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ZENODO
Dataset . 2025
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2024
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2025
License: CC BY
Data sources: ZENODO
ZENODO
Dataset . 2025
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2025
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2025
License: CC BY
Data sources: Datacite
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Data from: Inferring state-dependent diversification rates using approximate Bayesian computation (ABC)

Authors: Xie, Shu; Valente, Luis; Etienne, Rampal.S;

Data from: Inferring state-dependent diversification rates using approximate Bayesian computation (ABC)

Abstract

State-dependent speciation and extinction (SSE) models provide a framework for quantifying whether species traits have an impact on evolutionary rates and how this shapes the variation in species richness among clades in a phylogeny. However, SSE models are becoming increasingly complex, limiting the application of likelihood-based inference methods. Approximate Bayesian computation (ABC), a likelihood-free approach, is a potentially powerful alternative for estimating parameters. One of the key challenges in using ABC is the selection of efficient summary statistics, which can greatly affect the accuracy and precision of the parameter estimates. In state-dependent diversification models, summary statistics need to capture the complex relationships between rates of diversification and species traits. Here, we develop an ABC framework to estimate state-dependent speciation, extinction and transition rates in the BiSSE (binary state dependent speciation and extinction) model. Using different sets of candidate summary statistics, we then compare the inference ability of ABC with that of using likelihood-based maximum likelihood (ML) and Markov chain Monte Carlo (MCMC) methods. Our results show the ABC algorithm can accurately estimate state-dependent diversification rates for most of the model parameter sets we explored. The inference error of the parameters associated with the species-poor state is larger with ABC than in the likelihood estimations only when the speciation rate is highly asymmetric between the two states (λ1 / λ0 = 5). Furthermore, we find that the combination of normalized lineage-through-time (nLTT) statistics and phylogenetic signal in binary traits (Fitz and Purvis’s D) constitute efficient summary statistics for the ABC method. By providing insights into the selection of suitable summary statistics, our work aims to contribute to the use of the ABC approach in the development of complex state-dependent diversification models, for which a likelihood is not available.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
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