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Journal article
Phylogenomics and the rise of the angiosperms
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on...Zuntini, Alexandre R. ; Carruthers, Tom ; Maurin, Olivier ; Bailey, Paul C. ; Leempoel, Kevin …
Plant evolution, Angiosperms, Phylogenetics, Speciation, and Phylogenomics
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Journal article
Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling.
Mountains are among the most biodiverse places on Earth, and plant lineages that inhabit them have some of the highest speciation rates ever recorded. Plant diversity within the alpine zone - the elevation above which trees cannot grow—contributes significantly to overall diversity within mountain systems, but the origins of alpine... -
Journal article
Species as a Heuristic: Reconciling Theory and Practice.
Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the “species problem” stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and...Wells, Tom ; Carruthers, Tom ; Muñoz-Rodríguez, Pablo ; Sumadijaya, Alex ; Wood, John R I …
Heuristic, Species problem, Cohesion, Homeostasis, and Lineage
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Journal article
The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation.
Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences...Carruthers, Tom ; Sun, Miao ; Baker, William J. ; Smith, Stephen A. ; de Vos, Jurriaan M. …
Divergence time estimation, Species tree, Gene trees, and Topological incongruence
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Journal article
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding... -
Journal article
Uncertainty in Divergence Time Estimation.
Understanding and representing uncertainty is crucial in academic research because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field...Carruthers, Tom ; Scotland, Robert W
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Journal article
The Implications of Interrelated Assumptions on Estimates of Divergence Times and Rates of Diversification.
Phylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive...Carruthers, Tom ; Scotland, Robert W
Divergence time estimation, Phylogeny, Macroevolution, Diversification rates, and Macroevolutionary history
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Journal article
First person – Tom Carruthers.
First Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping early-career researchers promote themselves alongside their papers. Tom Carruthers is first author on ‘ exTREEmaTIME: a method for incorporating uncertainty into divergence time estimates’, published in BiO. Tom conducted...Carruthers, Tom
Carruthers, Tom, Biography, Assumptions, Early-career researchers, Uncertainty, Science careers, and Divergence times
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Journal article
exTREEmaTIME: a method for incorporating uncertainty into divergence time estimates.
We present a method of divergence time estimation (exTREEmaTIME) that aims to effectively account for uncertainty in divergence time estimates. The method requires a minimal set of assumptions, and, based on these assumptions, estimates the oldest possible divergence times and youngest possible divergence times that are consistent with the assumptions....Carruthers, Tom ; Scotland, Robert W.
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Journal article
A taxonomic monograph of Ipomoea integrated across phylogenetic scales
Taxonomic monographs have the potential to make a unique contribution to the understanding of global biodiversity. However, such studies, now rare, are often considered too daunting to undertake within a realistic time frame, especially as the world’s collections have doubled in size in recent times. Here, we report a global-scale...Muñoz-Rodríguez, Pablo ; Carruthers, Tom ; Wood, John R. I. ; Williams, Bethany R. M. ; Weitemier, Kevin …