4.8 Article

A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Evolution of the canonical sex chromosomes of the guppy and its relatives

Mark Kirkpatrick et al.

Summary: This study focuses on the sex chromosomes of the guppy and its close relatives, finding no evidence of a nonrecombining sex-determining region and suggesting that the evolution of sex-determining regions in certain relatives occurred independently. It also addresses conflicting results in previous studies and proposes best practices for future research.

G3-GENES GENOMES GENETICS (2022)

Article Ecology

On the genetic architecture of rapidly adapting and convergent life history traits in guppies

James R. Whiting et al.

Summary: The genetic basis of traits shapes and constrains how adaptation proceeds in nature. Guppy life history traits evolve rapidly and convergently in natural environments. Polygenic trait architectures may facilitate rapid phenotypic evolution but limit gene re-use across populations due to genetic redundancy.

HEREDITY (2022)

Article Biochemistry & Molecular Biology

Divergence and Remarkable Diversity of the Y Chromosome in Guppies

Pedro Almeida et al.

Summary: The study found that there is significant diversity and divergence in guppy Y chromosomes across different populations and species, with Y chromosome evolution linked to environmental pressures. Contrary to previous assumptions, the experiment results suggest that Y chromosome diversity is mainly influenced by gradual mechanisms of recombination suppression, rather than inversions for achieving sex chromosome recombination suppression.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Review Evolutionary Biology

The Genomic Architecture and Evolutionary Fates of Supergenes

Juanita Gutierrez-Valencia et al.

Summary: Supergenes are genomic regions controlling multi-trait phenotypic polymorphisms under balancing selection, with significant variation in genomic architecture and origin mode across diverse organisms. Differences in genomic architecture affect the evolutionary fate and degeneration rate of supergenes. Recent findings and simulations demonstrate the implications of genomic architecture on the evolution of supergenes and the long-term fate of balanced polymorphisms.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Genetics & Heredity

Studying models of balancing selection using phase-type theory

Kai Zeng et al.

Summary: Balancing selection is an important evolutionary force for maintaining genetic variability, and its effects on polymorphism patterns in linked neutral regions vary depending on the duration of the selection and recent population size changes. Long-term BLS has limited effects on polymorphism patterns, while new mutations subject to BLS initially reduce diversity and increase linkage disequilibrium in neutral regions.

GENETICS (2021)

Article Ecology

Using Delaunay triangulation to sample whole-specimen color from digital images

Jennifer J. Valvo et al.

Summary: Color variation is a common phenomenon in nature, but quantifying and interpreting it accurately can be challenging. This study introduced a new method called Colormesh, which combines unsupervised color quantification and geometric morphometrics to analyze complex color patterns. By applying Colormesh to digital images of Trinidadian guppies, the researchers found that the patterns of color variation did not align with previous expectations, demonstrating the utility of this approach for studying color pattern variation.

ECOLOGY AND EVOLUTION (2021)

Article Genetics & Heredity

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies

James R. Whiting et al.

Summary: Evidence of convergent evolution associated with HP-LP environments was found in the high- and low-predation populations of Trinidadian guppies, highlighting restrictions on the distribution of genetic variation between rivers. There was limited selection on common genes across drainages, but repeated selection on different genes involved in cadherin signaling. Constraints on genomic convergence were observed, but some repeatability in the genetic basis of convergent phenotypic evolution in this important model system was also demonstrated.

PLOS GENETICS (2021)

Article Biochemistry & Molecular Biology

Widespread intersex differentiation across the stickleback genome - The signature of sexually antagonistic selection?

Mirjam Bissegger et al.

MOLECULAR ECOLOGY (2020)

Review Genetics & Heredity

The genomics of coloration provides insights into adaptive evolution

Anna Orteu et al.

NATURE REVIEWS GENETICS (2020)

Article Evolutionary Biology

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)

Bonnie A. Fraser et al.

GENOME BIOLOGY AND EVOLUTION (2020)

Article Genetics & Heredity

Locating the Sex Determining Region of Linkage Group 12 of Guppy (Poecilia reticulata)

Deborah Charlesworth et al.

G3-GENES GENOMES GENETICS (2020)

Article Multidisciplinary Sciences

Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms

Roberta Bergero et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biotechnology & Applied Microbiology

Genetic mechanism underlying sexual plasticity and its association with colour patterning in zebrafish (Danio rerio)

Shahrbanou Hosseini et al.

