CHATROU, LARS, VINCENT SAVOLAINEN*, MARK W. CHASE, MARTYN POWELL, AND YIN-LONG QIU. Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS UK; Department of Botany, University of Massachusetts, Amherst, MA 01003-5810 USA. - Large-scale phylogeny of flowering plants 2: the faster the better.
It has been thought that higher-level taxonomic phylogenetic studies
focusing on ancient cladogenesis events would be better recovered
using slow-evolving genes, thereby avoiding multiple hits and
homoplasies. Furthemore, the distinction of "slow versus
fast" has long been confusing: lower numbers of variable sites
and lower frequency of change at variable sites being have both been
used when referring to slowly-evolving genes. Hillis has addressed
both issues using simulations of a 232-taxon 18S rDNA tree, and showed
that rapidly-evolving characters should perform better in phylogeny
reconstruction, providing that enough variable sites are used. Using a
six-gene data set (atpB, atp1, rbcL, matR, matK, and 18S rDNA, from
mitochondrial, plastid and nuclear genomes) for basal angiosperms, we
evaluated Hillis' expectations and reached the same conclusion.
Rapidly-evolving genes (i.e. those with more variable sites) performed
the best (e.g. matK), indicating that large-scale phylogenetic
analyses of plants will benefit from sequencing "fast"
genes. Contrary to what is generally assumed, none of these regions
differs much with respect to the frequencies of change at variable
sites (i.e. variable positions are all evolving at similar rates).
Key words: fast versus slow evolving genes, Large-scale phylogeny