Including Distorted Specimens in Allometric Studies: Linear Mixed Models Account for Deformation.

Allometry-patterns of relative change in body parts-is a staple for examining how clades exhibit scaling patterns representative of evolutionary constraint on phenotype, or quantifying patterns of ontogenetic growth within a species. Reconstructing allometries from ontogenetic series is one of the few methods available to reconstruct growth in fossil specimens. However, many fossil specimens are deformed (twisted, flattened, and displaced bones) during fossilization, changing their original morphology in unpredictable and sometimes undecipherable ways. To mitigate against post burial changes, paleontologists typically remove clearly distorted measurements from analyses. However, this can potentially remove evidence of individual variation and limits the number of samples amenable to study, which can negatively impact allometric reconstructions. Ordinary least squares (OLS) regression and major axis regression are common methods for estimating allometry, but they assume constant levels of residual variation across specimens, which is unlikely to be true when including both distorted and undistorted specimens. Alternatively, a generalized linear mixed model (GLMM) can attribute additional variation in a model (e.g., fixed or random effects). We performed a simulation study based on an empirical analysis of the extinct cynodont, Exaeretodon argentinus, to test the efficacy of a GLMM on allometric data. We found that GLMMs estimate the allometry using a full dataset better than simply using only non-distorted data. We apply our approach on two empirical datasets, cranial measurements of actual specimens of E. argentinus (n = 16) and femoral measurements of the dinosaur Tawa hallae (n = 26). Taken together, our study suggests that a GLMM is better able to reconstruct patterns of allometry over an OLS in datasets comprised of extinct forms and should be standard protocol for anyone using distorted specimens.

Alometria­el estudio de patrónes midiendo los cambios de proporciónes entre diferentes partes del cuerpo­es un método popularmente usado para estudiar como clados exhiben patrónes fenotípicos que representan restricciónes evolutivas, o para cuantificar patrónes de ontogenia entre una especie. Reconstruyendo alometrias para series ontogeneticas es uno de los pocos métodos disponibles para reconstruir el crecimiento de especies fósiles. Sin embargo, fósiles sufren de deformaciónes tafonomicas que alteran la morfología original y algunas veces en maneras no deseadas. Para mitigar estas alteraciones tafonomicas, paleontólogos excluyen mediciones alteradas de sus análisis. Desafortunadamente, esto limita el numero de muestras y potencialmente elimina evidencia de variación individual, impactando reconstrucciones alometricas. Mínimos Cuadrados Ordinarios (MCO) es un método frecuentemente usado para estimar alometria, pero asume niveles constantes de varición entre especímenes; esto es improbable cuando uno incluye especímenes deformados y especímenes indeformables. Alternativamente, Modelos Lineales Generalizados Mixtos (MLGM) pueden atribuir variciónes adicionales en un modelo. Nosotros corrimos simulaciones basadas en análisis empíricos del cinodonte extinto, Exaeretodon argentinus, para determinar la eficacia de MLGM con datos alometricos. Nosotros descubrimos que MLGM estima la alometria usando un conjunto de datos completos, en lugar de solo usar datos distorsionados. Aplicamos este método en dos conjuntos de datos empíricos: medidas craneales de especímenes de E. argentinus (n = 16) y medidas femorales del dinosaurio Tawa hallae (n = 26). Nuestros estudios indican que MLGM puede reconstruir mejor los patrónes de alometria sobre MCO con conjuntos de datos que incluyen especímenes extintos, y debería ser el protocolo estándar cuándo se usan especímenes que están deformados.

The effects of stochastic and episodic movement of the optimum on the evolution of the G-matrix and the response of the trait mean to selection.

Theoretical and empirical results demonstrate that the G-matrix, which summarizes additive genetic variances and covariances of quantitative traits, changes over time. Such evolution and fluctuation of the G-matrix could potentially have wide-ranging effects on phenotypic evolution. Nevertheless, no studies have yet addressed G-matrix stability and evolution when movement of an intermediate optimum includes large, episodic jumps or stochasticity. Here, we investigate such scenarios by using simulation-based models of G-matrix evolution. These analyses yield four important insights regarding the evolution and stability of the G-matrix. (i) Regardless of the model of peak movement, a moving optimum causes the G-matrix to orient towards the direction of net peak movement, so that genetic variance is enhanced in that direction (the variance enhancement effect). (ii) Peak movement skews the distribution of breeding values in the direction of movement, which impedes the response to selection. (iii) The stability of the G-matrix is affected by the overall magnitude and direction of peak movement, but modes and rates of peak movement have surprisingly small effects (the invariance principle). (iv) Both episodic and stochastic peak movement increase the probability that a population will fall below its carrying capacity and go extinct. We also present novel equations for the response of the trait mean to multivariate selection, which take into account the higher moments of the distribution of breeding values.

Molecular phylogeny of the subfamily Amphistichinae (Teleostei: Embiotocidae) reveals parallel divergent evolution of red pigmentation in two rapidly evolving lineages of sand-dwelling surfperch.

Pigment evolution was reconstructed in the subfamily Amphistichinae, a six-species clade of the surfperches, family Embiotocidae. Assignment was confirmed for all species within the subfamily, but low levels of differentiation were found among species within the subfamily, suggesting a recent radiation. The new phylogeny differs from previous hypotheses by the placement of the spotfin surfperch Hyperprosopon anale at the base of the subfamily, while still preserving the calico surfperch Amphistichus koelzi and the redtailed surfperch Amphistichus rhodoterus as sister species. Phenotypically, A. rhodoterus, A. koelzi and the silver surfperch Hyperprosopon ellipticum express high levels of red pigmentation. The barred surfperch, Amphistichus argenteus and the walleye surfperch Hyperprosopon argenteum express little to no red pigment, while basal H. anale expresses an intermediate amount of red pigment. Red pigmentation is proposed to have experienced parallel divergent evolution in each genus within the subfamily.