Evolution is coupled with branching across many granularities of life

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 synthetas..., , , # 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:**...,