Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Great journey of Great Tits (Parus major group): Origin, diversification and historical demographics of a broadly distributed bird lineage

(2020) Gang Song et al.   JOURNAL OF BIOGEOGRAPHY

Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae

(2020) Siri Birkeland et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Genomics Reveals Evolution of a Beak Morphology Locus in a High-Altitude Songbird

(2020) Yalin Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent changes in muscle metabolism depend on duration of high-altitude ancestry across Andean waterfowl

(2020) Neal J Dawson et al.   eLife

Little parallelism in genomic signatures of local adaptation in two sympatric, cryptic sister species

(2020) Juliane Hartke et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Parallel molecular evolution in pathways, genes, and sites in high-elevation hummingbirds revealed by comparative transcriptomics

(2019) Marisa C W Lim et al.   Genome Biology and Evolution

Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives

(2019) Yan Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows

(2019) Yanhua Qu et al.   National Science Review

Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis

(2018) Herman L. Mays et al.   CURRENT BIOLOGY

Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau

(2018) Xiaojia Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

(Non)Parallel Evolution

(2018) Daniel I. Bolnick et al.   Annual Review of Ecology Evolution and Systematics

Signatures of selection in embryonic transcriptomes of lizards adapting in parallel to cool climate

(2017) Nathalie Feiner et al.   EVOLUTION

Reconstruction of the late Miocene biogeographical history of tits and chickadees (Aves: Passeriformes: Paridae): A comparison between discrete area analyses and probabilistic diffusion approach

(2017) Ulf S. Johansson et al.   JOURNAL OF BIOGEOGRAPHY

Loss of Heterozygosity Drives Adaptation in Hybrid Yeast

(2017) Caiti S. Smukowski Heil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower

(2017) Federico Roda et al.   MOLECULAR ECOLOGY

Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates

(2016) Frank T. Burbrink et al.   ECOLOGY LETTERS

Evolution of body morphology and beak shape revealed by a morphometric analysis of 14 Paridae species

(2016) Shimiao Shao et al.   Frontiers in Zoology

The probability of parallel genetic evolution from standing genetic variation

(2016) A. MacPherson et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Predictable convergence in hemoglobin function has unpredictable molecular underpinnings

(2016) Chandrasekhar Natarajan et al.   SCIENCE

Evolutionary signals of selection on cognition from the great tit genome and methylome

(2016) Veronika N. Laine et al.   Nature Communications

Species diversification and phylogeographical patterns of birds in response to the uplift of the Qinghai-Tibet Plateau and Quaternary glaciations

(2016) Fumin Lei et al.   Current Zoology

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

(2015) Krystyna Nadachowska-Brzyska et al.   CURRENT BIOLOGY

Extent of QTL Reuse During Repeated Phenotypic Divergence of Sympatric Threespine Stickleback

(2015) G. L. Conte et al.   GENETICS

Adaptive Modifications of Muscle Phenotype in High-Altitude Deer Mice Are Associated with Evolved Changes in Gene Regulation

(2015) Graham R. Scott et al.   MOLECULAR BIOLOGY AND EVOLUTION

No Genome-Wide Protein Sequence Convergence for Echolocation

(2015) Z. Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas

(2015) Yanhua Qu et al.   Scientific Reports

Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level

(2015) Chandrasekhar Natarajan et al.   PLoS Genetics

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Niche filling slows the diversification of Himalayan songbirds

(2014) Trevor D. Price et al.   NATURE

A genetic mechanism for Tibetan high-altitude adaptation

(2014) Felipe R Lorenzo et al.   NATURE GENETICS

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

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Cytosolic functions of MORC2 in lipogenesis and adipogenesis

(2013) Beatriz Sánchez-Solana et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds

(2013) J. Projecto-Garcia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau

(2013) Yanhua Qu et al.   Nature Communications

Increase in Carbohydrate Utilization in High-Altitude Andean Mice

(2012) Marie-Pierre Schippers et al.   CURRENT BIOLOGY

Pleistocene climate changes shaped the divergence and demography of Asian populations of the great tit Parus major: evidence from phylogeographic analysis and ecological niche models

(2012) Na Zhao et al.   JOURNAL OF AVIAN BIOLOGY

Glacial expansion and diversification of an East Asian montane bird, the green-backed tit (Parus monticolus)

(2012) Wenjuan Wang et al.   JOURNAL OF BIOGEOGRAPHY

Lowered expression of heparan sulfate/heparin biosynthesis enzymeN-deacetylase/N-sulfotransferase 1 results in increased sulfation of mast cell heparin.

(2012) Anders Dagälv et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Regulatory changes contribute to the adaptive enhancement of thermogenic capacity in high-altitude deer mice

(2012) Z. A. Cheviron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel Molecular Evolution in an Herbivore Community

(2012) Y. Zhen et al.   SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Lineage diversification and historical demography of a montane bird Garrulax elliotii - implications for the Pleistocene evolutionary history of the eastern Himalayas

(2011) Yanhua Qu et al.   BMC EVOLUTIONARY BIOLOGY

Brain GLP-1 Signaling Regulates Femoral Artery Blood Flow and Insulin Sensitivity Through Hypothalamic PKC- 

(2011) C. Cabou et al.   DIABETES

Genomic insights into adaptation to high-altitude environments

(2011) Z A Cheviron et al.   HEREDITY

Elevated performance: the unique physiology of birds that fly at high altitudes

(2011) G. R. Scott   JOURNAL OF EXPERIMENTAL BIOLOGY

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

A multi-gene approach reveals a complex evolutionary history in the Cyanistes species group

(2011) JUAN CARLOS ILLERA et al.   MOLECULAR ECOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates

(2010) J. F. Storz et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

Evidence for an ancient adaptive episode of convergent molecular evolution

(2009) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of muscle phenotype for extreme high altitude flight in the bar-headed goose

(2009) G. R. Scott et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

QuickGO: a user tutorial for the web-based Gene Ontology browser

(2009) Rachael P. Huntley et al.   Database-The Journal of Biological Databases and Curation

An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics

(2008) James C. Zachos et al.   NATURE