Evolution: Family tree for γ-proteobacteria
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HIGHLIGHTS NATURE REVIEWS | MICROBIOLOGY VOLUME 1 | DECEMBER 2003 | 1 HIGHLIGHT ADVISORS ADRIANO AGUZZI UNIVERSITY HOSPITAL OF ZÜRICH, ZÜRICH, SWITZERLAND NORMA ANDREWS YALE UNIVERSITY SCHOOL OF MEDICINE, NEW HAVEN, CT, USA ARTURO CASADEVALL THE ALBERT EINSTEIN COLLEGE OF MEDICINE, BRONX, NY, USA CECILIA CHENG-MAYER ROCKEFELLER UNIVERSITY, NEW YORK, NY, USA RITA COLWELL UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE, BALTIMORE, MD, USA STANLEY FALKOW STANFORD UNIVERSITY SCHOOL OF MEDICINE, STANFORD, CA, USA TIMOTHY FOSTER TRINITY COLLEGE, DUBLIN, IRELAND KEITH GULL UNIVERSITY OF OXFORD, OXFORD, UK NEIL GOW UNIVERSITY OF ABERDEEN, ABERDEEN, UK HANS-DIETER KLENK PHILIPPS UNIVERSITY, MARBURG, GERMANY BERNARD MOSS NIAID, NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD, USA JOHN REX ASTRAZENECA, CHESHIRE, UK DAVID ROOS UNIVERSITY OF PENNSYLVANIA, PHILADELPHIA, PA, USA PHILIPPE SANSONETTI INSTITUT PASTEUR, PARIS, FRANCE CHIHIRO SASAKAWA UNIVERSITY OF TOKYO, TOKYO, JAPAN ROBIN WEISS UNIVERSITY COLLEGE LONDON, LONDON, UK The availability of whole-genome sequences for increasing numbers of related species makes studying evolu- tionary genetics in bacteria an attrac- tive prospect. By comparing sequence data between species in a group, the key genomic changes that led to the diversification of different species can be identified. But the high levels of lateral gene transfer (LGT) in bacte- ria, by which genetic material can be transferred between distantly related species, have cast doubt on whether accurate phylogenetic trees — a cru- cial starting point for studies of evo- lutionary genetics — could ever be drawn up for bacteria. In a recent paper, Nancy Moran and colleagues have now shown that reliable bacter- ial phylogenetic trees can be con- structed using a method that mini- mizes the impact of LGT events to determine taxonomic relationships among the γ-proteobacteria. The γ-proteobacteria are a diverse group that include free-living, patho- genic and endosymbiotic members, and more complete genome sequences are available for these organisms than for any other group of bacterial species. But the γ-pro- teobacteria also show an extremely high tendency for LGT. The most accurate way to determine phyloge- netic relationships between species is to compare the sequences of as many genes as possible that are common to all the members of the group being studied. But if this analysis includes genes that have been passed on by LGT rather than by vertical transmis- sion from one generation to the next, the results will be skewed, making it look like certain species are more closely related than they really are. Moran and colleagues attempted to construct a phylogenetic tree for the γ-proteobacteria using only sin- gle-copy orthologous genes — genes present in different species that have evolved from a single ancestor, but have become different from each other over time — to infer taxonomic relationships. Surprisingly, consider- ing the high level of LGT reported for this group, they found that out of 205 such gene families analysed, 203 were consistent with the same predicted family tree. Further analysis of the only two families that disagreed with the consensus tree showed that both of these are highly likely to have undergone LGT, explaining the differ- ent phylogenies for these genes. These results indicate that single-copy orthologues only very rarely undergo LGT events and can therefore be reli- ably used to determine taxonomic relationships between related species. This approach provides a new method for constructing accurate phyloge- netic trees for bacterial species, which will allow the changes that have dri- ven the diversification of bacterial genomes to be determined and ulti- mately shed light on the processes by which new species evolve. Louisa Flintoft References and links ORIGINAL RESEARCH PAPER Lerat, E., Daubin, V. & Moran, N. A. From gene trees to organismal phylogeny in prokaryotes: the case of the γ-proteobacteria. PLoS Biol. 1, 1–10 (2003) WEB SITE Nancy Moran’s laboratory: http://eebweb.arizona.edu/faculty/moran/lab/pag es/index2.html Family tree for γ-proteobacteria EVOLUTION
