scholarly journals Nothing Wrong with the Analysis of Clades in Comparative Evolutionary Studies: A Reply to Poe et al

2020 ◽  
Vol 70 (1) ◽  
pp. 197-201
Author(s):  
Joanna Baker ◽  
Andrew Meade ◽  
Mark Pagel ◽  
Chris Venditti
Keyword(s):  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Study ◽  
Evolutionary Studies ◽  
Clade Selection

Abstract In a recent paper, Poe et al. assert that scientists should abandon clade-based approaches, particularly those using named taxonomic ranks. Poe et al. attempt to demonstrate that clade selection can have effects on the results of evolutionary analyses but unfortunately fall short of making any robust conclusions. Here, we demonstrate that the assertions made by Poe et al. have two important flaws: (i) an erroneous view of modern phylogenetic comparative methods; and (ii) a lack of statistical rigor in their analyses. We repeat Poe et al.’s analysis but using appropriate phylogenetic comparative approaches. We demonstrate that results remain consistent regardless of the clade definition. We go on to discuss the value of taxonomic groupings and how they can provide meaningful units of comparison in evolutionary study. Unlike the disheartening suggestion to abandon the use of clades, scientists can instead continue to use phylogenetic “ corrections” that are already the standard for most comparative evolutionary analyses. [Comparative methods; evolution; phylogeny; taxonomy.]

scholarly journals Explaining large-scale patterns of vertebrate diversity

2015 ◽  
Vol 11 (7) ◽  
pp. 20150506 ◽  
Author(s):  
John J. Wiens
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Metabolic Rates ◽  
Diversification Rates ◽  
Richness Patterns ◽  
Current Species

The major clades of vertebrates differ dramatically in their current species richness, from 2 to more than 32 000 species each, but the causes of this variation remain poorly understood. For example, a previous study noted that vertebrate clades differ in their diversification rates, but did not explain why they differ. Using a time-calibrated phylogeny and phylogenetic comparative methods, I show that most variation in diversification rates among 12 major vertebrate clades has a simple ecological explanation: predominantly terrestrial clades (i.e. birds, mammals, and lizards and snakes) have higher net diversification rates than predominantly aquatic clades (i.e. amphibians, crocodilians, turtles and all fish clades). These differences in diversification rates are then strongly related to patterns of species richness. Habitat may be more important than other potential explanations for richness patterns in vertebrates (such as climate and metabolic rates) and may also help explain patterns of species richness in many other groups of organisms.

scholarly journals Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes

2019 ◽  
Vol 50 (1) ◽  
pp. 405-425 ◽  
Author(s):  
Dean C. Adams ◽  
Michael L. Collyer
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Biology ◽  
Generalized Least Squares ◽  
Comparative Methods ◽  
High Dimensional ◽  
Phenotypic Integration ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Trends ◽  
Phenotype Space ◽  
Multivariate Phenotypes

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

scholarly journals The evolution of parental care diversity in amphibians

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Andrew I. Furness ◽  
Isabella Capellini
Keyword(s):  
Parental Care ◽  
Developmental Stages ◽  
Comparative Methods ◽  
Biparental Care ◽  
Phylogenetic Comparative Methods ◽  
Amphibian Species ◽  
Full Spectrum

Abstract Parental care is extremely diverse across species, ranging from simple behaviours to complex adaptations, varying in duration and in which sex cares. Surprisingly, we know little about how such diversity has evolved. Here, using phylogenetic comparative methods and data for over 1300 amphibian species, we show that egg attendance, arguably one of the simplest care behaviours, is gained and lost faster than any other care form, while complex adaptations, like brooding and viviparity, are lost at very low rates, if at all. Prolonged care from the egg to later developmental stages evolves from temporally limited care, but it is as easily lost as it is gained. Finally, biparental care is evolutionarily unstable regardless of whether the parents perform complementary or similar care duties. By considering the full spectrum of parental care adaptations, our study reveals a more complex and nuanced picture of how care evolves, is maintained, or is lost.

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