Phylogenetic estimates of speciation and extinction rates for testing ecological and evolutionary hypotheses.

No abstract is available for this paper.

• Publication year

  2013

• Venue

  Trends in Ecology & Evolution

• Publication date

  2013-12-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1016/j.tree.2013.09.007PMID 24120478
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Early origin of viviparity and multiple reversions to oviparity in squamate reptiles.

  2014cited by this paper
• Coalescent species delimitation in milksnakes (genus Lampropeltis) and impacts on phylogenetic comparative analyses.

  2014cited by this paper
• Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

  2013cited by this paper
• WHAT CAN MULTIPLE PHYLOGENIES SAY ABOUT THE LATITUDINAL DIVERSITY GRADIENT? A NEW LOOK AT THE TROPICAL CONSERVATISM, OUT OF THE TROPICS, AND DIVERSIFICATION RATE HYPOTHESES

  2013cited by this paper
• The evolution of viviparity opens opportunities for lizard radiation but drives it into a climatic cul‐de‐sac

  2013cited by this paper
• Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

  2013cited by this paper
• Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes

  2013cited by this paper
• How can we improve accuracy of macroevolutionary rate estimates?

  2013cited by this paper
• DIVERSITY‐DEPENDENT CLADOGENESIS AND TRAIT EVOLUTION IN THE ADAPTIVE RADIATION OF THE AUKS (AVES: ALCIDAE)

  2013cited by this paper
• Diversification rates have declined in the Malagasy herpetofauna

  2013cited by this paper
• Estimating speciation and extinction rates for phylogenies of higher taxa.

  2013cited by this paper
• Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity

  2013cited by this paper
• INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION

  2012cited by this paper
• POSITIVE CORRELATION BETWEEN DIVERSIFICATION RATES AND PHENOTYPIC EVOLVABILITY CAN MIMIC PUNCTUATED EQUILIBRIUM ON MOLECULAR PHYLOGENIES

  2012cited by this paper
• Ecological opportunity and sexual selection together predict adaptive radiation

  2012cited by this paper
• A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence

  2012cited by this paper
• Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling.

  2012cited by this paper
• Prolonging the Past Counteracts the Pull of the Present: Protracted Speciation Can Explain Observed Slowdowns in Diversification

  2012cited by this paper
• Accelerated speciation in colour-polymorphic birds

  2012cited by this paper
• Diversitree: comparative phylogenetic analyses of diversification in R

  2012cited by this paper
• Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation

  2012cited by this paper
• The reconstructed evolutionary process with the fossil record.

  2012cited by this paper
• Linking the Investigations of Character Evolution and Species Diversification

  2012cited by this paper
• TEMPO AND MODE IN PLANT BREEDING SYSTEM EVOLUTION

  2012cited by this paper
• Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

  2012cited by this paper
• A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

  2012cited by this paper
• EXTINCTION, ECOLOGICAL OPPORTUNITY, AND THE ORIGINS OF GLOBAL SNAKE DIVERSITY

  2012cited by this paper
• Trait‐dependent diversification and the impact of palaeontological data on evolutionary hypothesis testing in New World ratsnakes (tribe Lampropeltini)

  2012cited by this paper
• Apparent signal of competition limiting diversification after ecological transitions from marine to freshwater habitats.

  2012cited by this paper
• TIME‐DEPENDENT SPECIATION AND EXTINCTION FROM PHYLOGENIES: A LEAST SQUARES APPROACH

  2011cited by this paper
• Multiple routes to mammalian diversity

  2011cited by this paper
• Interplay Between Changing Climate and Species’ Ecology Drives Macroevolutionary Dynamics

  2011cited by this paper
• Community assembly and diversification in Indo-Pacific coral reef fishes

  2011cited by this paper
• Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

  2011cited by this paper
• The Molecular Phylogenetic Signature of Clades in Decline

  2011cited by this paper
• Mammalian phylogeny reveals recent diversification rate shifts

  2011cited by this paper
• Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia.

