Evolution is coupled with branching across many granularities of life
Data files
Mar 14, 2025 version files 1.12 GB
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aars.gradual.log
106.22 MB
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aars.gradual.nexus
258.47 KB
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aars.gradual.trees
51 MB
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aars.spikes.log
121.74 MB
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aars.spikes.nexus
258.30 KB
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aars.spikes.trees
59.46 MB
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cephalopod.gradual.log
129.01 MB
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cephalopod.gradual.nexus
137.58 KB
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cephalopod.gradual.trees
146.03 MB
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cephalopod.spikes.log
147.96 MB
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cephalopod.spikes.nexus
137.36 KB
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cephalopod.spikes.trees
67.73 MB
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indoeuropean.gradual.log
24.18 MB
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indoeuropean.gradual.nexus
274.94 KB
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indoeuropean.gradual.trees
51.02 MB
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indoeuropean.spikes.log
68.93 MB
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indoeuropean.spikes.nexus
282.48 KB
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indoeuropean.spikes.trees
144.98 MB
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README.md
2.98 KB
Abstract
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.
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.