ArticleEcology and evolution2019
Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics.
Article in Ecology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Simultaneous Inference of Flora-Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data.Molecular ecology resources · 2026Article
- TreeHub: a comprehensive dataset of phylogenetic trees.Scientific data · 2025Article
- Potential predictive value of phylogenetic novelties in clinical fungi, illustrated byIMA fungus · 2025Article
- Environmental determinants of phylogenetic diversity in vernal pool habitats.Ecology and evolution · 2024Article
- Stability and Assembly Mechanisms of Butterfly Communities across Environmental Gradients of a Subtropical Mountain.Insects · 2024Article
- Characterization and organelle genome sequencing of Pyropia species from Myanmar.Scientific reports · 2023Article
- Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time.Plant diversity · 2023Article
- Community-level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in the northern Great Plains.Ecology and evolution · 2022Article
- Phylogenetic diversity and community assembly in a naturally fragmented system.Ecology and evolution · 2021Article
- Frequent ploidy changes in Salicaceae indicates widespread sharing of the salicoid whole genome duplication by the relatives of Populus L. and Salix L.BMC plant biology · 2021Article
- OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life.Systematic biology · 2021Article
- Clade composition of a plant community indicates its phylogenetic diversity.Ecology and evolution · 2020Article
- Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics.Ecology and evolution · 2019Article
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6 authors.
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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.
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