A more precise speciation and extinction rate estimator

  title={A more precise speciation and extinction rate estimator},
  author={John Alroy},
  • J. Alroy
  • Published in Paleobiology 1 September 2015
  • Environmental Science
Abstract A new turnover rate metric is introduced that combines simplicity and precision. Like the related three-timer and gap-filler equations, it involves first identifying a cohort of taxa sampled in the time interval preceding the one of interest (call the intervals i0 and i1). Taxa sampled in i0 and i1 are two-timers (t2); those sampled in i0 and i2 but not i1 are part-timers (p); and taxa sampled only in either i1, i2, or i3 are newly notated here as either s1, s2, or s3. The gap-filler… 

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.

The r package divDyn for quantifying diversity dynamics using fossil sampling data

Unbiased time series of diversity dynamics are vital for quantifying the grand history of life. Applications include identifying ancient mass extinctions and inferring both biotic and abiotic

An examination of the impact of Olson’s extinction on tetrapods from Texas

This study examines the best record available for the time of the extinction, the tetrapod-bearing formations of Texas, at a finer stratigraphic scale than those previously employed, indicating that Olson’s Extinction is not an artefact of the method used to bin data by time in previous analyses.

The R package divDyn for quantifying diversity dynamics using fossil sampling data

DivDyn is introduced, a new R package that facilitates the calculation of taxonomic richness, extinction and origination rates from time-binned fossil sampling data, and Phanerozoic-scale diversity dynamics of marine invertebrates is displayed using the divDyn package.

A framework for the integrated analysis of the magnitude, selectivity, and biotic effects of extinction and origination

Abstract. The taxonomic and ecologic composition of Earth's biota has shifted dramatically through geologic time, with some clades going extinct while others diversified. Here, we derive a metric

The effects of geographic range size and abundance on extinction during a time of “sluggish”' evolution

Abstract. Geographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not

Evaluating the accuracy of biodiversity changes through geologic times: from simulation to solution

Abstract. Estimating biodiversity and its variations through geologic time is a notoriously difficult task, due to several taphonomic and methodological effects that make the reconstructed signal

Evolutionary rates of mid-Permian tetrapods from South Africa and the role of temporal resolution in turnover reconstruction

Abstract. The Main Karoo Basin of South Africa contains a near-continuous sequence of continental deposition spanning ∼80 Myr from the mid-Permian to the Early Jurassic. The terrestrial vertebrates

Testing Character Evolution Models in Phylogenetic Paleobiology

The authors ultimately fit and use a joint tree and diversification model to estimate a dated phylogeny of the Cincta (Echinodermata), a morphologically distinct group of Cambrian echinoderms that lack the fivefold radial symmetry characteristic of extant members of the phylum.



Accurate and precise estimates of origination and extinction rates

  • J. Alroy
  • Environmental Science
  • 2014
Abstract Paleobiologists have used many different methods for estimating rates of origination and extinction. Unfortunately, all equations that consider entire age ranges are distorted by the Pull of

Constant extinction, constrained diversification, and uncoordinated stasis in North American mammals

  • J. Alroy
  • Environmental Science, Geography
  • 1996

Origination and extinction components of taxonomic diversity: general problems

  • M. Foote
  • Environmental Science, Geography
  • 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.

Dynamics of origination and extinction in the marine fossil record

  • J. Alroy
  • Environmental Science, Geography
    Proceedings of the National Academy of Sciences
  • 2008
The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The

Modeling bivalve diversification: the effect of interaction on a macroevolutionary system

Results of this analysis suggest that interactions with other taxa have substantially affected bivalve global diversity through the Phanerozoic, particularly during the initial Ordovician radiation and following the Late Permian and Late Cretaceous mass extinctions.

Temporal variation in extinction risk and temporal scaling of extinction metrics

Many areas of paleobiological research require reliable extinction metrics. Branching-and-extinction simulations and data on Phanerozoic marine families and genera are used to investigate the

Clams and brachiopods—ships that pass in the night

The presumed geometry of clam and brachiopod clades (brachiopod declines matched closely by clam increases) has long served as primary data for the classic case of gradual replacement by competition

A factor analytic description of the Phanerozoic marine fossil record

  • J. Sepkoski
  • Geography, Environmental Science
  • 1981
Data on numbers of marine families within 91 metazoan classes known from the Phanerozoic fossil record are analyzed. The distribution of the 2800 fossil families among the classes is very uneven,

On the potential for ocean acidification to be a general cause of ancient reef crises

Anthropogenic rise in the carbon dioxide concentration in the atmosphere leads to global warming and acidification of the oceans. Ocean acidification (OA) is harmful to many organisms but especially

Morphological diversity in the evolutionary radiation of Paleozoic and post-Paleozoic crinoids

  • M. Foote
  • Geography, Geology
  • 1999
Analysis of discrete-character data that cover the principal features of the crinoid skeleton shows that both Paleozoic and post-Paleozoic increases in morphological disparity were abrupt; this is consistent with rapid exploitation of open ecological opportunities in both cases.