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Recurrent gene amplification on Drosophila Y chromosomes suggests cryptic sex chromosome drive is common on young sex chromosomes

https://doi.org/10.1101/324368
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Phylogeny-aware alignment with PRANK
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Progress and prospects toward our understanding of the evolution of dosage compensation
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Sequencing the Mouse Y Chromosome Reveals Convergent Gene Acquisition and Amplification on Both Sex Chromosomes
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The hpRNA/RNAi Pathway Is Essential to Resolve Intragenomic Conflict in the Drosophila Male Germline
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The cellular basis of hybrid dysgenesis and Stellate regulation in Drosophila
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Adaptive Regulation of Testis Gene Expression and Control of Male Fertility by the Drosophila Hairpin RNA Pathway
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A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome
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Genetic conflict and sex chromosome evolution
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The Ecology and Evolutionary Dynamics of Meiotic Drive
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Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome
inferredcites →https://doi.org/10.1016/s0169-5347(98)01567-5openalex-snapshot
The Y chromosome as a battle ground for sexual selection
inferredcites →https://doi.org/10.1038/35084545openalex-snapshot
The role of selfish genetic elements in eukaryotic evolution
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The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
inferredcites →https://doi.org/10.1038/nature01723openalex-snapshot
Abundant gene conversion between arms of palindromes in human and ape Y chromosomes
inferredcites →https://doi.org/10.1038/nature06330openalex-snapshot
Demasculinization of X chromosomes in the Drosophila genus
inferredcites →https://doi.org/10.1038/nature06341openalex-snapshot
Evolution of genes and genomes on the Drosophila phylogeny
inferredcites →https://doi.org/10.1038/nature12235openalex-snapshot
Reversal of an ancient sex chromosome to an autosome in Drosophila
inferredcites →https://doi.org/10.1038/nature13151openalex-snapshot
Origins and functional evolution of Y chromosomes across mammals
inferredcites →https://doi.org/10.1038/nature13206openalex-snapshot
Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators
inferredcites →https://doi.org/10.1038/ng.126openalex-snapshot
The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression
inferredcites →https://doi.org/10.1038/ng.2705openalex-snapshot
Independent specialization of the human and mouse X chromosomes for the male germ line
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
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Fast and sensitive protein alignment using DIAMOND
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HISAT: a fast spliced aligner with low memory requirements
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The molecular evolutionary basis of species formation
inferredcites →https://doi.org/10.1038/nrg3366openalex-snapshot
Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration
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Massive gene amplification on a recently formed Drosophila Y chromosome
inferredcites →https://doi.org/10.1042/bst0340562openalex-snapshot
Sex-ratio meiotic drive in Drosophila simulans: cellular mechanism, candidate genes and evolution
inferredcites →https://doi.org/10.1073/pnas.101456898openalex-snapshot
Y chromosome polymorphism is a strong determinant of male fitness in Drosophila melanogaster
inferredcites →https://doi.org/10.1073/pnas.1519332113openalex-snapshot
Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive
inferredcites →https://doi.org/10.1093/bioinformatics/bti1003openalex-snapshot
PILER: identification and classification of genomic repeats
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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
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IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btv290openalex-snapshot
BFC: correcting Illumina sequencing errors
inferredcites →https://doi.org/10.1093/genetics/128.4.841openalex-snapshot
Causes of sex ratio bias may account for unisexual sterility in hybrids: a new explanation of Haldane's rule and related phenomena.
inferredcites →https://doi.org/10.1093/genetics/13.6.488openalex-snapshot
A NEW SEX-RATIO ABNORMALITY IN DROSOPHILA OBSCURA
inferredcites →https://doi.org/10.1093/genetics/130.1.229openalex-snapshot
Is Stellate a relict meiotic driver?
