geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

Pennell, Matthew W.; Eastman, Jonathan M.; Slater, Graham J.; Brown, Joseph W.; Uyeda, Josef C.; FitzJohn, Richard G.; Alfaro, Michael E.; Harmon, Luke J.

doi:10.1093/bioinformatics/btu181

Cited by 841 publications

(754 citation statements)

References 17 publications

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“…Diversifi cation rates -Th e rates reported in this study correspond to diff erent parts of the tree, known as breakpoints (e.g., nodes, stems, or both) that are evolving under diff erent parameter values, i.e., per-lineage net diversifi cation and relative extinction rates ( Pennell et al, 2014 ). Our analyses discovered six shift s in the rate of net diversifi cation ( r = speciation minus extinction) in the Rhinantheae clade when performed over the posterior distribution of trees; three of these were also identifi ed on the MCC tree.…”

Section: Resultsmentioning

confidence: 99%

“…Diversifi cation rates -Diversifi cation rate analyses were conducted on the same posterior distribution of 1000 trees, as well as on the maximum clade credibility (MCC) tree using MEDUSA ( Alfaro et al, 2009 ), which is an extension of the method described by Rabosky et al (2007) and is available in the R package geiger 2.0 ( Pennell et al, 2014 ). Th e method used by Rabosky et al (2007) estimates two likelihoods for a dated tree: (1) a phylogenetic likelihood that uses the timing of the splits on the backbone to estimate ML values for birth and death rates following the equations of Nee et al (1994) , and (2) a taxonomic likelihood that uses species richness along with the date of the splits, estimating diversifi cation rates following Magallón and Sanderson (2001) .…”

Section: Divergence Time Estimation -mentioning

confidence: 99%

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Shifts in diversification rates linked to biogeographic movement into new areas: An example of a recent radiation in the Andes

Uribe‐Convers

Tank

2015

American J of Botany

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PREMISE OF THE STUDY:Clade‐specific bursts in diversification are often associated with the evolution of key innovations. However, in groups with no obvious morphological innovations, observed upticks in diversification rates have also been attributed to the colonization of a new geographic environment. In this study, we explore the systematics, diversification dynamics, and historical biogeography of the plant clade Rhinantheae in the Orobanchaceae, with a special focus on the Andean clade of the genus Bartsia.METHODS:We sampled taxa from across Rhinantheae, including a representative sample of Andean Bartsia species. Using standard phylogenetic methods, we reconstructed evolutionary relationships, inferred divergence times among the clades of Rhinantheae, elucidated their biogeographic history, and investigated diversification dynamics.KEY RESULTS:We confirmed that the South American Bartsia species form a highly supported monophyletic group. The median crown age of Rhinantheae was determined to be ca. 30 Myr, and Europe played an important role in the biogeographic history of the lineages. South America was first reconstructed in the biogeographic analyses around 9 Myr ago, and with a median age of 2.59 Myr, this clade shows a significant uptick in diversification.CONCLUSIONS:Increased net diversification of the South American clade corresponds to biogeographic movement into the New World. This movement happened at a time when the Andes were reaching the necessary elevation to host an alpine environment. Although a specific route could not be identified with certainty, we provide plausible hypotheses to how the group colonized the New World.

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Section: Resultsmentioning

confidence: 99%

Section: Divergence Time Estimation -mentioning

confidence: 99%

Shifts in diversification rates linked to biogeographic movement into new areas: An example of a recent radiation in the Andes

Uribe‐Convers

Tank

2015

American J of Botany

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“…We compared divergence dates and ancestral placements between samples of 100 APT-dated MPTs to a random selection of 100 post-burn-in trees from the Bayesian analyses. We also used these samples to compare the outcomes of a comparative analysis, mimicking the analyses of [17], fitting models for Ornstein-Uhlenbeck (OU), early burst (EB), and Brownian motion (BM; via geiger [19]). Further details of our methods and convergence assessments for the tip-dating analyses are in the Methods section of the electronic supplementary material.…”

Section: Methodsmentioning

confidence: 99%

Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

et al. 2016

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An invited contribution to the special feature 'Putting fossils in trees: combining morphology, time, and molecules to estimate phylogenies and divergence times'. Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.

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“…In addition, following Mi et al (2012), we estimated phylogenetic signal for OR to determine phylogenetic distinctiveness between exotic and native species. We used Pagel's k (Pagel, 1999) to estimate phylogenetic signal through the 'fitDiscrete()' function from the geiger package (Pennell et al, 2014). Pagel's k is a multiplier of the off-diagonal elements of a variance-covariance matrix, which best fits the distribution of data at the tips of the phylogeny.…”

Section: Phylogenetic Signal and Community Structurementioning

confidence: 99%

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure

Escobedo

Ríos

Salgado‐Luarte

et al. 2017

Ann Bot

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Background and Aims Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles.Methods Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus, measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel's lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters.Key Results The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct.Conclusions Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated.

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geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 841 publications

References 17 publications

Shifts in diversification rates linked to biogeographic movement into new areas: An example of a recent radiation in the Andes

Shifts in diversification rates linked to biogeographic movement into new areas: An example of a recent radiation in the Andes

Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure

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