Abstract
Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel’s λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities.
Highlights
The explicit application of phylogenetics to understanding community assembly was proposed by Webb [1,2], and community phylogenetics has since become a rapidly expanding field in ecology
After trimming sequences so that at least 50% of species were represented at the beginning and the end of the alignment, c oxidase subunit I (COI) consisted of 658 bp, polymerase II (POL-II) 712 bp, EF1-α 483 bp, and CAD 730 bp
Our study investigated how different phylogenetic reconstruction methods applied to COI data can approximate net relatedness index (NRI) and nearest taxon index (NTI) calculated from a multi-gene tree, presumed here to provide the more robust phylogenetic hypothesis and branch lengths across the entire depth of the phylogeny
Summary
The explicit application of phylogenetics to understanding community assembly was proposed by Webb [1,2], and community phylogenetics has since become a rapidly expanding field in ecology. The sorting of species is facilitated through environmental and biotic pressures, which can act at various phylogenetic and spatial scales [3]. Given that these different pressures leave distinct phylogenetic patterns between locally co-occurring species, we can distinguish between different processes of community assembly. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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