  2011cited by this paper
• Phylogenetic inference of reciprocal effects between geographic range evolution and diversification.

  2011cited by this paper
• Reconciling molecular phylogenies with the fossil record

  2011cited by this paper
• THE IMPACT OF GENE‐TREE/SPECIES‐TREE DISCORDANCE ON DIVERSIFICATION‐RATE ESTIMATION

  2011cited by this paper
• Phylogenetic Insights on Adaptive Radiation

  2010cited by this paper
• Quantitative traits and diversification.

  2010cited by this paper
• Reinventing species selection with molecular phylogenies.

  2010cited by this paper
• EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

  2010cited by this paper
• Ecological opportunity and the origin of adaptive radiations

  2010cited by this paper
• Inferring the Dynamics of Diversification: A Coalescent Approach

  2010cited by this paper
• When can decreasing diversification rates be detected with molecular phylogenies and the fossil record?

  2010cited by this paper
• Equilibrium speciation dynamics in a model adaptive radiation of island lizards

  2010cited by this paper
• Problems detecting density-dependent diversification on phylogenies

  2009cited by this paper
• Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.

  2009cited by this paper
• Problems detecting density-dependent diversification on phylogenies: reply to Bokma

  2009cited by this paper
• Heritability of extinction rates links diversification patterns in molecular phylogenies and fossils.

  2009cited by this paper
• Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

  2009cited by this paper
• Extinction During Evolutionary Radiations: Reconciling the Fossil Record with Molecular Phylogenies

  2009cited by this paper
• HOW DOES ECOLOGICAL OPPORTUNITY INFLUENCE RATES OF SPECIATION, EXTINCTION, AND MORPHOLOGICAL DIVERSIFICATION IN NEW WORLD RATSNAKES (TRIBE LAMPROPELTINI)?

  2009cited by this paper
• Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory

  2009cited by this paper
• Density-Dependent Cladogenesis in Birds

  2008cited by this paper
• Explosive Evolutionary Radiations: Decreasing Speciation or Increasing Extinction Through Time?

  2008cited by this paper
• Detection of “Punctuated Equilibrium” by Bayesian Estimation of Speciation and Extinction Rates, Ancestral Character States, and Rates of Anagenetic and Cladogenetic Evolution on a Molecular Phylogeny

  2008cited by this paper
• Density-dependent diversification in North American wood warblers

  2008cited by this paper
• ASYMMETRIES IN PHYLOGENETIC DIVERSIFICATION AND CHARACTER CHANGE CAN BE UNTANGLED

  2007cited by this paper
• Estimating diversification rates from phylogenetic information.

  2007cited by this paper
• Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade

  2007cited by this paper
• Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography.

  2007cited by this paper
• Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions

  2007cited by this paper
• Estimating a binary character's effect on speciation and extinction.

  2007cited by this paper
• HOW DID LIFE BECOME SO DIVERSE? THE DYNAMICS OF DIVERSIFICATION ACCORDING TO THE FOSSIL RECORD AND MOLECULAR PHYLOGENETICS

  2007cited by this paper
• Diversification of Neoaves: integration of molecular sequence data and fossils

  2006cited by this paper
• LIKELIHOOD METHODS FOR DETECTING TEMPORAL SHIFTS IN DIVERSIFICATION RATES

  2006cited by this paper
• CONFOUNDING ASYMMETRIES IN EVOLUTIONARY DIVERSIFICATION AND CHARACTER CHANGE

  2006cited by this paper
• Birth-Death Models in Macroevolution

  2006cited by this paper
• Out of the Tropics: Evolutionary Dynamics of the Latitudinal Diversity Gradient

  2006cited by this paper
• LASER: A Maximum Likelihood Toolkit for Detecting Temporal Shifts in Diversification Rates From Molecular Phylogenies

  2006cited by this paper
• STATISTICAL ANALYSIS OF DIVERSIFICATION WITH SPECIES TRAITS

  2005cited by this paper
• A comprehensive framework for global patterns in biodiversity

  2004cited by this paper
• Can extinction rates be estimated without fossils?

