Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes

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.

Flower‐visitor communities of an arcto‐alpine plant—Global patterns in species richness, phylogenetic diversity and ecological functioning

“…Sequences under 500 base pairs were omitted from the final analysis, leaving 1,314 sequences. Our approach was based on the findings of Boyle and Adamowicz (), who investigated the utility of COI data for estimating phylogenetic community structure. They found that, in general, COI data will estimate the relative genetic distances between pairs of co‐occurring species very well.…”

“…In addition, phylogenies derived from single loci will always be subject to chance events and biases (Pamilo & Nei, 1988). Therefore, Boyle and Adamowicz (2015) recommended the use of an enforced backbone phylogeny-especially when dealing with data collected at a broader geographic scale and across more diverse taxonomic levels. Thus, we provided two sources of a priori information for the Bayesian analysis.…”

Forecasting pollination declines through DNA barcoding: the potential contributions of macroecological and macroevolutionary scales of inquiry

“…However, animal barcode data can increase the taxon density in a phylogenetic study when 'backbone' phylogenies constructed using multi-gene data or phylogenomics approaches constrain the deeper topology (e.g. genus or family-level relationships; see Trunz et al, 2016), in combination with barcode data, which are available for more species (Wilson, 2011;Boyle & Adamowicz, 2015). By incorporating barcode markers, phylogenetic trees have better phylogenetic resolution, which can yield more precise conclusions regarding community structuring and processes (Kress et al, 2009;Pei et al, 2011;Davies et al, 2012).…”

The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China

“…To constrain deep phylogenetic nodes and follow broadly accepted phylogenetic patterns, supertree methods (Bininda‐Emonds & Sanderson, ; Webb & Donoghue, ) can be combined with DNA barcode sequence data (Erickson et al, ; Kress et al, ) to provide more accurate depictions of topology. Furthermore, the incorporation of a backbone phylogeny can provide more accurate estimates of the branch lengths (Boyle & Adamowicz, ) and potentially affect the metrics of phylogenetic community diversity (Swenson, ). Since ecological and evolutionary processes might operate at different phylogenetic depths (Mazel et al, ), it seems reasonable that phylogenetic diversity metrics that are sensitive to processes operating at deep phylogenetic depths may be strongly influenced by combining supertree methods with DNA barcode sequence data, whereas those estimates that are largely capturing diversity at the tips of the phylogeny may be less influenced, although this remains to be tested.…”