Taxon sampling effects on the quantification and comparison of community phylogenetic diversity |
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Authors: | Daniel S Park Steven Worthington Zhenxiang Xi |
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Institution: | 1. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA;2. Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA;3. Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China |
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Abstract: | 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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Keywords: | community ecology community phylogeny divergence time estimates phylogenetic distance phylogenetic diversity taxon sampling |
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