Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

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.

Noise does not equal bias in assessing the evolutionary history of the angiosperm flora of China: A response to Qian (2019)

“…However, case studies have demonstrated that mode of phylogenetic inference has little influence on phylodiversity metrics. In other words, equivalent results have been obtained from purpose‐built and synthetic trees (Allen et al., 2019; Jantzen et al., 2019; Li, Trotta, et al, 2019). Nevertheless, the impact of limited sampling in a regional phylogeny on divergence times, using either a purpose‐built or pruned tree, compared to a global phylogeny remains to be assessed directly.…”

Clade composition of a plant community indicates its phylogenetic diversity

“…This is a welcome simplification, especially when dealing with hard to determine taxa. Second, phylogenetic diversity estimation using the clade indices requires less effort, expertise, and cost, as there is no need to obtain molecular data, performs a phylogenetic analysis and molecular dating (the latter is not necessary when phylograms are used, i.e., branch lengths in units substitutions per site; but see Jantzen et al, 2019 for discussion of how phylogenetic diversity measures can be affected by using either phylograms or dated phylogenies). As discussed in Li et al (2019), researchers have to decide what markers (Which genes to select?)…”

“…What fossil constraints for molecular dating?). All these difficult methodological decisions can be also avoided using phylogenies pruned from supertrees, for example, Daphne (Durka & Michalski, 2012) or the Open Tree of Life (Hinchliff et al, 2015), which have been shown to provide estimates of phylogenetic diversity well correlated to those derived from purpose‐built phylogenies (Li et al, 2019) and, additionally, have broader taxon sampling coverage that is important to correctly estimate phylogenetic diversity (Jantzen et al, 2019; Park et al, 2018). On the other hand, for many taxonomic groups, supertrees are poorly sampled and unavailable (e.g., Daphne covers only a part of the European flora) or do not include branch lengths (Open Tree of Life) that need to be additionally calculated (Li et al, 2019).…”

“…Simulation workflow was specifically designed to cover several aspects that can affect phylogenetic diversity estimation, that is, taxon sampling (Park et al, 2018), the number of taxa included in the regional phylogeny (Jantzen et al, 2019) or species richness of a community (Sandel, 2018; Swenson, 2014). Thus, these factors could also affect fit accuracy of the clade indices for all dimensions of phylogenetic diversity.…”

“…To construct dated phylogenies requires considerable effort, and the whole process is affected by methodological biases and subjective decisions (Jantzen et al, 2019; Li et al, 2019). Further, calculated phylogenetic diversity metrics depend on the attributes of phylogenies, such as the degree of balance, diversification rate, resolution, taxon sampling, or tree reconstruction methods (Jantzen et al, 2019; Park, Worthington, & Xi, 2018; Swenson, 2009; Vellend et al, 2011). Here, we propose and evaluate an approach based on the idea of considering species phylogeny as a categorical variable (i.e., affiliation to a phylogenetic clade) rather than continuous (i.e., phylogenetic distances among species).…”