An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology (Q34351365)

1 August 2017

An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology (English)

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1 August 2017

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2

Luke J Harmon

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1 August 2017

Matthew W Pennell

1

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PubMed ID

23773094

1 August 2017

language of work or name

English

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publication date

1 June 2013

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Annals of the New York Academy of Sciences

1 August 2017

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1 August 2017

1289

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1 August 2017

90-105

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PubMed ID

23773094

maintained by WikiProject

1 August 2017

1 reference

MrBayes 3: Bayesian phylogenetic inference under mixed models

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

BEAST: Bayesian evolutionary analysis by sampling trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Mammalian phylogeny reveals recent diversification rate shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Reconciling molecular phylogenies with the fossil record

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Macroevolutionary perspectives to environmental change

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

A novel comparative method for identifying shifts in the rate of character evolution on trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Modeling stabilizing selection: expanding the Ornstein-Uhlenbeck model of adaptive evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenies and the Comparative Method

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

The Phylogenetic Regression

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Tempo and mode of evolution revealed from molecular phylogenies

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

The reconstructed evolutionary process

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Tempo and mode of evolutionary radiation in iguanian lizards

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Estimating a binary character's effect on speciation and extinction

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Diversitree : comparative phylogenetic analyses of diversification in R

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Independent contrasts and PGLS regression estimators are equivalent.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Comparative methods for the analysis of continuous variables: geometric interpretations

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Testing for phylogenetic signal in comparative data: behavioral traits are more labile

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Inferring the historical patterns of biological evolution

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Comparative methods as a statistical fix: the dangers of ignoring an evolutionary model.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

The Phylogenetic Mixed Model

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

A Simple Method for Computing the Inverse of a Numerator Relationship Matrix Used in Prediction of Breeding Values

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Estimation of quantitative genetic parameters.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic logistic regression for binary dependent variables.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

A comparative method for both discrete and continuous characters using the threshold model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Fast likelihood calculations for comparative analyses

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Translating Between Microevolutionary Process and Macroevolutionary Patterns: The Correlation Structure of Interspecific Data

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Estimating the Rate of Phenotypic Evolution from Comparative Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

A likelihood approach to estimating phylogeny from discrete morphological character data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Reversible jump Markov chain Monte Carlo computation and Bayesian model determination

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Multiple routes to mammalian diversity

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Approximate Bayesian Computation in Evolution and Ecology

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Approximate Bayesian computation

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Simulation-based likelihood approach for evolutionary models of phenotypic traits on phylogeny.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Integrating fossils with molecular phylogenies improves inference of trait evolution.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic analysis using Lévy processes: finding jumps in the evolution of continuous traits

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

The role of diversification in causing the correlates of dioecy

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Floral symmetry affects speciation rates in angiosperms.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Which random processes describe the tree of life? A large-scale study of phylogenetic tree imbalance.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Whole-tree methods for detecting differential diversification rates.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

SYMMETREE: whole-tree analysis of differential diversification rates

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

A Bayesian approach for evaluating the impact of historical events on rates of diversification

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

The shifting balance of diversity among major marine animal groups

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Extinctions in ancient and modern seas

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Explosive evolutionary radiations: decreasing speciation or increasing extinction through time?

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Inferring the dynamics of diversification: a coalescent approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Extinction rates should not be estimated from molecular phylogenies

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Problems detecting density-dependent diversification on phylogenies

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Trees of unusual size: biased inference of early bursts from large molecular phylogenies

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Reinventing species selection with molecular phylogenies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Confounding asymmetries in evolutionary diversification and character change

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

ON PHYLOGENETIC TESTS OF IRREVERSIBLE EVOLUTION

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic inference of reciprocal effects between geographic range evolution and diversification

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Linking the investigations of character evolution and species diversification

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

The adaptive landscape as a conceptual bridge between micro- and macroevolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Comparing strengths of directional selection: how strong is strong?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phenotypic Selection in Natural Populations: What Limits Directional Selection?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Natural selection and the heritability of fitness components

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Evolutionary constraint and ecological consequences

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Heritability is not Evolvability

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Rates of evolution: effects of time and temporal scaling.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

The million-year wait for macroevolutionary bursts

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

On the Role of Species in Anagenesis

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Heritable genetic variation via mutation-selection balance: Lerch's zeta meets the abdominal bristle

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Resolving the paradox of stasis: models with stabilizing selection explain evolutionary divergence on all timescales

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

MIPoD: a hypothesis-testing framework for microevolutionary inference from patterns of divergence

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Convergent evolution of phenotypic integration and its alignment with morphological diversification in Caribbean Anolis ecomorphs

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

A phylogenetic comparative method for studying multivariate adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenies and Community Ecology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Rebuilding community ecology from functional traits.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

The merging of community ecology and phylogenetic biology

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

Opposing effects of competitive exclusion on the phylogenetic structure of communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Species interactions mediate phylogenetic community structure in a hyperdiverse lizard assemblage from arid Australia

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Generalized linear mixed models for phylogenetic analyses of community structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic signal, evolutionary process, and rate

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

The unified neutral theory of biodiversity and biogeography at age ten.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Neutral theory and the evolution of ecological equivalence

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogeny, niches, and relative abundance in natural communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

The newest synthesis: understanding the interplay of evolutionary and ecological dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Influence of phylogeny on fungal community assembly and ecosystem functioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic diversity and the functioning of ecosystems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic constraints on ecosystem functioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

The Red Queen and the Court Jester: species diversity and the role of biotic and abiotic factors through time

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Assessing the role of cladogenesis in macroevolution by integrating fossil and molecular evidence

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Effects of sampling standardization on estimates of Phanerozoic marine diversification

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phanerozoic trends in the global diversity of marine invertebrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phanerozoic Earth system evolution and marine biodiversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Species concepts and species delimitation

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12157

The meaning of birth and death (in macroevolutionary birth-death models)

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Species diversity in the Phanerozoic: a tabulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Taxonomic structure of the fossil record is shaped by sampling bias

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Diversity dynamics: molecular phylogenies need the fossil record

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Reconstructing ancestral character states under Wagner parsimony

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Reconstructing ancestral character states: a critical reappraisal

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Adaptive radiation, ecological opportunity, and evolutionary determinism. American Society of Naturalists E. O. Wilson award address

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Inferring speciation and extinction rates under different sampling schemes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Interplay between changing climate and species' ecology drives macroevolutionary dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Missing inaction: the dangers of ignoring missing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Nonrandom variation in within-species sample size and missing data in phylogenetic comparative studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Using the fossil record to estimate the age of the last common ancestor of extant primates

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Sampling-through-time in birth-death trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

The reconstructed evolutionary process with the fossil record

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Phylogenetic conservatism of extinctions in marine bivalves

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Heads or tails: staged diversification in vertebrate evolutionary radiations

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

High diversity, low disparity and small body size in plesiosaurs (Reptilia, Sauropterygia) from the Triassic-Jurassic boundary

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Uncertainty in the age of fossils and the stratigraphic fit to phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi).

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Evolutionary diversification of reef corals: a comparison of the molecular and fossil records

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

The Strength of Phenotypic Selection in Natural Populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Evolutionary Inferences from Phylogenies: A Review of Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

A NEW PHYLOGENETIC METHOD FOR IDENTIFYING EXCEPTIONAL PHENOTYPIC DIVERSIFICATION

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12157

21 January 2018

Identifiers

DOI

10.1111/NYAS.12157

1 reference

1 August 2017

1 reference

PubMed ID

23773094