Biology subjects

Revell, L. J.

Publications and source records attributed to Revell, L. J..

5 recordsLinked to original sources

bioRxiv2021

Testing for genetic assimilation with phylogenetic comparative analysis: Conceptual, methodological, and statistical considerations

Genetic assimilation is a process that leads to reduced phenotypic plasticity during adaptation to novel conditions, a potentially important phenomenon under global environmental change. Null expectations when testing for genetic assimilation, however, are not always clear. For instance, the statistical artifact of regression to the mean could bias us towards detecting genetic assimilation when it has not occurred. Likewise, the specific mechanism underlying plasticity expression may affect null expectations under neutral evolution. We used macroevolutionary numerical simulations to examine both of these important issues and their interaction, varying whether or not plasticity evolves, the evolutionary mechanism, trait measurement error, and experimental design. We also modified an existing reaction norm correction method to account for phylogenetic non-independence. We found: 1) regression to the mean is pervasive and can generate spurious support for genetic assimilation; 2) experimental design and post-hoc correction can minimize this spurious effect; and 3) neutral evolution can produce patterns consistent with genetic assimilation without constraint or selection, depending on the mechanism of plasticity expression. Additionally, we re-analyzed published macroevolutionary data supporting genetic assimilation, and found that support was lost after proper correction. Considerable caution is thus required whenever investigating genetic assimilation and reaction norm evolution at macroevolutionary scales.

evolutionary biology↗

bioRxiv2021

Testing for heterogeneous rates of discrete character evolution on phylogenies

Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. We present a method designed to test whether the rate of evolution of a discrete character has changed in one or more clades, lineages, or time periods. This method differs from other related approaches (such as the covarion model) in that the regimes in which the rate or process is postulated to have changed are specified a priori by the user, rather than inferred from the data. Similarly, it differs from methods designed to model a correlation between two binary traits in that the regimes mapped onto the tree are fixed. We apply our method to investigate the rate of dewlap color and/or caudal vertebra number evolution in Caribbean and mainland clades of the diverse lizard genus Anolis. We find little evidence to support any difference between mainland and island evolution in either character. We also examine the statistical properties of the method more generally and show that it has acceptable type I error, parameter estimation, and power. Finally, we discuss the relationship of our method to existing models of heterogeneity in the rate of discrete character evolution on phylogenies.

evolutionary biology↗

bioRxiv2021

A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree

Numerous questions in phylogenetic comparative biology revolve around the correlated evolution of two or more phenotypic traits on a phylogeny. In many cases, it may be sufficient to assume a constant value for the evolutionary correlation between characters across all the clades and branches of the tree. Under other circumstances, however, it is desirable or necessary to account for the possibility that the evolutionary correlation differs through time or in different sections of the phylogeny. Here, we present a method designed to fit a hierarchical series of models for heterogeneity in the evolutionary rates and correlation of two quantitative traits on a phylogenetic tree. We apply the method to two datasets: one for different attributes of the buccal morphology in sunfishes (Centrarchidae); and a second for overall body length and relative body depth in rock- and non-rock-dwelling South American iguanian lizards. We also examine the performance of the method for parameter estimation and model selection using a small set of numerical simulations.

evolutionary biology↗

bioRxiv2021

A variable-rate quantitative trait evolution model using penalized-likelihood

In recent years it has become increasingly popular to use phylogenetic comparative methods to investigate heterogeneity in the rate or process of quantitative trait evolution across the branches or clades of a phylogenetic tree. Here, I present a new method for modeling variability in the rate of evolution of a continuously-valued character trait on a reconstructed phylogeny. The underlying model of evolution is stochastic diffusion (Brownian motion), but in which the instantaneous diffusion rate ({sigma}2) also evolves by Brownian motion on a logarithmic scale. Unfortunately, its not possible to simultaneously estimate the rates of evolution along each edge of the tree and the rate of evolution of{sigma} 2 itself using Maximum Likelihood. As such, I propose a penalized-likelihood method in which the penalty term is equal to the log-transformed probability density of the rates under a Brownian model, multiplied by a smoothing coefficient,{lambda} , selected by the user.{lambda} determines the magnitude of penalty thats applied to rate variation between edges. Lower values of{lambda} penalize rate variation relatively little; whereas larger{lambda} values result in minimal rate variation among edges of the tree in the fitted model, eventually converging on a single value of{sigma} 2 for all of the branches of the tree. In addition to presenting this model here, I have also implemented it as part of my phytools R package in the function multirateBM. Using different values of the penalty coefficient,{lambda} , I fit the model to simulated data with: Brownian rate variation among edges (the model assumption); uncorrelated rate variation; rate changes that occur in discrete places on the tree; and no rate variation at all among the branches of the phylogeny. I then compare the estimated values of{sigma} 2 to their known true values. In addition, I use the method to analyze a simple empirical dataset of body mass evolution in mammals. Finally, I discuss the relationship between the method of this article and other models from the phylogenetic comparative methods and finance literature, as well as some applications and limitations of the approach.

evolutionary biology↗

bioRxiv2021

Molecular phylogeny of Puerto Rico Bank dwarf geckos (Squamata: Sphaerodactylidae: Sphaerodactylus)

AO_SCPLOWBSTRACTC_SCPLOWThe genus Sphaerodactylus is a very species-rich assemblage of sphaerodactylid lizards that has undergone a level of speciation in parallel to that of the well-known Anolis lizards. Nevertheless, molecular phylogenetic research on this group consists of a handful of smaller studies of regional focus (e.g., western Puerto Rico, the Lesser Antilles) or large-scale analyses based on relatively limited sequence data. Few medium-scale multi-locus studies exist-- for example, studies that encompass an entire radiation on an island group. Building upon previous work done in Puerto Rican Sphaerodactylus, we performed multi-locus sampling of Sphaerodactylus geckos from across the Puerto Rico Bank. We then used these data for phylogeny estimation with near-complete taxon sampling. We focused on sampling the widespread nominal species S. macrolepis and in so doing, we uncovered a highly divergent and morphologically distinct lineage of Sphaerodactylus macrolepis from Puerto Rico, Culebra, and Vieques islands, which we recognize as S. grandisquamis (Stejneger, 1904) on the basis of molecular and morphological characters. S. grandisquamis co-occurs with S. macrolepis only on Culebra Island but is highly genetically differentiated and morphologically distinct. Sphaerodactylus macrolepis is now restricted to the eastern Puerto Rico Bank, from Culebra east through the Virgin Islands and including the topotypic population on St. Croix. We include additional discussion of the evolutionary history and historical biogeography of the Sphaerodactylus of the Puerto Rican Bank in the context of these new discoveries.

evolutionary biology↗