TY - JOUR
T1 - Terraces in phylogenetic tree space
AU - Sanderson, Michael J.
AU - McMahon, Michelle M.
AU - Steel, Mike
PY - 2011/7/22
Y1 - 2011/7/22
N2 - A key step in assembling the tree of life is the construction of species-rich phylogenies from multilocus - but often incomplete - sequence data sets. We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic ambiguity within a terrace can be characterized efficiently and then ameliorated by new algorithms for obtaining a terrace's maximum-agreement subtree or by identifying the smallest set of new targets for additional sequencing. Algorithms to find optimal trees or estimate Bayesian posterior tree distributions may need to navigate strategically in the neighborhood of large terraces in tree space.
AB - A key step in assembling the tree of life is the construction of species-rich phylogenies from multilocus - but often incomplete - sequence data sets. We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic ambiguity within a terrace can be characterized efficiently and then ameliorated by new algorithms for obtaining a terrace's maximum-agreement subtree or by identifying the smallest set of new targets for additional sequencing. Algorithms to find optimal trees or estimate Bayesian posterior tree distributions may need to navigate strategically in the neighborhood of large terraces in tree space.
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U2 - 10.1126/science.1206357
DO - 10.1126/science.1206357
M3 - Article
C2 - 21680810
AN - SCOPUS:79960670940
SN - 0036-8075
VL - 333
SP - 448
EP - 450
JO - Science
JF - Science
IS - 6041
ER -