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