Methods for Estimating Extinction and Diversification Rates Ezra - - PowerPoint PPT Presentation

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Sep 17, 2023 50 likes •111 views

Methods for Estimating Extinction and Diversification Rates Ezra Winter-Nelson Motivation Phylogenetic estimation How do we gauge a models applicability at evolutionary timescales? Fossil records Environmental events

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Methods for Estimating Extinction and Diversification Rates

Ezra Winter-Nelson

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Motivation

Phylogenetic estimation
How do we gauge a model’s applicability

at evolutionary timescales?

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Fossil records

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Environmental events

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Current Methods

BAMM (Bayesian)
MEDUSA (Maximum Likelihood)
TreePar (Maximum Likelihood)
CoMET (Bayesian)

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Considerations

Molecular Clock

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Strict

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Relaxed

Extinction Type

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Global

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Lineage-Specific

Molecular Ecology Volume 23, Issue 24, pages 5947-5965, 30 OCT 2014 DOI: 10.1111/mec.12953 http://onlinelibrary.wiley.com/doi/10.1111/mec.12953/full#mec12953-fig-0002

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Goals

Comprehensive exploration of the field

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Pros/Cons of each method

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Major roadblocks

State of the field going forward

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New directions

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Predictive efficacy

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References

Ho, S. Y. W. and Duchêne, S. (2014), Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol, 23: 5947–

5965. doi:10.1111/mec.12953

Laurent, S., Robinson-Rechavi, M., Salamin, N. Are we able to detect mass extinction events using phylogenies? bioRxiv 004572; doi: https://doi.org/10.1101/004572 Laurent, S./ Robinson-Rechavi, M., Salamin, N. (2015). Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions. BMC Evolutionary Biology, 15:157. doi: 10.1186/s12862-015-0432-z. May, M. R., Höhna, S. and Moore, B. R. (2016). A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary. Methods Ecol Evol, 7: 947–959. doi:10.1111/2041-210X.12563. May, M. R., & Moore, B. R. (2016). How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods. Systematic Biology, 65(6), 1076–1084. http://doi.org/10.1093/sysbio/syw026 Vitti, J.J., Grossman, S.R., and Sabeti, P.C. (2013). Detecting natural selection in genomic data. Annual Review of Genetics, 47, 97–120.