Biology subjects

Meyer, X.

Publications and source records attributed to Meyer, X..

4 recordsLinked to original sources

bioRxiv2021

To draw or not to draw: understanding the temporal organization of drawing behaviour using fractal analyses

Studies on drawing often focused on spatial aspects of the finished products. Here, the drawing behaviour was studied by analysing its intermittent process, between drawing (i.e. marking a surface) and interruption (i.e. a pause in the marking gesture). To assess how this intermittence develops with age, we collected finger-drawings on a touchscreen by 185 individuals (children and adults). We measured the temporal structure of each drawing sequence to determine its complexity. To do this, we applied temporal fractal estimators to each drawing time series before combining them in a Principal Component Analysis procedure. The youngest children (3 years-old) drew in a more stereotypical way with long-range dependence detected in their alternations between states. Among older children and adults, the complexity of drawing sequences increased showing a less predictable behaviour as their drawings become more detailed and figurative. This study improves our understanding of the temporal aspects of drawing behaviour, and contributes to an objective understanding of its ontogeny.

animal behavior and cognition↗

bioRxiv2021

Western Amazon was a center of Neotropical fish dispersal, as evidenced by the continental-wide time-stratified biogeographic analysis of the hyper-diverse Hypostomus catfish

The Amazon is probably the most diverse realm on Earth, and is considered to be the primary source of diversity and a center of dispersal for Neotropical terrestrial organisms. Yet, the assumption that the Amazon basin is a primordial place of fish species origination and dispersal into other drainages still need to be tested. We addressed this issue by inferring a time-stratified biogeographic history and reconstructing the ancestral habitat preference of Hypostomus, a continentally widespread and species-rich Neotropical genus. We found that Hypostomus emerged in the Western Amazon ([~]14.7 Ma), when the Western Amazon River was flowing northwards and disconnected from the Eastern Amazon. We show that dispersal events in the first half of Hypostomus evolution occurred from the Western Amazon into adjacent basins, initiating its Neotropical radiation. The ancestral preferred habitat consisted in small rivers with running waters, a predominant habitat in river headwaters. Because of strong niche conservatism in the early evolution of Hypostomus, we suggest that most of the out-of-Western-Amazon dispersal occurred via headwater captures. The radiation of Hypostomus was further promoted by major reconfigurations of river basins, which opened dispersal opportunities into new drainages. Diversification in habitat preference coincided with colonization of basins already occupied by congenerics, indicative of niche shifts triggered by inter-specific competition and species coexistence. By analyzing the evolutionary history of Hypostomus, we show that Western Amazon was the main center of fish dispersal in the Neotropical Region from Middle Miocene to the present, supporting the cradle hypothesis of fish origination and dispersal.

evolutionary biology↗

bioRxiv2019

Adaptive Tree Proposals for Bayesian Phylogenetic Inference

Bayesian inference of phylogenies with MCMC is without a doubt a staple in the study of evolution. Yet, this method still suffers from a practical challenge identified more than two decades ago: designing tree topology proposals that efficiently sample the tree space. In this article, I introduce the concept of tree topology proposals that adapt to the posterior distribution as it is estimated. I use this concept to elaborate two adaptive variants of existing proposals and an adaptive proposal based on a novel design philosophy in which the structure of the proposal is informed by the posterior distribution of trees. I investigate the performance of these proposals by first presenting a metric that captures the performance of each proposals within a mixture. Using this metric, I then compare the adaptive proposals performance to the performance of standard and parsimony-guided proposals on 11 empirical datasets. Using adaptive proposals led to consistent performance gains and resulted in up to 18-fold increases in mixing efficiency and 6-fold increases in converge rate without increasing the computational cost of these analyses. [Bayesian inference; Adaptive tree proposals; Markov chain Monte Carlo; phylogenetics; posterior probability distribution.]

evolutionary biology↗

bioRxiv2018

Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

The estimation of origination and extinction rates and their temporal variation is central to understanding diversity patterns and the evolutionary history of clades. The fossil record provides the most direct evidence of extinction and biodiversity changes through time and has long been used to infer the dynamics of diversity changes in deep time. The software PyRate implements a Bayesian framework to analyze fossil occurrence data to estimate the rates of preservation, origination and extinction while incorporating several sources of uncertainty. This fully probabilistic approach allows us to explicitly assess the statistical support of alternative macroevolutionary hypotheses and to infer credible intervals around parameter estimates. Here, we present a major update of the software, which implements substantial methodological advancements, including more complex and realistic models of preservation, a reversible jump Markov chain Monte Carlo algorithm to estimate origination and extinction rates and their temporal variation, and a substantial boost in performance. We demonstrate the new functionalities through extensive simulations and with the analysis of a large dataset of Cenozoic marine mammals. We identify several significant shifts in origination and extinction rates of marine mammals, underlying a late Miocene diversity peak and a subsequent 50% diversity decline towards the present. Our analyses indicate that explicit statistical model testing, which is often neglected in fossil-based macroevolutionary analyses, is crucial to obtain accurate and robust results. PyRate provides a flexible, statistically sound analytical framework, which we think can serve as a useful toolkit for many future studies in paleobiology.

paleontology↗