Exploring the macroevolutionary signature of asymmetric inheritance at speciation
Data files
Aug 19, 2024 version files 32.94 KB
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README.md
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supp_data.zip
Abstract
Popular comparative phylogenetic models such as Brownian Motion, Ornstein-Ulhenbeck, and their extensions, assume that, at speciation, a trait value is inherited identically by two descendant species. This assumption contrasts with models of speciation at a micro-evolutionary scale where descendants’ phenotypic distributions are sub-samples of the ancestral distribution. Different speciation mechanisms can lead to a displacement of the ancestral phenotypic mean among descendants and an asymmetric inheritance of the ancestral phenotypic variance. In contrast, even macro-evolutionary models that account for intraspecific variance assume symmetrically conserved inheritance of ancestral phenotypic distribution at speciation. Here we develop an Asymmetric Brownian Motion model (ABM) that relaxes the assumption of symmetric and conserved inheritance of the ancestral distribution at the time of speciation. The ABM jointly models the evolution of both intra- and inter-specific phenotypic variation. It also infers the mode of phenotypic inheritance at speciation, which can range from a symmetric and conserved inheritance, where descendants inherit the ancestral distribution, to an asymmetric and displaced inheritance, where descendants inherit divergent phenotypic means and variances. To demonstrate this model, we analyze the evolution of beak morphology in Darwin finches, finding evidence of displacement at speciation. The ABM model helps to bridge micro- and macro-evolutionary models of trait evolution by providing a more robust framework for testing the effects of ecological speciation, character displacement, and niche partitioning on trait evolution at the macro-evolutionary scale.
README: Exploring the macroevolutionary signature of asymmetric inheritance at speciation
This dataset contains what is needed to reproduce the application of the ABM model on the Coerebinae dataset.
Description of the Data and file structure
Data/Coerebinae.csv: Trait dataset in a .csv format. This file contains individual measurements of 4 beak traits as well as information about the measured individual (Species name, specimen ring number, sex, and whether the individual was a juvenile or not). Bill total culmen (cm) refers to the length of the upper part of the beak from the tip to the skull. Bill nares (cm) refers to the length of the upper part of the beak from the tip to the nares. Bill width (cm) refers to the width of the upper part of the beak at the nares. Bill depth (cm) refers to the height of the beak at the nares. Missing data is marked as NA.
Data/Coerebinae.tre. Phylogenetic tree file in Newick format with branch lengths representing divergence time in my.
Scripts/Analysis_thraupidae.R: to run the analyses in R
Scripts/mcmc_ADIM.R: script with the implementation of the ABM model.
Scripts/sim_data_ABM.R can be used to reproduce the simulations. The model can then be run with the function mcmc_ADIM() and the tuning provided in the manuscript.
Sharing/Access Information
The data is derived from Reaney, A. M., Y. Bouchenak-Khelladi, J. A. Tobias, and A. Abzhanov. 2020. Ecological and morphological determinants of evolutionary diversification in Darwin’s finches and their relatives. Ecology and Evolution 10:14020–14032.
The scripts are original.
The ABM model is maintained and developed further in the repository https://github.com/theogab/ABM