Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 55,138 bioRxiv papers from 254,399 authors.

A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates

By Joelle Barido-Sottani, Timothy G Vaughan, Tanja Stadler

Posted 11 Oct 2018
bioRxiv DOI: 10.1101/440982

Heterogeneous populations can lead to important differences in birth and death rates across a phylogeny. Taking this heterogeneity into account is thus critical to obtain accurate estimates of the underlying population dynamics. We present a new multi-state birth-death model (MSBD) that can estimate lineage-specific birth and death rates. For species phylogenies, this corresponds to estimating lineage-dependent speciation and extinction rates. Contrary to existing models, we do not require a prior hypothesis on a trait driving the rate differences and we allow the same rates to be present in different parts of the phylogeny. Using simulated datasets, we show that the MSBD model can reliably infer the presence of multiple evolutionary regimes, their positions in the tree, and the birth and death rates associated with each. We also present a re-analysis of two empirical datasets and compare the results obtained by MSBD and by the existing software BAMM. The MSBD model is implemented as a package in the Bayesian inference software BEAST2, which allows joint inference of the phylogeny and the model parameters.

Download data

  • Downloaded 493 times
  • Download rankings, all-time:
    • Site-wide: 16,335 out of 55,165
    • In evolutionary biology: 1,251 out of 3,820
  • Year to date:
    • Site-wide: 14,554 out of 55,165
  • Since beginning of last month:
    • Site-wide: 7,583 out of 55,165

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide

Sign up for the Rxivist weekly newsletter! (Click here for more details.)