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

  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},
  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… 

Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data

It is proved mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversisation is zero.

Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades.

The results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to yield potentially unreliable inferences about the diversification of extinct clades.

Global diversity dynamics in the fossil record are regionally heterogeneous

Global diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and

Fossil data support a pre-Cretaceous origin of flowering plants.

A Bayesian method is developed to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity and indicates that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group.

Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process

This work uses a combination of analytical and simulation techniques to explore phylogenetic network space under a birth-death-hybridization process and finds that the growth of phylogenetic networks and class membership is largely affected by the assumptions about macroevolutionary patterns of gene flow.

The SITE-100 Project: Site-Based Biodiversity Genomics for Species Discovery, Community Ecology, and a Global Tree-of-Life

The SITE-100 program is presented, which is an attempt at building the Tree-of-Life from whole-community sampling of high-biodiversity sites around the globe, and it is argued in favor of site-based sampling as an unorthodox but logistically efficient way to construct large phylogenetic trees.

Sustained high rates of morphological evolution during the rise of tetrapods.

It is shown that combining osteological and ichnological calibration data results in major shifts on the time of origin of all major groups of tetrapodomorphs (up to 25 million years) and that low rates of net diversification, not fossilization, explain long ghost lineages in the early tetrapdomorph fossil record.

Accounting for uncertainty from zero inflation and overdispersion in paleoecological studies of predation using a hierarchical Bayesian framework

Abstract. The effects of overdispersion and zero inflation (e.g., poor model fits) can result in misinterpretation in studies using count data. These effects have not been evaluated in

Marine plankton show threshold extinction response to Neogene climate change

It is shown that one significant zooplankton group, the radiolaria, underwent a severe decline in high latitude species richness presaged by ecologic reorganization during the late Neogene, a time of amplified polar cooling.



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.


  • 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
  • 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.


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