Evolution of the immune system influences speciation rates in teleost fishes

Alternative adaptive immunity strategies: coelacanth, cod and shark immunity

(2016) Francesco Buonocore et al.   MOLECULAR IMMUNOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A comprehensive analysis of teleost MHC class I sequences

(2015) Unni Grimholt et al.   BMC EVOLUTIONARY BIOLOGY

Coevolution of MHC genes (LMP/TAP/class Ia, NKT-class Ib, NKp30-B7H6): lessons from cold-blooded vertebrates

(2015) Yuko Ohta et al.   IMMUNOLOGICAL REVIEWS

Co-evolution of lymphocyte receptors with MHC class I

(2015) Peter Parham   IMMUNOLOGICAL REVIEWS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Matthew W. Pennell et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Statistical binning enables an accurate coalescent-based estimation of the avian tree

(2014) S. Mirarab et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

A Novel Bayesian Method for Inferring and Interpreting the Dynamics of Adaptive Landscapes from Phylogenetic Comparative Data

(2014) Josef C. Uyeda et al.   SYSTEMATIC BIOLOGY

BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

(2014) Daniel L. Rabosky et al.   Methods in Ecology and Evolution

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Absence of major histocompatibility complex class II mediated immunity in pipefish, Syngnathus typhle: evidence from deep transcriptome sequencing

(2013) D. Haase et al.   Biology Letters

Evolution of Hox gene clusters in deuterostomes

(2013) Juan Pascual-Anaya et al.   BMC DEVELOPMENTAL BIOLOGY

Unraveling the Evolution of the Atlantic Cod’s (Gadus morhua L.) Alternative Immune Strategy

(2013) Martin Malmstrøm et al.   PLoS One

Why does the immune system of Atlantic cod lack MHC II?

(2012) Bastiaan Star et al.   BIOESSAYS

Divergent selection on locally adapted major histocompatibility complex immune genes experimentally proven in the field

(2012) Christophe Eizaguirre et al.   ECOLOGY LETTERS

Ecological opportunity and sexual selection together predict adaptive radiation

(2012) Catherine E. Wagner et al.   NATURE

The Evolution of Pharyngognathy: A Phylogenetic and Functional Appraisal of the Pharyngeal Jaw Key Innovation in Labroid Fishes and Beyond

(2012) P. C. Wainwright et al.   SYSTEMATIC BIOLOGY

Diversitree: comparative phylogenetic analyses of diversification in R

(2012) Richard G. FitzJohn   Methods in Ecology and Evolution

Inferring Speciation and Extinction Rates under Different Sampling Schemes

(2011) S. Hohna et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Major histocompatibility complex polymorphism: dynamics and consequences of parasite-mediated local adaptation in fishes

(2010) C. Eizaguirre et al.   JOURNAL OF FISH BIOLOGY

Evolution of Thermal Physiology in Liolaemus Lizards: Adaptation, Phylogenetic Inertia, and Niche Tracking

(2009) Antonieta Labra et al.   AMERICAN NATURALIST

Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data

(2009) Adela Roa-Varón et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Origin and evolution of the adaptive immune system: genetic events and selective pressures

(2009) Martin F. Flajnik et al.   NATURE REVIEWS GENETICS

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

(2009) M. E. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Speciation accelerated and stabilized by pleiotropic major histocompatibility complex immunogenes

(2008) Christophe Eizaguirre et al.   ECOLOGY LETTERS

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Does intra-individual major histocompatibility complex diversity keep a golden mean?

(2008) B. Woelfing et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Lifetime reproductive success is maximized with optimal major histocompatibility complex diversity

(2008) M. Kalbe et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Testing Congruence in Phylogenomic Analysis

(2008) Jessica W. Leigh et al.   SYSTEMATIC BIOLOGY