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Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism
Author(s) -
Davies T. Jonathan,
Kraft Nathan J. B.,
Salamin Nicolas,
Wolkovich Elizabeth M.
Publication year - 2012
Publication title -
ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.144
H-Index - 294
eISSN - 1939-9170
pISSN - 0012-9658
DOI - 10.1890/11-1360.1
Subject(s) - phylogenetic tree , phylogenetics , biology , phylogenetic comparative methods , evolutionary biology , ecology , biochemistry , gene
The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co‐vary with phylogeny can significantly impact how we analyze cross‐species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species‐rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction‐based solution that can reliably retrieve unbiased estimates of K , and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).