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

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 met...

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Bibliographic Details
Published in:PloS one 2015-06, Vol.10 (6), p.e0126662-e0126662
Main Authors: Boyle, Elizabeth E, Adamowicz, Sarah J
Format: Article
Language:English
Subjects:
Animals
Aquatic insects
Bar codes
Biodiversity
Bioinformatics
Biology
Body size
Communities
Community structure
Cytochrome
Cytochrome-c oxidase
Deoxyribonucleic acid
DNA
DNA - analysis
DNA barcoding
DNA Barcoding, Taxonomic - methods
Electron Transport Complex IV - genetics
Evolution
Gene sequencing
Genes
Insecta
Insecta - enzymology
Insecta - genetics
Insecta - growth & development
Larva - genetics
Lepidoptera
Manitoba
Nucleotide sequence
Phylogenetics
Phylogeny
Reconstruction
Sequence Analysis, DNA - methods
Studies
Trees
Vegetation
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0126662