Journal
MOLECULAR ECOLOGY
Volume 27, Issue 5, Pages 1296-1308Publisher
WILEY
DOI: 10.1111/mec.14520
Keywords
community ecology; community phylogeny; divergence time estimates; phylogenetic distance; phylogenetic diversity; taxon sampling
Funding
- National Natural Science Foundation of China [31600172]
- Harvard University Herbaria
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Ecologists are increasingly making use of molecular phylogenies, especially in the fields of community ecology and conservation. However, these phylogenies are often used without full appreciation of their underlying assumptions and uncertainties. A frequent practice in ecological studies is inferring a phylogeny with molecular data from taxa only within the community of interest. These inferred community phylogenies are inherently biased in their taxon sampling. Despite the importance of comprehensive sampling in constructing phylogenies, the implications of using inferred community phylogenies in ecological studies have not been examined. Here, we evaluate how taxon sampling affects the quantification and comparison of community phylogenetic diversity using both simulated and empirical data sets. We demonstrate that inferred community trees greatly underestimate phylogenetic diversity and that the probability of incorrectly ranking community diversity can reach up to 25%, depending on the dating methods employed. We argue that to reach reliable conclusions, ecological studies must improve their taxon sampling and generate the best phylogeny possible.
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