Transcript of Evolution: Family tree for γ-proteobacteria
HIGHLIGHTS
NATURE REVIEWS | MICROBIOLOGY VOLUME 1 | DECEMBER 2003 | 1
HIGHLIGHT ADVISORS
ADRIANO AGUZZIUNIVERSITY HOSPITAL OFZÜRICH, ZÜRICH, SWITZERLAND
NORMA ANDREWSYALE UNIVERSITY SCHOOL OFMEDICINE, NEW HAVEN, CT, USA
ARTURO CASADEVALLTHE ALBERT EINSTEIN COLLEGEOF MEDICINE, BRONX, NY, USA
CECILIA CHENG-MAYERROCKEFELLER UNIVERSITY,NEW YORK, NY, USA
RITA COLWELLUNIVERSITY OF MARYLANDBIOTECHNOLOGY INSTITUTE,BALTIMORE, MD, USA
STANLEY FALKOWSTANFORD UNIVERSITYSCHOOL OF MEDICINE,STANFORD, CA, USA
TIMOTHY FOSTERTRINITY COLLEGE, DUBLIN,IRELAND
KEITH GULLUNIVERSITY OF OXFORD,OXFORD, UK
NEIL GOWUNIVERSITY OF ABERDEEN,ABERDEEN, UK
HANS-DIETER KLENKPHILIPPS UNIVERSITY,MARBURG, GERMANY
BERNARD MOSSNIAID, NATIONAL INSTITUTES OFHEALTH, BETHESDA, MD, USA
JOHN REXASTRAZENECA, CHESHIRE, UK
DAVID ROOSUNIVERSITY OF PENNSYLVANIA,PHILADELPHIA, PA, USA
PHILIPPE SANSONETTIINSTITUT PASTEUR, PARIS, FRANCE
CHIHIRO SASAKAWAUNIVERSITY OF TOKYO, TOKYO, JAPAN
ROBIN WEISSUNIVERSITY COLLEGE LONDON,LONDON, UK
The availability of whole-genomesequences for increasing numbers ofrelated species makes studying evolu-tionary genetics in bacteria an attrac-tive prospect. By comparing sequencedata between species in a group, thekey genomic changes that led to thediversification of different species canbe identified. But the high levels oflateral gene transfer (LGT) in bacte-ria, by which genetic material can betransferred between distantly relatedspecies, have cast doubt on whetheraccurate phylogenetic trees — a cru-cial starting point for studies of evo-lutionary genetics — could ever bedrawn up for bacteria. In a recentpaper, Nancy Moran and colleagueshave now shown that reliable bacter-ial phylogenetic trees can be con-structed using a method that mini-mizes the impact of LGT events todetermine taxonomic relationshipsamong the γ-proteobacteria.
The γ-proteobacteria are a diversegroup that include free-living, patho-genic and endosymbiotic members,and more complete genomesequences are available for theseorganisms than for any other groupof bacterial species. But the γ-pro-teobacteria also show an extremelyhigh tendency for LGT. The mostaccurate way to determine phyloge-netic relationships between species isto compare the sequences of as manygenes as possible that are common toall the members of the group beingstudied. But if this analysis includesgenes that have been passed on byLGT rather than by vertical transmis-
sion from one generation to the next,the results will be skewed, making itlook like certain species are moreclosely related than they really are.
Moran and colleagues attemptedto construct a phylogenetic tree forthe γ-proteobacteria using only sin-gle-copy orthologous genes — genespresent in different species that haveevolved from a single ancestor, buthave become different from eachother over time — to infer taxonomicrelationships. Surprisingly, consider-ing the high level of LGT reported forthis group, they found that out of 205
such gene families analysed, 203 wereconsistent with the same predictedfamily tree. Further analysis of theonly two families that disagreed withthe consensus tree showed that bothof these are highly likely to haveundergone LGT, explaining the differ-ent phylogenies for these genes. Theseresults indicate that single-copyorthologues only very rarely undergoLGT events and can therefore be reli-ably used to determine taxonomicrelationships between related species.This approach provides a new methodfor constructing accurate phyloge-netic trees for bacterial species, whichwill allow the changes that have dri-ven the diversification of bacterialgenomes to be determined and ulti-mately shed light on the processes bywhich new species evolve.
Louisa Flintoft
References and linksORIGINAL RESEARCH PAPER Lerat, E.,Daubin, V. & Moran, N. A. From gene trees toorganismal phylogeny in prokaryotes: the case ofthe γ-proteobacteria. PLoS Biol. 1, 1–10 (2003)WEB SITE Nancy Moran’s laboratory:http://eebweb.arizona.edu/faculty/moran/lab/pages/index2.html
Family tree for γ-proteobacteria
E V O L U T I O N
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