M. Alfaro

Publications163
h-index50
Citations10,454
Highly Influential Citations986
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  • Publications
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Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates
The uneven distribution of species richness is a fundamental and unexplained pattern of vertebrate biodiversity. Although species richness in groups like mammals, birds, or teleost fishes is often…
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Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.
TLDR
Computer simulation is used to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony boot strap proportion (MP-BP).
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Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation.
TLDR
It is demonstrated that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fishes that comprise the majority of vertebrate biological diversity.
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Geiger V2.0: an Expanded Suite of Methods for Fitting Macroevolutionary Models to Phylogenetic Trees
TLDR
This work presents geiger v2.0, a complete overhaul of the popular R package geiger, which reimplemented existing methods with more efficient algorithms and developed several new approaches for accomodating heterogeneous models and data types.
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Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.
TLDR
The reversible jump Markov chain Monte Carlo algorithm described here allows estimation of phylogeny (and other phylogenetic model parameters) to be performed while accounting for uncertainty in the model of DNA substitution.
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An inverse latitudinal gradient in speciation rate for marine fishes
TLDR
It is shown that the fastest rates of speciation occur in species-poor regions outside the tropics, and that high-latitude fish lineages form new species at much faster rates than their tropical counterparts.
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The Posterior and the Prior in Bayesian Phylogenetics
TLDR
The behavior of the PP in Bayesian and frequentist terms and its relationship to parametric and nonparametric bootstrapping are discussed.
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A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES
TLDR
A Bayesian approach for identifying complex patterns in the evolution of continuous traits, which uses reversible‐jump Markov chain Monte Carlo sampling and performs well in recovering simulated rate shifts and simulated rates for datasets nearing the size typical for comparative phylogenetic study.
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Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes
TLDR
The results suggest that the causes of diversification in large clades are likely to be complex and not easily ascribed to a single event, even a dramatic one such as a whole genome duplication.
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Diversity versus disparity and the radiation of modern cetaceans
TLDR
It is concluded that the signature of adaptive radiations may be retained within morphological traits even after equilibrium diversity has been reached and high extinction or fluctuations in net diversification have erased any signature of an early burst of diversification in the structure of the phylogeny.
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