phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things)

Revell, Liam J.

doi:10.1101/2023.03.08.531791

Cited by 61 publications

(87 citation statements)

References 145 publications

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“…It is widely held that correcting or controlling or accounting for phylogeny (methodology summarized in Box 1) should be mandatory when ecologists consider present‐day functionality of traits in combination with each other or with different environments (e.g. Garamszegi, 2014; Losos, 2011; Revell & Harmon, 2022; Swenson, 2020). Reviewers and editors of ecology journals commonly require authors to control for phylogeny.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetically conservative trait correlation: Quantification and interpretation

et al. 2023

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Correlation across species between two quantitative traits, or between a trait and a habitat property, can suggest that a trait value is effective in sustaining populations in some contexts but not others. It is widely held that such correlations should be controlled for phylogeny, via phylogenetically independent contrasts (PICs) or phylogenetic generalized least squares (PGLS). A weakness of this idea is that a clade's traits tend to confer success in particular habitats or ways of life, and those niches in turn tend to select for the same traits to continue in the clade. This feedback mechanism can bind phylogeny and niche together as a unified cause for present‐day trait configurations. Accordingly, the phylogenetically conservative share of a trait correlation ought not to be excluded from consideration as potentially ecologically functional. Another weakness is that PGLS does not yield a complete or accurate breakdown of covariation between traits A and B because it corresponds to a generating model where B predicts variation in A but not the reverse, and phylogenetic signal in B is not modelled. Multi‐response mixed models using phylogenetic covariance matrices can quantify conservative trait correlation (CTC), a share of A‐B covariation that is phylogenetically conservative. Because the evidence is from correlative data, it is not possible to split CTC into causation by phylogenetic history versus causation by continuing reciprocal selection between A and B. Moreover, it is quite likely biologically that the two influences have acted in concert, through phylogenetic niche conservatism. Synthesis: The CTC concept treats phylogenetic conservatism as a conjoint interpretation alongside ongoing influence of other traits. CTC can be quantified via multi‐response phylogenetic mixed models.

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Section: Introductionmentioning

confidence: 99%

Phylogenetically conservative trait correlation: Quantification and interpretation

et al. 2023

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“…Results were compared using Akaike's information criterion for small sample sizes (AICc) and Akaike weights were calculated to identify the best combination of explanatory variables from those tested. AICc was calculated using the function AICc() of the R package qpcR [58], and Akaike weights calculated using the aic.w() function of the R package phytools [59].…”

Section: Methodsmentioning

confidence: 99%

Deep-time biodiversity patterns and the dinosaurian fossil record of the Late Cretaceous Western Interior, North America

et al. 2021

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In order for palaeontological data to be informative to ecologists seeking to understand the causes of today's diversity patterns, palaeontologists must demonstrate that actual biodiversity patterns are preserved in our reconstructions of past ecosystems. During the Late Cretaceous, North America was divided into two landmasses, Laramidia and Appalachia. Previous work has suggested strong faunal provinciality on Laramidia at this time, but these arguments are almost entirely qualitative. We quantitatively investigated faunal provinciality in ceratopsid and hadrosaurid dinosaurs using a biogeographic network approach and investigated sampling biases by examining correlations between dinosaur occurrences and collections. We carried out a model-fitting approach using generalized least-squares regression to investigate the sources of sampling bias we identified. We find that while the raw data strongly support faunal provinciality, this result is driven by sampling bias. The data quality of ceratopsids and hadrosaurids is currently too poor to enable fair tests of provincialism, even in this intensively sampled region, which probably represents the best-known Late Cretaceous terrestrial ecosystem on Earth. To accurately reconstruct biodiversity patterns in deep time, future work should focus on smaller scale, higher resolution case studies in which the effects of sampling bias can be better controlled.

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“…These methods continued to develop and allowed linear morphometric work to be placed in a phylogenetic context for the first time. Incorporating phylogenetic signal into multivariate datasets were developed in the last two decades (e.g., Adams, 2014a; Adams, 2014b; Adams & Felice, 2014; Revell & Harmon, 2008) for which numerous excellent reviews now exist (Adams & Collyer, 2018; Adams & Collyer, 2019; Revell & Harmon, 2022). Along with the development of morphometric techniques, the ability to assess the relevance of phylogenetic signal through PCMs has helped to revolutionize macroevolutionary studies across numerous groups in the tree of life.…”

Section: The Morphometrics Of Nonavian Dinosaursmentioning

confidence: 99%

Dots on a screen: The past, present, and future of morphometrics in the study of nonavian dinosaurs

Hedrick

2023

The Anatomical Record

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Using morphometrics to study nonavian dinosaur fossils is a practice that predates the origin of the word “dinosaur.” By the 1970s, linear morphometrics had become established as a valuable tool for analyzing intra‐ and interspecific variation in nonavian dinosaurs. With the advent of more recent techniques such as geometric morphometrics and more advanced statistical approaches, morphometric analyses of nonavian dinosaurs have proliferated, granting unprecedented insight into many aspects of their biology and evolution. I outline the past, present, and future of morphometrics as applied to the study of nonavian dinosaurs zeroing in on five aspects of nonavian dinosaur paleobiology where morphometrics has been widely utilized to advance our knowledge: systematics, sexual dimorphism, locomotion, macroevolution, and trackways. Morphometric methods are especially susceptible to taphonomic distortion. As such, the impact of taphonomic distortion on original fossil shape is discussed as are current and future methods for quantifying and accounting for distortion with the goal of reducing the taphonomic noise to biological signal ratio. Finally, the future of morphometrics in nonavian dinosaur paleobiology is discussed as paleobiologists move into a “virtual paleobiology” framework, whereby digital renditions of fossils are captured via methods such as photogrammetry and computed tomography. These primary data form the basis for three‐dimensional (3D) geometric morphometric analyses along with a slew of other forms of analyses. These 3D specimen data form part of the extended specimen and help to democratize paleobiology, unlocking the specimen from the physical museum and making the specimen available to researchers across the world.

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phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things)

Cited by 61 publications

References 145 publications

Phylogenetically conservative trait correlation: Quantification and interpretation

Phylogenetically conservative trait correlation: Quantification and interpretation

Deep-time biodiversity patterns and the dinosaurian fossil record of the Late Cretaceous Western Interior, North America

Dots on a screen: The past, present, and future of morphometrics in the study of nonavian dinosaurs

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