Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions

GT Lloyd - Biological Journal of the Linnean Society, 2016 - academic.oup.com
Discrete character-taxon matrices are increasingly being used in an attempt to understand
the pattern and tempo of morphological evolution; however, methodological sophistication …

Integrating fossil observations into phylogenetics using the fossilized birth–death model

AM Wright, DW Bapst, J Barido-Sottani… - Annual Review of …, 2022 - annualreviews.org
Over the past decade, a new set of methods for estimating dated trees has emerged.
Originally referred to as the fossilized birth–death (FBD) process, this single model has …

Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage

RBJ Benson, NE Campione, MT Carrano… - PLoS …, 2014 - journals.plos.org
Large-scale adaptive radiations might explain the runaway success of a minority of extant
vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological …

paleotree: an R package for paleontological and phylogenetic analyses of evolution

DW Bapst - Methods in Ecology and Evolution, 2012 - Wiley Online Library
paleotree is a library of functions for the R statistical computing environment dedicated to
analyses that combine paleontological and phylogenetic data sets, particularly the time …

[HTML][HTML] Gradual assembly of avian body plan culminated in rapid rates of evolution across the dinosaur-bird transition

SL Brusatte, GT Lloyd, SC Wang, MA Norell - Current Biology, 2014 - cell.com
The evolution of birds from theropod dinosaurs was one of the great evolutionary transitions
in the history of life [1–22]. The macroevolutionary tempo and mode of this transition is …

strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

MA Bell, GT Lloyd - 2015 - Wiley Online Library
Abstract strap (S tratigraphic T ree A nalysis for P alaeontology) is a new package for the
freely available statistical programming language R designed to perform three main …

Confluence, synnovation, and depauperons in plant diversification

MJ Donoghue, MJ Sanderson - New Phytologist, 2015 - Wiley Online Library
We review the empirical phylogenetic literature on plant diversification, highlighting
challenges in separating the effects of speciation and extinction, in specifying diversification …

A new method for testing evolutionary rate variation and shifts in phenotypic evolution

S Castiglione, G Tesone, M Piccolo… - Methods in Ecology …, 2018 - Wiley Online Library
Quantifying phenotypic evolutionary rates and their variation across phylogenetic trees is a
major issue in evolutionary biology. A number of phylogenetic comparative methods (PCM …

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

MW Pennell, LJ Harmon - Annals of the New York Academy of …, 2013 - Wiley Online Library
Recent innovations in phylogenetic comparative methods (PCMs) have spurred a
renaissance of research into the causes and consequences of large‐scale patterns of …

Five hundred million years of extinction and recovery: a Phanerozoic survey of large‐scale diversity patterns in fishes

M Friedman, LC Sallan - Palaeontology, 2012 - Wiley Online Library
Fishes include more than half of all living animals with backbones, but large‐scale
palaeobiological patterns in this assemblage have not received the same attention as those …