Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates

@article{Warnock2020AssessingTI,
  title={Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates},
  author={Rachel C. M. Warnock and Tracy A. Heath and Tanja Stadler},
  journal={Paleobiology},
  year={2020},
  volume={46},
  pages={137 - 157}
}
Abstract. Estimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates based on the observed branching times in a given phylogeny of living species. The fossilized birth–death (FBD) process is a model that… 

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References

SHOWING 1-10 OF 53 REFERENCES

Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.

A new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record is presented and represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.

Bias in phylogenetic measurements of extinction and a case study of end‐Permian tetrapods

Here, simulations are used to investigate the adequacy of measures of phylogenetic clustering of extinction when applied to phylogenies of fossil taxa while assuming a Brownian motion model of trait evolution, and expected biases under a variety of evolutionary and analytical scenarios are characterized.

PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data

PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data is presented and a new birth–death model is developed to correlate the variation of speciation/extinction rates with changes of a continuous trait.

EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

  • D. Rabosky
  • Biology, Environmental Science
    Evolution; international journal of organic evolution
  • 2010
It is shown that when diversification rates vary among lineages, simple estimators based on the birth–death process are unable to recover true extinction rates, suggesting that extinction rates should not be estimated in the absence of fossil data.

Origination and extinction components of taxonomic diversity: general problems

  • M. Foote
  • Environmental Science, Geography
    Paleobiology
  • 2000
Modeling supports intuitive and empirical arguments that single-interval taxa, being especially sensitive to variation in preservation and interval length, produce many undesirable distortions of the fossil record, and suggests which rate measures are likely to be most accurate in principle.

Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

A major update of the software PyRate is presented, which implements substantial methodological advancements, including more complex and realistic models of preservation, a reversible jump Markov chain Monte Carlo algorithm to estimate origination and extinction rates and their temporal variation, and a substantial boost in performance.

Reconciling molecular phylogenies with the fossil record

It is shown that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies, and it is suggested that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr.

When Can Clades Be Potentially Resolved with Morphology?

  • D. Bapst
  • Biology, Environmental Science
    PloS one
  • 2013
Using branching simulations, intrinsic resolution is quantified across several models of morphological differentiation and taxonomic sampling, suggesting that poor phylogenetic resolution occasionally observed in morphological phylogenetics may result from a lack of intrinsic resolvability within groups.

The fossilized birth–death process for coherent calibration of divergence-time estimates

The fossilized birth–death process is introduced—a fossil calibration method that unifies extinct and extant species with a single macroevolutionary model, eliminating the need for ad hoc calibration priors and yielding more accurate node age estimates while providing a coherent measure of statistical uncertainty.

FAIR SAMPLING OF TAXONOMIC RICHNESS AND UNBIASED ESTIMATION OF ORIGINATION AND EXTINCTION RATES

Paleobiologists are reaching a consensus that biases in diversity curves, origination rates, and extinction rates need to be removed using statistical estimation methods. Diversity estimates are
...