Phylomatic: tree assembly for applied phylogenetics

By Campbell O. Webb, Michael J. Donoghue. 2005

1,045 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f595202a0e1b34578c582b029ae834bd3a8a0384

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology, Evolution, Behavior and Systematics

1. Francesco de Bello
2. Peter B. Reich
3. Jeannine Cavender-Bares
4. A. Moles
5. A. Chao
6. N. Mason
7. Wilfried Thuiller
8. J. Lepš

In Molecular Biology

1. W. John Kress
2. Olivier J. Hardy
3. Hong Qian
4. Jeannine Cavender-Bares
5. Peter B. Reich
6. Yi Jin
7. A. Chao
8. Steven W. Kembel

Citations in the corpus

• Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change (2008, background): “with Phylomatic version 1 (46) and was further resolved above the generic level”
• Interspecific variation in functional traits, not climatic differences among species ranges, determines demographic rates across 44 temperate and Mediterranean tree species (2010, methodology): “A phylogenetic tree for the study species was constructed using Phylomatic (Webb & Donogue 2005) based on the maximally resolved tree (Davies et al. 2004).”
• Functional traits explain variation in plant life history strategies (2013, methodology): “Consequently, we resorted to running the species list with their recognized families in PHYLOMATIC v2 (53) (discontinued January 10, 2013; Phylomatic v3 is now at http://phylodiversity.”
• Interspecific integration of trait dimensions at local scales: the plant phenotype as an integrated network (2017, methodology): “To examine the effects of phylogeny on the trait correlation structure, we generated a phylogeny for our species list using Phylomatic (Webb & Donoghue 2005) based on the Bell, Soltis & Soltis’s (2010) supertree (Fig.”
• Life‐history traits are correlated with geographical distribution patterns of western European forest herb species (2007, methodology): “To develop PICs, the 271 angiosperm species in the data set were first arrayed on a phylogenetic supertree based on the family-level phylogeny of Davies et al. (2004) using the webbased program phylomatic (http://www.phylodiversity.net/ phylomatic; see also Webb & Donoghue, 2005).”
• Shocks to the system: community assembly of the oak savanna in a 40-year fire frequency experiment (2012, methodology): “The third tree, previously reported in Willis et al. (2010), was constructed based on the Davies et al. (2004) backbone tree using Phylomatic (Webb and Donoghue 2005).”
• Uses and misuses of meta‐analysis in plant ecology (2014, methodology): “First, free online tools such as Phylomatic (Webb & Donoghue 2004) and Phylografter (http://phylografter.googlecode.com) have been created to allow assembly of comprehensive phylogenetic trees for land plants based on published studies.”
• What we (don’t) know about global plant diversity (2018, neutral): “2016), Phylomatic which uses taxonomic data to fill-in missing phylogenetic data (Webb and Donoghue 2005), and approaches which use taxonomic information to ‘gap-fill’ our knowledge of plant functional diversity (FitzJohn et al.”
• Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities (2012, methodology): “…Lavergne et al. 2010; Swenson 2011), in addition to statistical methods and software for the integration of phylogenetic trees into eco- logical analyses (Webb & Donoghue 2005; Hardy & Senterre 2007;Helmus et al. 2007;Webb, Ackerly&Kembel 2008; Pau- sas & Verdú 2010; Eastman, Paine & Hardy 2011).”
• Phylogenetic community structure in Minnesota oak savanna is influenced by spatial extent and environmental variation (2009, methodology): “Initial phylogenetic structure was determined using Phylomatic (Webb and Donoghue 2005).”
• Geographic patterns and environmental correlates of taxonomic and phylogenetic beta diversity for large‐scale angiosperm assemblages in China (2020, methodology): “This approach of adding taxa to a megaphylogeny is broadly used in community phylogenetics (Webb and Donoghue 2005, Shiono et al.”
• Interactions between hawkmoths and flowering plants in East Africa: polyphagy and evolutionary specialization in an ecological context (2013, methodology): “S1) was based on existing published trees and was constructed using PHYLOMATIC (Webb & Donoghue, 2005).”