Synthesis of phylogeny and taxonomy into a comprehensive tree of life
- Cody E. Hinchliff, Stephen A. Smith, K. Cranston
- Biology, Environmental ScienceProceedings of the National Academy of Sciences
- 8 December 2014
This study is the first, to the knowledge, to apply an efficient and automated process for assembling published trees into a complete tree of life, and presents a draft tree containing 2.3 million tips—the Open Tree of Life.
Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications.
- David C. Tank, J. Eastman, L. Harmon
- Biology, Environmental ScienceNew Phytologist
- 1 July 2015
Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time, and it is suggested that stochastically changing diversification rates across the phylogeny explain these patterns.
Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life.
- J. Pease, Joseph W. Brown, Joseph F. Walker, Cody E. Hinchliff, Stephen A. Smith
- BiologyAmerican-Eurasian journal of botany
- 1 March 2018
The Quartet Sampling method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.
The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database
- Brian Salvin Maitner, B. Boyle, B. Enquist
- Environmental Science
- 6 September 2017
An r package that provides easy access to large-scale botanical data in the BIEN database by turning user inputs into optimised PostgreSQL functions and developing a protocol for providing customised citations and herbarium acknowledgements for data downloaded through the bien r package.
Using supermatrices for phylogenetic inquiry: an example using the sedges.
- Cody E. Hinchliff, E. Roalson
- BiologySystematic Biology
- 1 March 2013
The reconstruction of a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank is used to show that supermatrix methods offer powerful means of pursuing phylogenetic study and these tools have high potential value for many systematic biologists.
The origins of Eleocharis (Cyperaceae) and the status of Websteria, Egleria, and Chillania
- Cody E. Hinchliff, Ariel Lliully, Timothy S Carey, E. Roalson
- Biology
- 1 June 2010
The phylogenetic reconstructions indicate several other instances of generic paraphyly in other Cyperaceae lineages, including Egleria and Websteria, and that this clade, representing the Eleocharideae, is sister to the Abildgaardieae.
Phylogenetic Relationships in Eleocharis (Cyperaceae): C4 Photosynthesis Origins and Patterns of Diversification in the Spikerushes
- E. Roalson, Cody E. Hinchliff, R. Trevisan, C. R. D. da Silva
- Biology
- 20 September 2010
The results suggest that in Eleocharis C4 photosynthesis has been derived at least three times, with several cases of possible reversion to C3-like or intermediate pathways and several additional origins of C3–C4 intermediate photosynthetic pathways, as inferred by carbon isotope ratio measurements.
Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants)
- Cody E. Hinchliff, Stephen A. Smith
- BiologyPLoS ONE
- 7 July 2014
It is concluded that public databases have exceptional value for modern systematics and evolutionary biology, and that a continued emphasis on expanding taxonomic and genomic coverage will play a critical role in developing these resources to their full potential.
Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs
- Stephen A. Smith, Joseph W. Brown, Cody E. Hinchliff
- Computer SciencePLoS Comput. Biol.
- 1 September 2013
Methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG), are introduced and serve as a basis for an alternative to consensus tree and supertree methods.
Phylesystem: a git-based data store for community-curated phylogenetic estimates
- E. J. McTavish, Cody E. Hinchliff, Stephen A. Smith
- Computer Science, BiologyBioinform.
- 4 May 2015
The development of software infrastructure to support the open curation of phylogenetic data by the community of biologists is reported, including a server running the ‘phylesystem-api’, which wraps the interactions with git and GitHub.
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