Systematics and the Origin of Species On Ernst Mayr's 100th Anniversary (2005) / Chapter Skim
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12 Examining Bacterial Species Under the Specter of Gene Transfer and Exchange--HOWARD OCHMAN, EMMANUELLE LERAT, AND VINCENT DAUBIN
12 Examining Bacterial Species Under the Specter of Gene Transfer and Exchange--HOWARD OCHMAN, EMMANUELLE LERAT, AND VINCENT DAUBIN
Pages 229-242
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From page 229... ...
By adopting a whole-genome approach, which examined the history of every gene in numerous bacterial genomes, we show that LGT does not hamper phylogenetic reconstruction at many of the shallower taxonomic levels. Despite the high levels of gene acquisition, the only taxonomic group for which appreciable amounts of homolo gous recombination were detected was within bacterial species.
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From page 230... ...
These new data allow us to follow the origin and ancestry of every gene in a genome to resolve the degree to which gene transfer has shaped the contents of bacterial genomes and has obscured the history of bacterial groups at different phylogenetic depths. THE SCOPE OF GENE TRANSFER IN BACTERIA There are several means by which bacteria can acquire genes: by conjugal transfer, by phage-mediated insertions and by the update of native DNA from the outside sources (Ochman et al., 2000; Redfield, 2001)
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From page 231... ...
Because acquired regions often manifest multiple features that denote their ancestry, it is thus not perhaps surprising that many genes with sporadic distributions, as might occur from a history of lateral transfer, have anomalous base compositions. To illustrate the utility and accuracy of these methods for recognizing acquired genes, Fig.
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From page 232... ...
But this method divulges predominantly one class of acquired sequences, i.e., unique genes obtained from very divergent sources, and might vastly underestimate the full extent of LGT-affecting bacterial genomes. Gene exchange can also occur between close relatives and/or between genes that are conserved among organisms.
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From page 233... ...
Thus, there is a need to establish whether LGT is resorting the genes in bacterial genomes, eradicating the vestiges of bacterial species, and confounding attempts at phylogenetic classification. To assess the extent to which LGT is linked phylogenetic disruption, we considered the relationship between DNA acquisition and phylogenetic incongruence in fully sequenced bacteria at several taxonomic levels, including that occurring within species (E.
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. DETERMINANTS OF GENE EXCHANGE IN BACTERIAL SPECIES Despite the massive influx of new genes into bacterial genomes, the only taxonomic group for which appreciable amounts of homologous recombination were detected was within bacterial species.
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. If similar mechanisms that limit homologous recombination are operating in other taxa, then bacterial species can be viewed as assemblages of lineages that are sufficiently closely related to potentially exchange shared genes.
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Bacterial species are typically recognized according to their cellular properties and metabolic capabilities; for example, E coli, a mammalian commensal, ferments lactose but not citrate, whereas Salmonella enterica, a mammalian pathogen, is lactose negative and citrate positive.
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(A) Neighbor-joining tree based on the concatenation of 205 singlecopy genes common to all 13 Gammaproteobacterial species.
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From page 238... ...
. These groupings are the result of a nonarbitrary process of gene acquisition in which divergent organisms serve as a persistent source of novel genes in a genome, and the levels of recombinational exchange among homologs shared by related species are low.
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239 13 2 were 205 00 00.98 tree. 12 Different 98 05 05.10 Orthologs reference with shown.
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(1997) Using codon usage to predict genes origin: Is the Escherichia coli outer membrane a patchwork of products from different genomes?
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(1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
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(1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon.
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