DOI: 10.5061/dryad.sxksn03dj
title: Evolution is coupled with branching across many granularities of life

description: Across many scales of life, the rate of evolutionary change is often
 accelerated at the time when one lineage splits into two. The emergence of
 novel protein function can be facilitated by gene duplication
 (neofunctionalisation); rapid morphological change is often accompanied
 with speciation (punctuated equilibrium); and the establishment of
 cultural identity is frequently driven by sociopolitical division
 (schismogenesis). In each case, the changes resist re-homogenisation;
 promoting assortment into distinct lineages that are susceptible to
 different selective pressures, leading to rapid divergence. The
 traditional gradualistic view of evolution struggles to detect this
 phenomenon. We propose a probabilistic framework that constructs
 phylogenies, tests for saltative branching, and improves divergence time
 estimation by estimating the independent contributions of gradual and
 abrupt change on each lineage. We provide evidence of saltative branching
 for proteins (aminoacyl-tRNA synthetases), animal morphologies
 (cephalopods), and human languages (Indo-European). These three cases
 provide unique insights: for aminoacyl-tRNA synthetases, the trees are
 substantially different from those obtained under gradualist models; we
 estimate that 99% of Cephalopod morphological changes coincided with
 speciation events; and Indo-European dispersal is estimated to have
 started around 6000 BCE, corroborating the recently proposed hybrid
 explanation. Our open-source code is available under a GPL license.
description: # Evolution is coupled with branching across many granularities of life
 [https://doi.org/10.5061/dryad.sxksn03dj](https://doi.org/10.5061/dryad.sxksn03dj) ## Description of the data and file structure This repository contains the following files for each dataset (aaRS amino acid sequences, cephalopod morphologies, and Indo-European cognates): `.log file:` The posterior distribution log file produced by BEAST 2. These files are combined across two or more MCMC chains, and are all post-burnin. `.trees file:`The posterior distribution tree files produced by BEAST 2.These files are combined across two or more MCMC chains, and are all post-burnin. `.nexus file:`The CCD-0 summary tree of the respective `.trees` file, using median tree heights. Note that the `log`, `trees`, and `nexus` files are available from both the `gradual` and `spikes` models, produced under the gradual and gradual+abrupt models respectively. ### Files and variables #### File: aars.gradual.log \**Description:**aaRS log file(gradual clock model) #### File: aars.spikes.log \**Description:**aaRS log file(gradual+abrupt clock model) #### File: cephalopod.gradual.log \**Description:**cephalopod log file(gradual clock model) #### File: cephalopod.spikes.log \**Description:**cephalopod log file(gradual+abrupt clock model) #### File: indoeuropean.gradual.log \**Description:**Indo-European log file(gradual clock model) #### File: indoeuropean.spikes.log \**Description:**Indo-European log file(gradual+abrupt clock model) #### File: aars.gradual.trees \**Description:**aaRS tree log file(gradual clock model) #### File: aars.spikes.trees \**Description:**aaRS tree log file(gradual+abrupt clock model) #### File: cephalopod.gradual.trees \**Description:**cephalopod tree log file(gradual clock model) #### File: cephalopod.spikes.trees \**Description:**cephalopod tree log file(gradual+abrupt clock model) #### File: indoeuropean.gradual.trees \**Description:**Indo-European tree log file(gradual clock model) #### File: indoeuropean.spikes.trees \**Description:**Indo-European tree log file(gradual+abrupt clock model) #### File: aars.gradual.nexus \**Description:**aaRS summary tree (gradual clock model) #### File: aars.spikes.nexus \**Description:**aaRS summary tree (gradual+abrupt clock model) #### File: cephalopod.gradual.nexus \**Description:**cephalopod summary tree (gradual clock model) #### File: cephalopod.spikes.nexus \**Description:**cephalopod summary tree (gradual+abrupt clock model) #### File: indoeuropean.gradual.nexus \**Description:**Indo-European summary tree (gradual clock model) #### File: indoeuropean.spikes.nexus \**Description:**Indo-European summary tree (gradual+abrupt clock model) ## Code/software The results of the manuscript were generated using v1.0.0 of the Gamma Spike Clock model for BEAST 2, found at [https://github.com/jordandouglas/GammaSpikeModel.](https://github.com/jordandouglas/GammaSpikeModel)