scholarly journals Peer Review #1 of "Realistic scenarios of missing taxa in phylogenetic comparative methods and their effects on model selection and parameter estimation (v0.1)"

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7917 ◽  
Author(s):  
Rafael S. Marcondes

Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree’s terminal taxa, but rarely do a tree and dataset include all taxa within a clade. Because the probability that a taxon is included in a dataset depends on ecological traits that have phylogenetic signal, missing taxa in real datasets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but the problem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work.


2021 ◽  
pp. 004912412199555
Author(s):  
Michael Baumgartner ◽  
Mathias Ambühl

Consistency and coverage are two core parameters of model fit used by configurational comparative methods (CCMs) of causal inference. Among causal models that perform equally well in other respects (e.g., robustness or compliance with background theories), those with higher consistency and coverage are typically considered preferable. Finding the optimally obtainable consistency and coverage scores for data [Formula: see text], so far, is a matter of repeatedly applying CCMs to [Formula: see text] while varying threshold settings. This article introduces a procedure called ConCovOpt that calculates, prior to actual CCM analyses, the consistency and coverage scores that can optimally be obtained by models inferred from [Formula: see text]. Moreover, we show how models reaching optimal scores can be methodically built in case of crisp-set and multi-value data. ConCovOpt is a tool, not for blindly maximizing model fit, but for rendering transparent the space of viable models at optimal fit scores in order to facilitate informed model selection—which, as we demonstrate by various data examples, may have substantive modeling implications.


2015 ◽  
Vol 11 (7) ◽  
pp. 20150506 ◽  
Author(s):  
John J. Wiens

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.


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