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 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.