BMC GENOMICS (2019)

Article Multidisciplinary Sciences

Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird

Kang-Wook Kim et al.

NATURE COMMUNICATIONS (2019)

Letter Multidisciplinary Sciences

On the power to detect rare recombination events

Alison E. Wright et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

Sean Stankowski et al.

PLOS BIOLOGY (2019)

Article Genetics & Heredity

Limits to Genomic Divergence Under Sexually Antagonistic Selection

Katja R. Kasimatis et al.

G3-GENES GENOMES GENETICS (2019)

Article Genetics & Heredity

Mapping of the Sex Determining Region on Linkage Group 12 of Guppy (Poecilia reticulata)

Lior Dor et al.

G3-GENES GENOMES GENETICS (2019)

Review Immunology

The NLRP1 inflammasome: new mechanistic insights and unresolved mysteries

Patrick S. Mitchell et al.

CURRENT OPINION IN IMMUNOLOGY (2019)

Article Biochemistry & Molecular Biology

Hematopoietic and neural crest defects in zebrafish shoc2 mutants: a novel vertebrate model for Noonan-like syndrome

Hyein Jang et al.

HUMAN MOLECULAR GENETICS (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemical Research Methods

Accurate detection of complex structural variations using single-molecule sequencing

Fritz J. Sedlazeck et al.

NATURE METHODS (2018)

Review Genetics & Heredity

The Colorful Sex Chromosomes of Teleost Fish

Verena A. Kottler et al.

GENES (2018)

Article Genetics & Heredity

A One-Penny Imputed Genome from Next-Generation Reference Panels

Brian L. Browning et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2018)

Article Genetics & Heredity

Measuring Genetic Differentiation from Pool-seq Data

Valentin Hivert et al.

GENETICS (2018)

Article Multidisciplinary Sciences

Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish

Paolo Franchini et al.

NATURE COMMUNICATIONS (2018)

Article Anthropology

Frequency of folate-related polymorphisms varies by skin pigmentation

Patrice Jones et al.

AMERICAN JOURNAL OF HUMAN BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Back to basics: using colour polymorphisms to study evolutionary processes

Erik I. Svensson

MOLECULAR ECOLOGY (2017)

Article Multidisciplinary Sciences

Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation

Alison E. Wright et al.

NATURE COMMUNICATIONS (2017)

Article Ecology

A sex-linked supergene controls sperm morphology and swimming speed in a songbird

Kang-Wook Kim et al.

NATURE ECOLOGY & EVOLUTION (2017)

Article Biochemistry & Molecular Biology

Sexually dimorphic expression in developing and adult gonads shows an important role of gonadal soma-derived factor during sex differentiation in olive flounder (Paralichthys olivaceus)

Yuezhong Liu et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY (2017)

Article Biochemical Research Methods

Sambamba: fast processing of NGS alignment formats

Artem Tarasov et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

SpeedSeq: ultra-fast personal genome analysis and interpretation

Colby Chiang et al.

NATURE METHODS (2015)

Article Developmental Biology

Sex Chromosome Synapsis and Recombination in Male Guppies

Artem P. Lisachov et al.

ZEBRAFISH (2015)

Article Multidisciplinary Sciences

Mutations in PNPLA6 are linked to photoreceptor degeneration and various forms of childhood blindness

S. Kmoch et al.

NATURE COMMUNICATIONS (2015)

Article Psychology, Biological

Mate Preference for Novel Phenotypes: A Fresh Face Matters

Robin E. Graber et al.

ETHOLOGY (2015)

Article Statistics & Probability

changepoint: AnRPackage for Changepoint Analysis

Rebecca Killick et al.

Journal of Statistical Software (2015)

Article Biochemistry & Molecular Biology

Sex chromosome polymorphism in guppies

Indrajit Nanda et al.

CHROMOSOMA (2014)

Article Biochemistry & Molecular Biology

Epistatic and Combinatorial Effects of Pigmentary Gene Mutations in the Domestic Pigeon

Eric T. Domyan et al.

CURRENT BIOLOGY (2014)

Article Genetics & Heredity

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

Catherine A. Wilson et al.

