Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows

Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

(2022) Ching-Ho Chang et al.   eLife

Gene regulation by gonadal hormone receptors underlies brain sex differences

(2022) B. Gegenhuber et al.   NATURE

Oleic acid is an endogenous ligand of TLX/NR2E1 that triggers hippocampal neurogenesis

(2022) Prasanna Kandel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recurring adaptive introgression of a supergene variant that determines social organization

(2022) Eckart Stolle et al.   Nature Communications

A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes

(2022) Emily R. Hager et al.   SCIENCE

Genome‐wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white‐throated sparrows

(2021) Dan Sun et al.   MOLECULAR ECOLOGY

pixy : Unbiased estimation of nucleotide diversity and divergence in the presence of missing data

(2021) Katharine L Korunes et al.   Molecular Ecology Resources

Balancing selection in self‐fertilizing populations

(2021) Sylvain Glémin   EVOLUTION

Kcns3 deficiency disrupts Parvalbumin neuron physiology in mouse prefrontal cortex: Implications for the pathophysiology of schizophrenia

(2021) Takeaki Miyamae et al.   NEUROBIOLOGY OF DISEASE

Massive genome inversion drives coexistence of divergent morphs in common quails

(2021) Ines Sanchez-Donoso et al.   CURRENT BIOLOGY

A supergene underlies linked variation in color and morphology in a Holarctic songbird

(2021) Erik R. Funk et al.   Nature Communications

BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data

(2020) Katherine M Siewert et al.   Genome Biology and Evolution

Evolution of a supergene that regulates a trans-species social polymorphism

(2020) Zheng Yan et al.   Nature Ecology & Evolution

Vasoactive intestinal peptide as a mediator of the effects of a supergene on social behaviour

(2020) Brent M. Horton et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants

(2020) Carlos Martinez-Ruiz et al.   eLife

A supergene-linked estrogen receptor drives alternative phenotypes in a polymorphic songbird

(2020) Jennifer R. Merritt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular architecture of the zebra finch arcopallium

(2019) Claudio V Mello et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Little Evidence of Antagonistic Selection in the Evolutionary Strata of Fungal Mating-Type Chromosomes (Microbotryum lychnidis-dioicae)

(2019) Anna Liza Bazzicalupo et al.   G3-Genes Genomes Genetics

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds

(2019) Luohao Xu et al.   Nature Ecology & Evolution

Transcriptome Analyses of Heart and Liver Reveal Novel Pathways for Regulating Songbird Migration

(2019) William J. Horton et al.   Scientific Reports

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

(2019) Tony Kess et al.   Science Advances

Sex-dependent dominance maintains migration supergene in rainbow trout

(2019) Devon E. Pearse et al.   Nature Ecology & Evolution

Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes

(2018) Dan Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene

(2018) Yu-Ching Huang et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Eco-Evolutionary Genomics of Chromosomal Inversions

(2018) Maren Wellenreuther et al.   TRENDS IN ECOLOGY & EVOLUTION

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

Esrrb, an estrogen-related receptor involved in early development, pluripotency, and reprogramming

(2017) Nicola Festuccia et al.   FEBS LETTERS

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman et al.   GENOME RESEARCH

The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB

(2017) Rodrigo Pracana et al.   MOLECULAR ECOLOGY

Supergenes: The Genomic Architecture of a Bird with Four Sexes

(2016) Leonardo Campagna   CURRENT BIOLOGY

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

(2016) Elaina M. Tuttle et al.   CURRENT BIOLOGY

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era

(2016) Feng Gao et al.   G3-Genes Genomes Genetics

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data: Table 1.

(2015) Chase W. Nelson et al.   BIOINFORMATICS

The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex adaptations

(2015) Deborah Charlesworth   Evolutionary Applications

Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows

(2015) W. M. Zinzow-Kramer et al.   GENES BRAIN AND BEHAVIOR

Estrogen Receptor Alpha as a Mediator of Life-History Trade-offs

(2015) Donna L. Maney et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

(2015) Florencia Schlamp et al.   MOLECULAR ECOLOGY

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Extreme selective sweeps independently targeted the X chromosomes of the great apes

(2015) Kiwoong Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication

(2015) Brandon S. Gaut et al.   TRENDS IN GENETICS

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

Positive and Purifying Selection on the Drosophila Y Chromosome

(2014) Nadia D. Singh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

Estrogen receptor   polymorphism in a species with alternative behavioral phenotypes

(2014) B. M. Horton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

(2014) Christopher N. Balakrishnan et al.   PeerJ

Lower Gene Expression for KCNS3 Potassium Channel Subunit in Parvalbumin-Containing Neurons in the Prefrontal Cortex in Schizophrenia

(2013) Danko Georgiev et al.   AMERICAN JOURNAL OF PSYCHIATRY

Genetic mapping of the female mimic morph locus in the ruff

(2013) Lindsay L Farrell et al.   BMC GENETICS

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

On the importance of balancing selection in plants

(2013) Lynda F. Delph et al.   NEW PHYTOLOGIST

Behavioral Characterization of a White-Throated Sparrow Homozygous for the ZAL2m Chromosomal Rearrangement

(2012) Brent M. Horton et al.   BEHAVIOR GENETICS

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

Morph Matters: Aggression Bias in a Polymorphic Sparrow

(2012) Brent M. Horton et al.   PLoS One

An aggression-specific cell type in the anterior hypothalamus of finches

(2012) J. L. Goodson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila

(2012) Q. Zhou et al.   SCIENCE

Small but mighty: the evolutionary dynamics of W and Y sex chromosomes

(2011) Judith E. Mank   CHROMOSOME RESEARCH

Haplotype-Based Genomic Sequencing of a Chromosomal Polymorphism in the White-Throated Sparrow (Zonotrichia albicollis)

(2011) J. K. Davis et al.   JOURNAL OF HEREDITY

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis)

(2010) Lynn Y Huynh et al.   BMC GENETICS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Sexual Conflict Resolved by Invasion of a Novel Sex Determiner in Lake Malawi Cichlid Fishes

(2009) R. B. Roberts et al.   SCIENCE

Endocrine and genomic architecture of life history trade-offs in an avian model of social behavior

(2008) Donna L. Maney   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Meiotic Recombination at the Ends of Chromosomes in Saccharomyces cerevisiae

(2008) A. B. Barton et al.   GENETICS

The Chromosomal Polymorphism Linked to Variation in Social Behavior in the White-Throated Sparrow (Zonotrichia albicollis) Is a Complex Rearrangement and Suppressor of Recombination

(2008) J. W. Thomas et al.   GENETICS