CSIRO Publishing blank image blank image blank image blank imageBooksblank image blank image blank image blank imageJournalsblank image blank image blank image blank imageAbout Usblank image blank image blank image blank imageShopping Cartblank image blank image blank image You are here: Journals > Australian Systematic Botany   
Australian Systematic Botany
Journal Banner
  Taxonomy, Biogeography & Evolution of Plants
blank image Search
blank image blank image
blank image
  Advanced Search

Journal Home
About the Journal
Editorial Board
Current Issue
Just Accepted
All Issues
Special Issues
LAS Johnson Review Series
Sample Issue
For Authors
General Information
Notice to Authors
Submit Article
Open Access
For Referees
Referee Guidelines
Review an Article
Annual Referee Index
For Subscribers
Subscription Prices
Customer Service
Print Publication Dates

blue arrow e-Alerts
blank image
Subscribe to our Email Alert or RSS feeds for the latest journal papers.

red arrow Connect with us
blank image
facebook twitter youtube


Article << Previous     |     Next >>   Contents Vol 20(4)

L. A. S. JOHNSON REVIEW No. 9Construction and annotation of large phylogenetic trees

Michael J. Sanderson

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
PDF (327 KB) $40
 Export Citation


Broad availability of molecular sequence data allows construction of phylogenetic trees with 1000s or even 10 000s of taxa. This paper reviews methodological, technological and empirical issues raised in phylogenetic inference at this scale. Numerous algorithmic and computational challenges have been identified surrounding the core problem of reconstructing large trees accurately from sequence data, but many other obstacles, both upstream and downstream of this step, are less well understood. Before phylogenetic analysis, data must be generated de novo or extracted from existing databases, compiled into blocks of homologous data with controlled properties, aligned, examined for the presence of gene duplications or other kinds of complicating factors, and finally, combined with other evidence via supermatrix or supertree approaches. After phylogenetic analysis, confidence assessments are usually reported, along with other kinds of annotations, such as clade names, or annotations requiring additional inference procedures, such as trait evolution or divergence time estimates. Prospects for partial automation of large-tree construction are also discussed, as well as risks associated with ‘outsourcing’ phylogenetic inference beyond the systematics community.

Subscriber Login

Legal & Privacy | Contact Us | Help


© CSIRO 1996-2015