Abstract
The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods.To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway‐Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of (a) the number of taxa included in the regional phylogeny; (b) random versus targeted sampling of species to assemble the regional species pool; (c) including only species from specific clades rather than broad sampling; (d) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and (e) using phylograms compared to chronograms.We found that including more taxa in a study increases the likelihood of observing significantly nonrandom phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms.The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.
Highlights
The field of community phylogenetics uses patterns of phylodiversity to understand community assembly and the coexistence of related species, incorporating a phylogenetic framework into the study of community ecology (Ackerly, 2003; Cavender‐Bares, Kozak, Fine, & Kembel, 2009; Webb, 2000; Webb, Ackerly, McPeek, & Donoghue, 2002)
We studied the effects of (a) the number of taxa included in the regional phylogeny; (b) random versus targeted sampling of species to assemble the regional species pool; (c) including only species from specific clades rather than broad sampling; (d) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and (e) using phylograms compared to chronograms
Recent studies have investigated patterns of community phylogenetic structure in diverse lineages including vertebrates (e.g., Gómez, Bravo, Brumfield, Tello, & Cadena, 2010; Patrick & Stevens, 2016), invertebrates (e.g., Lessard, Fordyce, Gotelli, & Sanders, 2009; Saito, Valente‐Neto, Rodrigues, de Oliveira Roque & Siqueira, 2016), algae (e.g., Fritschie, Cardinale, Alexandrou, & Oakley, 2014), zooplankton (e.g., Gianuca et al, 2017), and vascular plants (e.g., Kembel & Hubbell, 2006; Willis et al, 2010). These studies rely on measures of phylodiversity, a quantification of the evolutionary history represented by the taxa in a given community, based on the branches connecting these taxa on a regional phylogeny, often referred to as “phylogenetic diversity” (Faith, 1992)
Summary
The field of community phylogenetics uses patterns of phylodiversity to understand community assembly and the coexistence of related species, incorporating a phylogenetic framework into the study of community ecology (Ackerly, 2003; Cavender‐Bares, Kozak, Fine, & Kembel, 2009; Webb, 2000; Webb, Ackerly, McPeek, & Donoghue, 2002). Recent studies have investigated patterns of community phylogenetic structure in diverse lineages including vertebrates (e.g., Gómez, Bravo, Brumfield, Tello, & Cadena, 2010; Patrick & Stevens, 2016), invertebrates (e.g., Lessard, Fordyce, Gotelli, & Sanders, 2009; Saito, Valente‐Neto, Rodrigues, de Oliveira Roque & Siqueira, 2016), algae (e.g., Fritschie, Cardinale, Alexandrou, & Oakley, 2014), zooplankton (e.g., Gianuca et al, 2017), and vascular plants (e.g., Kembel & Hubbell, 2006; Willis et al, 2010) These studies rely on measures of phylodiversity, a quantification of the evolutionary history represented by the taxa in a given community, based on the branches connecting these taxa on a regional phylogeny, often referred to as “phylogenetic diversity” (Faith, 1992). We test five questions related to this gap in understanding how taxon sampling and tree reconstruction methods can affect estimated patterns of phylodiversity, focusing on metrics that are commonly used to understand community structure
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
