers. Thus, it is likely that human population growth and expansion during the Neolithic created a selective pressure that favoured pathogens that specialized in human hosts, originating what was probably the first wave of emerging human diseases [4]. One of the features that has emerged from fully sequenced genomes is that species that have specialized their niche undergo a process of reductive evolution through gene elimination [5–8]. Mobile elements such as insertion sequences (ISs) greatly increase in number following host restriction [9] and influence the process of genome reduction. After a niche change, many genes become obsolete and the selective pressure to preserve their function is dramatically reduced. In addition, host restriction can reduce the efficiency of selection in bacterial specialists because of reduced population sizes and genetic drift [10,11]. ISs might inactivate unnecessary or redundant genes in the new environment [12,13] by rapidly increasing the number of IS copies. The number of IS elements in bacterial pathogens could, therefore, indicate a recent host adaptation [14] or restriction [9]. Here, we show that recent expansions of ISs in bacteria are associated with humans or human activities that were developed in the Neolithic. The cultural revolution of the Neolithic can be dated precisely (for evolutionary time scales) at w10 000 years before present, which provides an outstanding model for prokaryotic evolution in the short-to-medium time scale. Recent expansions of mobile elements We investigated paralogous genes, including IS elements, across 255 fully sequenced prokaryotic genomes. Para- logues are defined as protein-coding sequences within a genome that have at least 30% sequence identity over Corresponding author: Mira, A. (alex.mira@umh.es). Available online 29 March 2006 Update TRENDS in Microbiology Vol.14 No.5 May 2006 200 www.sciencedirect.com