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List of works by Michael E. Alfaro

A Comparative Study in Ancestral Range Reconstruction Methods: Retracing the Uncertain Histories of Insular Lineages

scientific article (publication date: 16 October 2008)

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

scientific article

A clinical research pathway towards developing new insights into cardiomyopathy

scientific article published on 28 September 2015

A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes).

scientific article

A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy

scientific article published on 28 March 2013

A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes).

scientific article

A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes).

scientific article

A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci

scientific article

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

scientific article published on 24 August 2011

A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America.

scientific article published on 12 March 2018

Adaptive evolution of facial colour patterns in Neotropical primates.

scientific article published on 11 January 2012

Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships

scientific article published on 03 July 2020

An inverse latitudinal gradient in speciation rate for marine fishes

scientific article published in Nature

Anointing variation across wild capuchin populations: a review of material preferences, bout frequency and anointing sociality in Cebus and Sapajus

scientific article

Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.

scientific article

Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate

scientific article published on 8 October 2014

Biogeography of the marmosets and tamarins (Callitrichidae).

scientific article published on 20 May 2014

Biologically inspired phylogenetic models strongly outperform the no common mechanism model.

scientific article

Biting disrupts integration to spur skull evolution in eels.

scientific article published on 17 November 2014

Body fineness ratio as a predictor of maximum prolonged-swimming speed in coral reef fishes

scientific article

Body shape convergence driven by small size optimum in marine angelfishes.

scientific article published on June 2017

Boxfish swimming paradox resolved: forces by the flow of water around the body promote manoeuvrability.

scientific article published on February 2015

Capuchin monkey biogeography: understanding Sapajus Pleistocene range expansion and the current sympatry between Cebus and Sapajus

scholarly article by Marcela G. M. Lima et al published 29 January 2017 in Journal of Biogeography

Cebus phylogenetic relationships: a preliminary reassessment of the diversity of the untufted capuchin monkeys

scientific article

Clade age and species richness are decoupled across the eukaryotic tree of life

scientific article (publication date: August 2012)

Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty.

scientific article published in February 2006

Contemporaneous radiations of fungi and plants linked to symbiosis

scientific article published in Nature Communications

Convergence in trophic morphology and feeding performance among piscivorous natricine snakes.

scientific article published on 6 April 2009

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

scientific article (publication date: 8 August 2009)

Dietary breadth is positively correlated with venom complexity in cone snails

scientific article

Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates

scientific article

Diversity versus disparity and the radiation of modern cetaceans

scientific article (publication date: 22 October 2010)

Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae).

scientific article published on 15 March 2013

Do reefs drive diversification in marine teleosts? Evidence from the pufferfishes and their allies (Order Tetraodontiformes).

scientific article

Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?

scientific article

Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences.

scientific article published on 8 September 2017

Elongation of the body in eels.

scientific article published on 16 June 2010

Evolution: Bioluminescent Courtship as an Engine of Diversity.

scientific article

Evolutionary bangs and whimpers: methodological advances and conceptual frameworks for studying exceptional diversification

scientific article published on 14 October 2010

Evolutionary biology: A flourishing of fish forms

scientific article published in April 2010

Explosive Pleistocene range expansion leads to widespread Amazonian sympatry between robust and gracile capuchin monkeys

scientific article

Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary

scientific article published on 12 March 2018

Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements

scientific article published on 04 April 2018

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

scientific article

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

scientific article published on 12 June 2015

Imperfect morphological convergence: variable changes in cranial structures underlie transitions to durophagy in moray eels

scientific article published on 24 April 2014

Integrated diversification of locomotion and feeding in labrid fishes.

scientific article published on February 2008

Integrating fossils with molecular phylogenies improves inference of trait evolution.

scientific article

Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae).

scientific article

Life in the unthinking depths: energetic constraints on encephalization in marine fishes

scientific article

Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae.

scientific article published in May 2005

Molecular systematics and evolution of Regina and the thamnophiine snakes.

scientific article published in December 2001

Morphological convergence as a consequence of extreme functional demands: examples from the feeding system of natricine snakes.

scientific article

Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae.

scientific article

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

scientific article

Phylogenetic Factor Analysis

scientific article published on 7 August 2017

Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic

scientific article published on 10 September 2007

Phylogenetic relationships and evolutionary history of the reef fish family Labridae

scientific article

Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes

scientific article (publication date: October 2008)

Phylogenetics and geography of speciation in New World Halichoeres wrasses

scientific article published on 28 December 2017

Phylogenomic Systematics of Ostariophysan fishes: Ultraconserved Elements Support the Surprising Non-monophyly of Characiformes

scientific article

Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit.

scientific article

Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

scientific article

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

scientific article

Phylogeny and biogeography of hogfishes and allies (Bodianus, Labridae).

scientific article published on 2 March 2016

Phylogeny, evolutionary history, and biogeography of Oriental-Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences

scientific article published on 21 November 2007

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

scientific article (publication date: 13 May 2013)

Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

scientific article published in 2022

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation.

scientific article

Relationships of the temperate Australasian labrid fish tribe Odacini (Perciformes; Teleostei).

scientific article published in August 2004

Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

scientific article

Resolving the ray-finned fish tree of life

scientific article published on 30 May 2018

Roosting ecology and the evolution of pelage markings in bats

scientific article

Spatial and temporal patterns of diversification on the Amazon: A test of the riverine hypothesis for all diurnal primates of Rio Negro and Rio Branco in Brazil

scientific article published on 5 October 2014

Sweeping and striking: a kinematic study of the trunk during prey capture in three thamnophiine snakes

scientific article published in July 2003

Systemic iridovirus from threespine stickleback Gasterosteus aculeatus represents a new megalocytivirus species (family Iridoviridae).

scientific article

Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom.

scientific article

The Posterior and the Prior in Bayesian Phylogenetics

scholarly article by Michael E. Alfaro & Mark Holder published December 2006 in Annual Review of Ecology, Evolution, and Systematics

The effect of habitat on modern shark diversification

scientific article published on 30 May 2014

The effects of ecology and evolutionary history on robust capuchin morphological diversity.

scientific article

The evolution of capture myopathy in hooved mammals: a model for human stress cardiomyopathy?

scientific article

The evolution of island gigantism and body size variation in tortoises and turtles

scientific article

The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfish (family: Balistidae).

scientific article published on 25 March 2011

The influence of model averaging on clade posteriors: an example using the triggerfishes (Family Balistidae).

scientific article

Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes

scientific article

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

scientific article

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