  2004cited by this paper
• Historical biogeography, ecology and species richness.

  2004cited by this paper
• Tempo and Mode of Evolutionary Radiation in Iguanian Lizards

  2003cited by this paper
• Sri Lanka: an amphibian hot spot.

  2002cited by this paper
• Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales

  2002cited by this paper
• Detection of punctuated equilibrium from molecular phylogenies

  2002cited by this paper
• ABSOLUTE DIVERSIFICATION RATES IN ANGIOSPERM CLADES

  2001cited by this paper
• GENE DIVERGENCE , POPULATION DIVERGENCE , AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES

  2001cited by this paper
• The Ecology of Adaptive Radiation

  2000cited by this paper
• Reconstructing shifts in diversification rates on phylogenetic trees.

  1996cited by this paper
• The reconstructed evolutionary process.

  1994cited by this paper
• ADAPTIVE RADIATION AND THE TOPOLOGY OF LARGE PHYLOGENIES

  1993cited by this paper
• Community Diversity: Relative Roles of Local and Regional Processes

  1987cited by this paper
• A kinetic model of Phanerozoic taxonomic diversity. III. Post-Paleozoic families and mass extinctions

  1984cited by this paper
• Equilibrium Models of Evolutionary Species Diversity and the Number of Empty Niches

  1984cited by this paper
• A kinetic model of Phanerozoic taxonomic diversity II. Early Phanerozoic families and multiple equilibria

  1979cited by this paper
• A kinetic model of Phanerozoic taxonomic diversity I. Analysis of marine orders

  1978cited by this paper
• Evolutionary Paleoecology of the Marine Biosphere

  1974cited by this paper
• Maximum likelihood estimation in the birth-and-death process

  1974cited by this paper
• Major Features Of Evolution

  1954cited by this paper
• RATES OF EVOLUTION

  1950cited by this paper

• Graph Neural Networks for Likelihood-Free Inference in Diversification Models

  2025cites this paper
• Bayesian Model Averaging of Parametric Coalescent Models for Phylodynamic Inference

  2025cites this paper
• Diversification and extinction of Hemiptera in deep time

  2025cites this paper
• Link between the Birth-Death process and the Kingman Coalescent - Applications to Phylogenetic Epidemiology.

  2025cites this paper
• Unraveling the genomic landscape of Campylorhynchus wrens along western Ecuador's precipitation gradient: Insights into hybridization, isolation by distance, and isolation by the environment

  2024cites this paper
• Understanding species limits through the formation of phylogeographic lineages

  2024cites this paper
• Anciently duplicated genes continuously recruited to heart expression in vertebrate evolution are associated with heart chamber increase.

  2024cites this paper
• Effects of the interaction between Linnean and Darwinian shortfalls on diversification gradients

  2024cites this paper
• Opening the species box: What parsimonious microscopic models of speciation have to say about macroevolution

  2024cites this paper
• Whether niche changes promote the evolution of species: a case study of Paeonia in Asia and North America

  2024cites this paper
• Exploring The Role Of Isolation By Distance, Isolation By Environment, And Hybridization In Campylorhynchus Wrens Along A Precipitation Gradient In Western Ecuador

  2023cites this paper
• Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes

  2023cites this paper
• Strong floral morphology conservatism during the rapid diversification of the genus Helianthemum.

  2023cites this paper
• Unraveling the Genomic Landscape of Campylorhynchus Wrens along Western Ecuador’s Precipitation Gradient: Insights into Isolation by Distance, Isolation by Environment, and Hybridization

  2023cites this paper
• A Comparison of Deep Learning Architectures for Inferring Parameters of Diversification Models from Extant Phylogenies

  2023cites this paper
• Species Richness and Speciation Rates for all Terrestrial Animals Emerge from a Synthesis of Ecological Theories

  2022cites this paper
• A road map for phylogenetic models of species trees.

