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by: Dr. Jayda Mayert


Dr. Jayda Mayert
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Class Notes
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This 2 page Class Notes was uploaded by Dr. Jayda Mayert on Saturday September 12, 2015. The Class Notes belongs to MIBO 8610 at University of Georgia taught by Staff in Fall. Since its upload, it has received 52 views. For similar materials see /class/202393/mibo-8610-university-of-georgia in Microbiology at University of Georgia.




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Date Created: 09/12/15
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY Oct 1997 p 114571156 002077139704000 Copyright 1997 International Union of Microbiological Societies Vol 47 No 4 Discovery and Classi cation of Ecological Diversity in the Bacterial World the Role of DNA Sequence Data THOMAS PALYS1 L K NAKAMURA2 AND FREDERICK M COHANlquot Department of Biology Wesleyan University Middletown Connecticut 0645901701 and Microbial National Center for Agricultural Utilization Researc Properties Research Agricultural Research Service US Department of Agriculture Peoria Illinois 616042 All living organisms fall into discrete clusters of closely related individuals on the basis of gene sequence similarity Evolutionary genetic theory predicts that in the bacterial world each sequence similarity cluster should correspond to an ecologically distinct population Indeed surveys of sequence diversity in protein coding genes show that sequence clusters correspond to ecological populations Future population surveys of proteincoding gene sequences can be expected to disclose many previously unknown ecological populations of bacteria Sequence similarity clustering in proteincoding genes is recommended as a primary criterion for demarcating taxa For two decades systematists have applied wholegenome hybridization as a universal criterion for demarcating species of bacteria systematists have widely recognized bacterial spe cies as phenotypically distinct groups of strains with 70 or greater annealing of genomic fragments in DNADNA hybrid ization 36 85 This criterion has been widely used because it can be easily applied to any taxon and most importantly the groupings of bacteria based on DNADNA hybridization are often the same as those based on phenotypic characters and ecology 36 However it is becoming increasingly evident that any par ticular cutoff value such as 70 is arbitrary and not guar anteed to yield groups of bacteria that correspond to real ecological units 82 Also it is not clear what determines the fraction of genomic segments that anneal in hybridization ex periments 82 but see reference 43 is it the fraction of genes that are shared or the sequence similarity at shared gene loci Accordingly no evolutionary genetic theory predicts why groups of strains with greater than 70 annealing should cor respond to ecologically distinct populations There is however another molecular approach that may provide a universal criterion for classifying bacterial diversity This approach relies on the observation that all living organ isms both prokaryotic and eukaryotic fall into clusters of closely related organisms based on the sequence similarity of shared genes 1 15 48 That is bacteria and other organisms fall into clearly distinct sequence clusters where the average sequence divergence between strains of different clusters is far greater than the average divergence between strains of the same cluster Recent theory has suggested that each sequence similarity cluster observed in the bacterial world might corre spond to an ecologically distinct population 14 15 17 18 If this conjecture is correct then a classi cation system based on sequence clusters would have a theoretical grounding that is lacking in the genomic hybridization approach In this study we will demonstrate that the DNA sequences of proteincoding genes are more effective than DNADNA hybridization for classifying the ecological diversity of bacteria We rst extend the theoretical argument of Cohan 14 that Corresponding author Mailing address Department of Biology Wesleyan University 237 Church St Middletown CT 064590170 Phone 860 6853482 Fax 860 6852141 Email FCohanWes leyan edu 1145 each sequence cluster in the bacterial world should correspond to an ecologically distinct population We then present empir ical evidence that sequences of proteincoding genes have suc cessfully separated populations of bacteria into distinct se quence similarity clusters that correspond to ecological units Finally we argue that taxon demarcations should be based on the sequence similarity clusters emerging from sequence sur veys of proteincoding genes Theoretical background A model of sequence divergence in bacteria must take into account that the genes typically se quenced by bacterial systematists eg 16S rRNA nucleic acid polymerases and ribosomal proteins are not likely to be in volved in ecological differences between bacterial populations Many of these genes appear to perform the same housekeep ing duties in every species as alleles of these genes are func tionally interchangeable across taxa 35 51 63 73 89 A model of sequence diversity must also take into account the fact that nearly all nucleotide substitutions and amino acid substitutions detected in surveys are likely to be neutral in their tness effects 40 Therefore the patterns of sequence divergence observed by systematists largely involve substitu tions that have no tness consequence in genes that are not involved in populationspeci c adaptations Cohan 14 16 has developed a model of neutral sequence divergence within and between ecological populations of bac teria The model posits that each adaptive mutation within a population confers a competitive advantage upon a mutant cell and its clonal or nearly clonal descendants this advantage allows the mutants to replace all competing cells of the same population However because different populations use at least somewhat different resources an adaptive mutant from one population is not expected to outcompete members of other populations even if the populations are sympatric In this model an ecological population is de ned as the domain of competitive superiority of an adaptive mutant This de nition leads to two predictions about sequence di vergence within and between ecological populations 14 15 First natural selection favoring each adaptive mutation in a given population is expected to purge that population of its genetic diversity at all loci This is because recombination is rare in bacteria 50 69 75 86 so that the entire genome originally associated with the adaptive mutation remains intact as it sweeps through the population Therefore the population loses all or nearly all its genetic diversity at all loci This


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