Ancestral Reconstruction

Joy, Jeffrey B.; Liang, Richard; McCloskey, Rosemary M.; Nguyen, Thuy; Poon, Art F. Y.

doi:10.1371/journal.pcbi.1004763

Cited by 150 publications

(118 citation statements)

References 93 publications

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“…For a review and comparison of the methods of character state reconstruction, see Royer‐Carenzi (), Joy et al . () and Royer‐Carenzi & Didier ().…”

Section: Beyond Topologies: Unravelling Patterns Of Biodiversitymentioning

confidence: 98%

“…Bayesian character state estimation is preferred over ML approaches as it accounts for uncertainty in both model parameters and phylogeny (Pagel, 2004;Vanderpoorten & Goffinet, 2006). For a review and comparison of the methods of character state reconstruction, see Royer-Carenzi (2013), Joy et al (2016) and Royer-Carenzi & Didier (2016).…”

Section: Ancestral State Reconstructionmentioning

confidence: 99%

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Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

Young

Gillung

2019

Systematic Entomology

155

104

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“…For a review and comparison of the methods of character state reconstruction, see Royer‐Carenzi (), Joy et al . () and Royer‐Carenzi & Didier ().…”

Section: Beyond Topologies: Unravelling Patterns Of Biodiversitymentioning

confidence: 98%

Section: Ancestral State Reconstructionmentioning

confidence: 99%

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

Young

Gillung

2019

Systematic Entomology

155

104

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“…Ancestral reconstruction is a challenging and important question in evolutionary biology. As such, it motivated the development of several approaches [5,9,8,6,13]. They all rely on two general points of view which are quite different.…”

Section: Introductionmentioning

confidence: 99%

Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction

Didier

2016

Preprint

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The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost).A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony.This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated to the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

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“…Ancestral reconstruction can be used to recover the values of the ancestral character states of a trait (Finarelli & Flynn, 2006;Joy, Liang, McCloskey, Nguyen, & Poon, 2016). In this study, we inferred the ancestral character state for body mass and body length using our phylogenetic tree for Trochilidae.…”

Section: Ancestral Character State Estimationmentioning

confidence: 99%

Body mass as a supertrait linked to abundance and behavioral dominance in hummingbirds: A phylogenetic approach

Bribiesca

Herrera‐Alsina

Ruíz-Sánchez

et al. 2019

Ecology and Evolution

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Body mass has been considered one of the most critical organismal traits, and its role in many ecological processes has been widely studied. In hummingbirds, body mass has been linked to ecological features such as foraging performance, metabolic rates, and cost of flying, among others. We used an evolutionary approach to test whether body mass is a good predictor of two of the main ecological features of hummingbirds: their abundances and behavioral dominance. To determine whether a species was abundant and/or behaviorally dominant, we used information from the literature on 249 hummingbird species. For abundance, we classified a species as “plentiful” if it was described as the most abundant species in at least part of its geographic distribution, while we deemed a species to be “behaviorally dominant” when it was described as pugnacious (notably aggressive). We found that plentiful hummingbird species had intermediate body masses and were more phylogenetically related to each other than expected by chance. Conversely, behaviorally dominant species tended to have larger body masses and showed a random pattern of distribution in the phylogeny. Additionally, small‐bodied hummingbird species were not considered plentiful by our definition and did not exhibit behavioral dominance. These results suggest a link between body mass, abundance, and behavioral dominance in hummingbirds. Our findings indicate the existence of a body mass range associated with the capacity of hummingbird species to be plentiful, behaviorally dominant, or to show both traits. The mechanisms behind these relationships are still unclear; however, our results provide support for the hypothesis that body mass is a supertrait that explains abundance and behavioral dominance in hummingbirds.

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Ancestral Reconstruction

Cited by 150 publications

References 93 publications

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction

Body mass as a supertrait linked to abundance and behavioral dominance in hummingbirds: A phylogenetic approach

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