On the mapping between evolutionary scenarios and governing rules in state-dependent speciation-extinction models
- 1Washington University in Saint Louis
Abstract
Biologists often wish to explain why one trait is more common than its alternatives among species in a clade: is it due to asymmetries in diversification or character evolution processes? State-dependent speciation-extinction (SSE) models provide a flexible framework for jointly modeling such processes. Here, we derive mathematical results that define functional relationships (``rulesets") among rate parameters, establish a mapping between rulesets and evolutionary scenarios, and characterize how these scenarios give rise to different long-term tip state distributions. In particular, we show that multiple evolutionary scenarios can produce identical stationary distributions of tip state frequencies. Performing inference on simulated data from extant-only trees, we find that not all scenarios are equally favored for explaining datasets constructed solely from extant species. This bias could arise from the interplay between mixing rates, elapsed time, and the conditioning inherent in tree likelihoods. As a proof of concept, we apply our framework to the binary SSE (BiSSE) model across multiple Squamate clades and conduct a literature survey of previous BiSSE analyses on Angiosperm phylogeny. We show that, to some extent, the preference for certain scenarios observed in simulations is also reflected in analyses of empirical trees. This study provides a theoretical ground to directly link data-generating process and observed tip state frequencies under an SSE framework.
Related
- The Principle of Natural Selection and its Governing Interactions of Reproduction and Speciation: A Formal Framework for Reproductive Architecture and Ancestry
- Speciation, extinction and explosions induced by sudden environmental changes
- fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
- Unmasking the large and highly repetitive genome of Phlox reveals a complex evolutionary history of speciation with gene flow
- Eco-evolutionary dynamics create extinction avalanches in mutualistic-antagonistic networks
BibTeX
@misc{soewongsono2026mapping,
title = {{On the mapping between evolutionary scenarios and governing rules in state-dependent speciation-extinction models}},
author = {A. C. Soewongsono and M. J. Landis},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.24.754193},
url = {https://www.biorxiv.org/content/10.64898/2026.09.24.754193v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - On the mapping between evolutionary scenarios and governing rules in state-dependent speciation-extinction models
AU - A. C. Soewongsono
AU - M. J. Landis
PY - 2026
DA - 2026/09/24
PB - bioRxiv
DO - 10.64898/2026.09.24.754193
UR - https://www.biorxiv.org/content/10.64898/2026.09.24.754193v1
AB - Biologists often wish to explain why one trait is more common than its alternatives among species in a clade: is it due to asymmetries in diversification or character evolution processes? State-dependent speciation-extinction (SSE) models provide a flexible framework for jointly modeling such processes. Here, we derive mathematical results that define functional relationships (``rulesets") among rate parameters, establish a mapping between rulesets and evolutionary scenarios, and characterize how these scenarios give rise to different long-term tip state distributions. In particular, we show that multiple evolutionary scenarios can produce identical stationary distributions of tip state frequencies. Performing inference on simulated data from extant-only trees, we find that not all scenarios are equally favored for explaining datasets constructed solely from extant species. This bias could arise from the interplay between mixing rates, elapsed time, and the conditioning inherent in tree likelihoods. As a proof of concept, we apply our framework to the binary SSE (BiSSE) model across multiple Squamate clades and conduct a literature survey of previous BiSSE analyses on Angiosperm phylogeny. We show that, to some extent, the preference for certain scenarios observed in simulations is also reflected in analyses of empirical trees. This study provides a theoretical ground to directly link data-generating process and observed tip state frequencies under an SSE framework.
ER -