GENETICS (2014)

Article Biochemistry & Molecular Biology

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

Bastian Pfeifer et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Biochemistry & Molecular Biology

deepTools: a flexible platform for exploring deep-sequencing data

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biotechnology & Applied Microbiology

LUMPY: a probabilistic framework for structural variant discovery

Ryan M. Layer et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Ecology

WHY EPISTASIS IS IMPORTANT FOR SELECTION AND ADAPTATION

Thomas F. Hansen

EVOLUTION (2013)

Review Biochemistry & Molecular Biology

The SLC24 gene family of Na+/Ca2+-K+ exchangers: From sight and smell to memory consolidation and skin pigmentation

Paul P. M. Schnetkamp

MOLECULAR ASPECTS OF MEDICINE (2013)

Article Multidisciplinary Sciences

Mating advantage for rare males in wild guppy populations

Kimberly A. Hughes et al.

NATURE (2013)

Letter Biochemical Research Methods

Improved whole-chromosome phasing for disease and population genetic studies

Olivier Delaneau et al.

NATURE METHODS (2013)

Review Genetics & Heredity

Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration

Doris Bachtrog

NATURE REVIEWS GENETICS (2013)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Biochemical Research Methods

The variant call format and VCFtools

Petr Danecek et al.

BIOINFORMATICS (2011)

Review Genetics & Heredity

Xeroderma pigmentosum

Alan R. Lehmann et al.

ORPHANET JOURNAL OF RARE DISEASES (2011)

Article Multidisciplinary Sciences

Tudor domain containing 7 (Tdrd7) is essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis

Takashi Tanaka et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Editorial Material Mathematical & Computational Biology

BioMart: driving a paradigm change in biological data management

Arek Kasprzyk

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2011)

Article Biochemistry & Molecular Biology

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies

Eva-Maria Willing et al.

MOLECULAR ECOLOGY (2010)

Review Biochemistry & Molecular Biology

Colour polymorphism and correlated characters: genetic mechanisms and evolution

Jeffrey S. McKinnon et al.

MOLECULAR ECOLOGY (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Review Genetics & Heredity

Genetic and molecular insights into the development and evolution of sexual dimorphism

Thomas M. Williams et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemical Research Methods

adegenet:: a R package for the multivariate analysis of genetic markers

Thibaut Jombart

BIOINFORMATICS (2008)

Article Developmental Biology

Potential role of Nanos3 in maintaining the undifferentiated spermatogonia population

Francesca Lolicato et al.

DEVELOPMENTAL BIOLOGY (2008)

Review Fisheries

The evolution of teleost pigmentation and the fish-specific genome duplication

I. Braasch et al.

JOURNAL OF FISH BIOLOGY (2008)

Article Multidisciplinary Sciences

Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences

Bernardo Lemos et al.

SCIENCE (2008)

Review Biochemistry & Molecular Biology

Population genomics:: Whole-genome analysis of polymorphism and divergence in Drosophila simulans

David J. Begun et al.

PLOS BIOLOGY (2007)

Article Genetics & Heredity

PLINK: A tool set for whole-genome association and population-based linkage analyses

Shaun Purcell et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2007)

Article Biochemistry & Molecular Biology

Absence of tektin 4 causes asthenozoospermia and subfertility in male mice

Angshumoy Roy et al.

FASEB JOURNAL (2007)

Article Cell Biology

Keratin finction in skin epithelia: a broadening palette with surprising shades

Li-Hong Gu et al.

CURRENT OPINION IN CELL BIOLOGY (2007)

Article Multidisciplinary Sciences

Frequency-dependent survival in natural guppy populations

Robert Olendorf et al.

NATURE (2006)

Article Ecology

Genetic and environmental effects on secondary sex traits in guppies (Poecilia reticulata)

KA Hughes et al.

JOURNAL OF EVOLUTIONARY BIOLOGY (2005)

Article Ecology

Sex chromosomes and sexual selection in poeciliid fishes

A Lindholm et al.

AMERICAN NATURALIST (2002)

Article Behavioral Sciences

Ultraviolet reflectance patterns of male guppies enhance their attractiveness to females

A Kodric-Brown et al.

ANIMAL BEHAVIOUR (2002)

Review Ornithology

The evolution of cooperative and pair breeding in thornbills Acanthiza (Pardalotidae)

JA Nicholls et al.

JOURNAL OF AVIAN BIOLOGY (2000)