Comparative linkage mapping uncovers recombination suppression across massive chromosomal inversions associated with local adaptation in Atlantic silversides

Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation

(2021) Anna Tigano et al.   Genome Biology and Evolution

BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

(2021) Yasmine Mansour et al.   BMC BIOINFORMATICS

Constraint and divergence in the evolution of male and female recombination rates in fishes

(2021) Christopher R. Cooney et al.   EVOLUTION

A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia

(2020) Nina Overgaard Therkildsen et al.   Marine Genomics

Balancing selection via life-history trade-offs maintains an inversion polymorphism in a seaweed fly

(2020) Claire Mérot et al.   Nature Communications

Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

(2020) Enrique J. Schwarzkopf et al.   BMC GENOMICS

Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura

(2020) Kieran Samuk et al.   CURRENT BIOLOGY

From molecules to populations: appreciating and estimating recombination rate variation

(2020) Joshua V. Peñalba et al.   NATURE REVIEWS GENETICS

Making the most of population genomic data to understand the importance of chromosomal inversions for adaptation and speciation

(2020) Claire Mérot   MOLECULAR ECOLOGY

Massive haplotypes underlie ecotypic differentiation in sunflowers

(2020) Marco Todesco et al.   NATURE

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

(2020) Aryn P. Wilder et al.   Evolution Letters

Evolving Inversions

(2019) Rui Faria et al.   TRENDS IN ECOLOGY & EVOLUTION

Going beyond SNPs: the role of structural genomic variants in adaptive evolution and species diversification

(2019) Maren Wellenreuther et al.   MOLECULAR ECOLOGY

Sex differences in the recombination landscape

(2019) Jason M. Sardell et al.   AMERICAN NATURALIST

Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

(2019) Nina O. Therkildsen et al.   SCIENCE

Otolith-based growth reconstructions in young-of-year Atlantic silversides Menidia menidia and their implications for sex-selective survival

(2019) JW Pringle et al.   MARINE ECOLOGY PROGRESS SERIES

Full mitochondrial genome sequences reveal new insights about post-glacial expansion and regional phylogeographic structure in the Atlantic silverside (Menidia menidia)

(2018) Runyang Nicolas Lou et al.   MARINE BIOLOGY

Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics

(2018) Quiterie Haenel et al.   MOLECULAR ECOLOGY

Eco-Evolutionary Genomics of Chromosomal Inversions

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

Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes

(2018) Rui Faria et al.   MOLECULAR ECOLOGY

Chromosomal inversions associated with environmental adaptation in honeybees

(2018) Matthew J. Christmas et al.   MOLECULAR ECOLOGY

Connecting theory and data to understand recombination rate evolution

(2017) Amy L. Dapper et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recombination rate plasticity: revealing mechanisms by design

(2017) Laurie S. Stevison et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

(2017) Jessica Stapley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Variation in Recombination Rate: Adaptive or Not?

(2017) Kathryn R. Ritz et al.   TRENDS IN GENETICS

“Islands of Divergence” in the Atlantic Cod Genome Represent Polymorphic Chromosomal Rearrangements

(2016) Marte Sodeland et al.   Genome Biology and Evolution

Consequences of elevated CO2exposure across multiple life stages in a coastal forage fish

(2016) Christopher S. Murray et al.   ICES JOURNAL OF MARINE SCIENCE

Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod

(2016) Tina Graceline Kirubakaran et al.   MOLECULAR ECOLOGY

Genomics of local adaptation with gene flow

(2016) Anna Tigano et al.   MOLECULAR ECOLOGY

Pattern and scale of geographic variation in environmental sex determination in the Atlantic silverside,Menidia menidia

(2015) Tara A. Duffy et al.   EVOLUTION

Vulnerability of early life stage Northwest Atlantic forage fish to ocean acidification and low oxygen

(2015) E DePasquale et al.   MARINE ECOLOGY PROGRESS SERIES

An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

(2015) G. J. McKinney et al.   Molecular Ecology Resources

The genomics of ecological vicariance in threespine stickleback fish

(2015) Marius Roesti et al.   Nature Communications

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Vulnerability of early life stage Northwest Atlantic forage fish to ocean acidification and low oxygen

(2015) E DePasquale et al.   MARINE ECOLOGY PROGRESS SERIES

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Decadal Changes in the World's Coastal Latitudinal Temperature Gradients

(2013) Hannes Baumann et al.   PLoS One

Genomic rearrangements and the evolution of clusters of locally adaptive loci

(2013) S. Yeaman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Scrambling Eggs: Meiotic Drive and the Evolution of Female Recombination Rates

(2011) Yaniv Brandvain et al.   GENETICS

Recombination rate variation in closely related species

(2011) C S Smukowski et al.   HEREDITY

Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary

(2011) X. Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

The landscape of recombination in African Americans

(2011) Anjali G. Hinch et al.   NATURE

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

(2011) A. Branca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species

(2010) Elena Sarropoulou et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

How and Why Chromosome Inversions Evolve

(2010) Mark Kirkpatrick   PLOS BIOLOGY

The Covariance between Genetic and Environmental Influences across Ecological Gradients

(2009) David O. Conover et al.   Annals of the New York Academy of Sciences

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Chemical signatures in the otoliths of a coastal marine fish, Menidia menidia, from the northeastern United States: spatial and temporal differences

(2009) LM Clarke et al.   MARINE ECOLOGY PROGRESS SERIES

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Revisiting the Impact of Inversions in Evolution: From Population Genetic Markers to Drivers of Adaptive Shifts and Speciation?

(2008) Ary A. Hoffmann et al.   Annual Review of Ecology Evolution and Systematics