inferredcites →https://doi.org/10.1093/genetics/14.1.127openalex-snapshot
A NEW SEX-RATIO ABNORMALITY IN DROSOPHILA OBSCURA
inferredcites →https://doi.org/10.1093/genetics/154.1.229openalex-snapshot
Sex-ratio Meiotic Drive in Drosophila simulans Is Related to Equational Nondisjunction of the Y Chromosome
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/nar/20.14.3731openalex-snapshot
Structural organization and diversification of Y-linked sequences comprising Su(Ste) genes in Drosophila melanogaster
inferredcites →https://doi.org/10.1093/nar/gkw1016openalex-snapshot
FlyBase at 25: looking to the future
inferredcites →https://doi.org/10.1098/rspb.2001.1863openalex-snapshot
The X chromosome is a hot spot for sexually antagonistic fitness variation
inferredcites →https://doi.org/10.1098/rstb.2000.0717openalex-snapshot
The degeneration of Y chromosomes
inferredcites →https://doi.org/10.1098/rstb.2009.0264openalex-snapshot
The role of meiotic drive in hybrid male sterility
inferredcites →https://doi.org/10.1100/tsw.2010.168openalex-snapshot
Multiple Roles of the Y Chromosome in the Biology ofDrosophila melanogaster
inferredcites →https://doi.org/10.1101/gr.088609.108openalex-snapshot
General gene movement off the X chromosome in the Drosophila genus
inferredcites →https://doi.org/10.1101/gr.159384.113openalex-snapshot
Comparative validation of the D. melanogaster modENCODE transcriptome annotation
inferredcites →https://doi.org/10.1111/j.1558-5646.1984.tb00346.xopenalex-snapshot
SEX CHROMOSOMES AND THE EVOLUTION OF SEXUAL DIMORPHISM
inferredcites →https://doi.org/10.1111/j.1558-5646.1991.tb04401.xopenalex-snapshot
DIVERGENCE OF MEIOTIC DRIVE‐SUPPRESSION SYSTEMS AS AN EXPLANATION FOR SEX‐BIASED HYBRID STERILITY AND INVIABILITY
inferredcites →https://doi.org/10.1126/science.1090042openalex-snapshot
Extensive Gene Traffic on the Mammalian X Chromosome
inferredcites →https://doi.org/10.1126/science.169.3948.888openalex-snapshot
"Sex Ratio" in Drosophila pseudoobscura : Spermiogenic Failure
inferredcites →https://doi.org/10.1126/science.283.5408.1742openalex-snapshot
Truncated RanGAP Encoded by the Segregation Distorter Locus of Drosophila
inferredcites →https://doi.org/10.1126/science.715437openalex-snapshot
Gene Dosage Compensation and the Evolution of Sex Chromosomes
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110411-160242openalex-snapshot
Nothing in Genetics Makes Sense Except in Light of Genomic Conflict
inferredcites →https://doi.org/10.1146/annurev.ecolsys.32.081501.113958openalex-snapshot
Sex Chromosome Meiotic Drive
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-6-31openalex-snapshot
Automated generation of heuristics for biological sequence comparison
inferredcites →https://doi.org/10.1186/1471-2148-7-87openalex-snapshot
Molecular phylogeny of the Drosophila obscura species group, with emphasis on the Old World species
inferredcites →https://doi.org/10.1186/1471-2164-12-177openalex-snapshot
Expansion and functional diversification of a leucyl aminopeptidase family that encodes the major protein constituents of Drosophila sperm
inferredcites →https://doi.org/10.1186/s12862-019-1425-0openalex-snapshot
Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group
inferredcites →https://doi.org/10.1242/jcs.108.4.1419openalex-snapshot
Heterochromatin protein 1 is required for correct chromosome segregation in Drosophila embryos
inferredcites →https://doi.org/10.1242/jeb.148148openalex-snapshot
Genetic conflicts: the usual suspects and beyond
inferredcites →https://doi.org/10.1371/journal.pbio.0050292openalex-snapshot
A sex-ratio Meiotic Drive System in Drosophila simulans. I: An Autosomal Suppressor
inferredcites →https://doi.org/10.1371/journal.pbio.0050293openalex-snapshot
A sex-ratio Meiotic Drive System in Drosophila simulans. II: An X-linked Distorter
inferredcites →https://doi.org/10.1371/journal.pbio.1000244openalex-snapshot
The Multicopy Gene Sly Represses the Sex Chromosomes in the Male Mouse Germline after Meiosis
inferredcites →https://doi.org/10.1371/journal.pbio.1000335openalex-snapshot
The Sexually Antagonistic Genes of Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pbio.1001899openalex-snapshot
Sex Determination: Why So Many Ways of Doing It?
inferredcites →https://doi.org/10.1371/journal.pbio.1002499openalex-snapshot
Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline
inferredcites →https://doi.org/10.1371/journal.pbio.2006348openalex-snapshot
De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
inferredcites →https://doi.org/10.1371/journal.pgen.1002900openalex-snapshot
A Genetic Basis for a Postmeiotic X Versus Y Chromosome Intragenomic Conflict in the Mouse
inferredcites →https://doi.org/10.1371/journal.pgen.1005073openalex-snapshot
Sex Ratio Meiotic Drive as a Plausible Evolutionary Mechanism for Hybrid Male Sterility
inferredcites →https://doi.org/10.1534/genetics.110.115444openalex-snapshot
Nonallelic Gene Conversion in the Genus Drosophila
inferredcites →https://doi.org/10.1534/genetics.112.147561openalex-snapshot
Mutations to the piRNA Pathway ComponentAubergineEnhance Meiotic Drive of Segregation Distorter inDrosophila melanogaster
inferredcites →https://doi.org/10.1534/genetics.116.192336openalex-snapshot
Repeated Duplication of Argonaute2 Is Associated with Strong Selection and Testis Specialization in Drosophila

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41559-019-1009-9openalex-snapshot
Massive gene amplification on a recently formed Drosophila Y chromosome
inferred← citeshttps://doi.org/10.1186/s12862-019-1425-0openalex-snapshot
Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group
inferred← citeshttps://doi.org/10.1371/journal.pbio.2005609openalex-snapshot
Haploid selection, sex ratio bias, and transitions between sex-determining systems
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