  2022cites this paper
• Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability

  2022cites this paper
• Agricultural habitats are dominated by rapidly evolving nematodes revealed through phylogenetic comparative methods

  2021cites this paper
• Patterns of Pelagic Fish Diversity in Floodplain Lakes of Whitewater and Blackwater Drainage Systems Within the Central Amazon River Basin of Brazil

  2021cites this paper
• Towards a global perspective for Salvia L: Phylogeny, diversification, and floral evolution

  2021cites this paper
• Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia.

  2021cites this paper
• Geo-Climatic Changes and Apomixis as Major Drivers of Diversification in the Mediterranean Sea Lavenders (Limonium Mill.)

  2021cites this paper
• Universal probabilistic programming offers a powerful approach to statistical phylogenetics

  2021cites this paper
• Exploring diversification drivers in golden orbweavers

  2021cites this paper
• Probabilistic programming: a powerful new approach to statistical phylogenetics

  2020cites this paper
• Changing Only Slowly: The Role of Phylogenetic Niche Conservatism in Caviidae (Rodentia) Speciation

  2020cites this paper
• Recent accelerated diversification in rosids occurred outside the tropics

  2020cites this paper
• Genetic diversity of cytochrome b in Iberian ibex from Andalusia

  2020cites this paper
• Are Skyline Plot-Based Demographic Estimates Overly Dependent on Smoothing Prior Assumptions?

  2020cites this paper
• Changing Only Slowly: The Role of Phylogenetic Niche Conservatism in Caviidae (Rodentia) Speciation

  2020cites this paper
• Spider Diversification Through Space and Time.

  2020cites this paper
• A computationally tractable birth-death model that combines phylogenetic and epidemiological data

  2020cites this paper
• Biotic and abiotic factors driving the diversification dynamics of Crocodylia

  2019cites this paper
• Morphological Innovations and Vast Extensions of Mountain Habitats Triggered Rapid Diversification Within the Species-Rich Irano-Turanian Genus Acantholimon (Plumbaginaceae)

  2019cites this paper
• The State of the World’s Biodiversity

  2019cites this paper
• Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

  2019cites this paper
• Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts

  2019cites this paper
• Digging their own macroevolutionary grave: fossoriality as an evolutionary dead end in snakes

  2018cites this paper
• The Biogeography of Deep Time Phylogenetic Reticulation

  2018cites this paper
• Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates

  2018cites this paper
• Microevolutionary processes impact macroevolutionary patterns

  2018cites this paper
• Neotropical Diversification: Historical Overview and Conceptual Insights

  2018cites this paper
• Phylogenetic Comparative Methods can Provide Important Insights into the Evolution of Toxic Weaponry

  2018cites this paper
• The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

  2018cites this paper
• The genomic view of diversification

  2018cites this paper
• Exact Bayesian inference for phylogenetic birth‐death models

  2018influential citation
• Cryptic species as a window into the paradigm shift of the species concept

  2018cites this paper
• Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome.

  2017cites this paper
• Fossils matter - understanding modes and rates of trait evolution in Musteloidea (Carnivora)

  2017cites this paper
• Horizontal gene transfer constrains the timing of methanogen evolution

  2017cites this paper
• Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea).

  2017cites this paper
• Time and environment explain the current richness distribution of non‐marine turtles worldwide

  2017cites this paper
• Geographical diversification and the effect of model and data inadequacies: the bat diversity gradient as a case study

  2017cites this paper
• Optimal Point Process Filtering for Birth-Death Model Estimation

  2017influential citation
• Why sex? Darevskia answers

  2017cites this paper
• A major shift in diversification rate helps explain macroevolutionary patterns in primate species diversity

  2017cites this paper
• A latitudinal phylogeographic diversity gradient in birds

  2017cites this paper
• Phylogenetic Paleoecology: Tree-Thinking and Ecology in Deep Time.

