ArticleEcology2019
For common community phylogenetic analyses, go ahead and use synthesis phylogenies.
Article in Ecology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Simultaneous Inference of Flora-Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data.Molecular ecology resources · 2026Article
- Fossil record biases skew inferences of mammal trait evolution.Nature communications · 2026Article
- Colonization and extinction mediate environmental effects on the phylogenetic diversity of invertebrate communities.Ecology · 2026Article
- Scale-dependent decoupling of leaf traits and phylogeny reveals dimension-specific environmental filtering in Polyspora chrysandra-associated montane forests.BMC plant biology · 2026Article
- Informing spatial conservation prioritization with species' traits.Conservation biology : the journal of the Society for Conservation Biology · 2026Article
- Diel activity correlates with colour pattern morphology of heterobranch sea slugs.The Journal of animal ecology · 2025Article
- Long-term nitrogen deposition reduces the diversity of nitrogen-fixing plants.Science advances · 2024Article
- Environmental determinants of phylogenetic diversity in vernal pool habitats.Ecology and evolution · 2024Article
- Variations and trade-offs in leaf and culm functional traits among 77 woody bamboo species.BMC plant biology · 2024Article
- Climate change and land use threaten global hotspots of phylogenetic endemism for trees.Nature communications · 2023Article
- A latitudinal gradient in Darwin's naturalization conundrum at the global scale for flowering plants.Nature communications · 2023Article
- U.PhyloMaker: An R package that can generate large phylogenetic trees for plants and animals.Plant diversity · 2023Article
- Range restricted old and young lineages show the southern Western Ghats to be both a museum and a cradle of diversity for woody plants.Proceedings. Biological sciences · 2023Article
- Global beta-diversity of angiosperm trees is shaped by Quaternary climate change.Science advances · 2023Article
- Evolutionary history of marginal habitats regulates the diversity of tree communities in the Atlantic Forest.Annals of botany · 2023Article
- Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time.Plant diversity · 2023Article
- Environmental stress influences Malesian Lamiaceae distributions.Ecology and evolution · 2022Article
- Community-level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in the northern Great Plains.Ecology and evolution · 2022Article
- Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species-rich rainforest in Borneo.Ecology and evolution · 2022Article
- Phylogenetic diversity and community assembly in a naturally fragmented system.Ecology and evolution · 2021Article
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Authors and funding
9 authors.
Funding
Abstract
Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel's λ and Blomberg's K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman's
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