DOI: 10.5061/dryad.5m9n159
title: Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

description: 1. 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. 2.
 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 1)
 the number of taxa included in the regional phylogeny; 2) random vs.
 targeted sampling of species to assemble the regional species pool; 3)
 including only species from specific clades rather than broad sampling; 4)
 using trees reconstructed directly for the taxa under study compared to
 trees pruned from a larger reconstructed tree; and 5) using phylograms
 compared to chronograms. 3. We found that including more taxa in a study
 increases the likelihood of observing significantly non-random
 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. 4. 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.
description: Ordway_572_phylogramMaximum likelihood phylogeny for 572 vascular plants occurring at the Ordway-Swisher Biological Station (Florida) based on rbcL and matK sequences; includes taxa designated as "complete dataset" in manuscriptOrdway_572_chronogramDated phylogeny for 572 vascular plants occurring at the Ordway-Swisher Biological Station (Florida) based on maximum likelihood phylogeny using rbcL and matK sequences, dated using treePL; includes taxa designated as "complete dataset" in manuscript572_taxa_alignmentMultiple sequence alignment of rbcL and matK sequences for 572 vascular plants occurring at the Ordway-Swisher Biological Station; used to reconstruct the Ordway_572 phylogeniesCommunity_designationsMatrix of taxa (columns) and communities (rows) where 0 represents absence and 1 represents presence of each taxon in each community; community designations were used for all phylodiversity calculationsRandom_subsets_prunedPruned phylogenies for each random subset described in the manuscript; taxa were randomly selected from the 572 taxon dataset and phylogenies were pruned from the 572-taxon phylogramTargeted_subsets_prunedPruned phylogenies for each targeted subset described in the manuscript, with taxa targeted proportional to species representation by family from the 572 taxon dataset; phylogenies were pruned from the 572 taxon phylogramRandom_subsets_reconstructedPruned phylogenies for each random subset described in the manuscript; taxa were randomly selected from the 572 taxon dataset and phylogenies were reconstructed based on a reduced-taxon alignment of rbcL and matKConstraints572Nexus file of constraints used for phylogeny reconstruction of full dataset; constraint file was modified for subsets using a custom R scriptREADMEREADME file for all data files in package