  2017cites this paper
• Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes.

  2017cites this paper
• Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards

  2016cites this paper
• Irrational exuberance for resolved species trees

  2016cites this paper
• How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods

  2016cites this paper
• Origin of origami cockroach reveals long-lasting (11 Ma) phenotype instability following viviparity

  2016cites this paper
• The Species Problem from the Modeler’s Point of View

  2016cites this paper
• Dating the emergence of truffle-like fungi in Australia, by using an augmented meta-analysis

  2016cites this paper
• Not going with the flow: a comprehensive time‐calibrated phylogeny of dragonflies (Anisoptera: Odonata: Insecta) provides evidence for the role of lentic habitats on diversification

  2016cites this paper
• Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage

  2016cites this paper
• Version dated : August 24 , 2016 1 RH : THE SPECIES PROBLEM IN MODELING

  2016cites this paper
• Mutualism Persistence and Abandonment during the Evolution of the Mycorrhizal Symbiosis

  2016cites this paper
• Molecular paleobiology - progress and perspectives

  2016cites this paper
• Ecological opportunities, habitat, and past climatic fluctuations influenced the diversification of modern turtles.

  2016cites this paper
• Reproductive isolation and the causes of speciation rate variation in nature

  2016cites this paper
• Integrating Paleontological and Phylogenetic Approaches to Macroevolution

  2016cites this paper
• Species selection and random drift in macroevolution

  2016cites this paper
• Species diversity is dynamic and unbounded at local and continental scales.

  2015cites this paper
• The Anthropocene Speciation Hypothesis Remains Valid: Reply to Hulme et al.

  2015cites this paper
• Relative roles of ecological and energetic constraints, diversification rates and region history on global species richness gradients.

  2015cites this paper
• Quantifying Age-dependent Extinction from Species Phylogenies

  2015influential citation
• Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae.

  2015cites this paper
• An introduction to phylogenetic analyses and modelling in ecology

  2015cites this paper
• How Ecology and Landscape Dynamics Shape Phylogenetic Trees.

  2015cites this paper
• Estimating the normal background rate of species extinction

  2015cites this paper
• Rapid acceleration of plant speciation during the Anthropocene.

  2015cites this paper
• When do plant radiations influence community assembly? The importance of historical contingency in the race for niche space.

  2015cites this paper
• How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics?

  2015cites this paper
• Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods.

  2015cites this paper
• Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications.

  2015cites this paper
• Putative floral brood-site mimicry, loss of autonomous selfing, and reduced vegetative growth are significantly correlated with increased diversification in Asarum (Aristolochiaceae).

  2015cites this paper
• Post-molecular systematics and the future of phylogenetics.

  2015cites this paper
• Coordinated Dispersal and Pre-Isthmian Assembly of the Central American Ichthyofauna

  2015cites this paper
• Integrating phylogenomics, biogeography and systematics to explore the taxonomy and the rise of the ratsnakes

  2015cites this paper
• Phylogenetic relationships, systematics, character-associated diversification, and chloroplast genome evolution in Asarum (Aristolochiaceae)

  2015cites this paper
• How traits shape trees: new approaches for detecting character state‐dependent lineage diversification

  2014cites this paper
• Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts

  2014cites this paper
• SYNTHES IS Phylogenetic approaches for studying diversification

  2014influential citation
• The Roles of Stochasticity and Life History in the Evolutionary Population Dynamics of Pathogens

  2014cites this paper
• for Trends in Ecology and Evolution ( TREE ) 1 2 Title :

  2014cites this paper
• Molecular Phylogeny and Biogeographic History of the Armored Neotropical Catfish Subfamilies Hypoptopomatinae, Neoplecostominae and Otothyrinae (Siluriformes: Loricariidae)

  2014cites this paper
• Clade Age and Diversification Rate Variation Explain Disparity in Species Richness among Water Scavenger Beetle (Hydrophilidae) Lineages

  2014cites this paper