[1]

Ellegren H, Sheldon BC. 2008. Genetic basis of fitness differences in natural populations. Nature 452:169−75

doi: 10.1038/nature06737
[2]

Carvalho CMB, Lupski JR. 2016. Mechanisms underlying structural variant formation in genomic disorders. Nature Reviews Genetics 17(4):224−38

doi: 10.1038/nrg.2015.25
[3]

Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, et al. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55−61

doi: 10.1038/nature10944
[4]

Yoshida K, Rödelsperger C, Röseler W, Riebesell M, Sun S, et al. 2023. Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. Nature Ecology & Evolution 7(3):424−39

doi: 10.1038/s41559-022-01980-z
[5]

Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, et al. 2010. Origins and functional impact of copy number variation in the human genome. Nature 464:704−12

doi: 10.1038/nature08516
[6]

Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. 2007. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315:848−53

doi: 10.1126/science.1136678
[7]

Aguilera A, Gómez-González B. 2008. Genome instability: a mechanistic view of its causes and consequences. Nature Reviews Genetics 9(3):204−17

doi: 10.1038/nrg2268
[8]

Kaufmann P, Wiberg RAW, Papachristos K, Scofield DG, Tellgren-Roth C, et al. 2023. Y-linked copy number polymorphism of target of rapamycin is associated with sexual size dimorphism in seed beetles. Molecular Biology and Evolution 40:msad167

doi: 10.1093/molbev/msad167
[9]

Wang Y, Gasser RB, Charlesworth D, Zhou Q. 2022. Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms. Nature Communications 13:3239

doi: 10.1038/s41467-022-30578-z
[10]

Tosto NM, Beasley ER, Wong BBM, Mank JE, Flanagan SP. 2023. The roles of sexual selection and sexual conflict in shaping patterns of genome and transcriptome variation. Nature Ecology & Evolution 7(7):981−93

doi: 10.1038/s41559-023-02019-7
[11]

Chen S, Krinsky BH, Long M. 2013. New genes as drivers of phenotypic evolution. Nature Reviews Genetics 14(9):645−60

doi: 10.1038/nrg3521
[12]

Sayadi A, Martinez Barrio A, Immonen E, Dainat J, Berger D, et al. 2019. The genomic footprint of sexual conflict. Nature Ecology & Evolution 3(12):1725−30

doi: 10.1038/s41559-019-1041-9
[13]

Harrison PW, Wright AE, Zimmer F, Dean R, Montgomery SH, et al. 2015. Sexual selection drives evolution and rapid turnover of male gene expression. Proceedings of the National Academy of Sciences of the United States of America 112(14):4393−98

doi: 10.1073/pnas.1501339112
[14]

Catalán A, Macias-Muñoz A, Briscoe AD. 2018. Evolution of sex-biased gene expression and dosage compensation in the eye and brain of Heliconius butterflies. Molecular Biology and Evolution 35(9):2120−34

doi: 10.1093/molbev/msy111
[15]

Charlesworth B, Charlesworth D. 2000. The degeneration of Y chromosomes. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 355:1563−72

doi: 10.1098/rstb.2000.0717
[16]

Angus RB, Dellow J, Winder C, Credland PF. 2011. Karyotype differences among four species of Callosobruchus Pic (Coleoptera: Bruchidae). Journal of Stored Products Research 47(2):76−81

doi: 10.1016/j.jspr.2010.10.003
[17]

Nina Wilson SCT. 1997. Female genotype affects male success in sperm competition. Proceedings: Biological Sciences 264(1387):1491−95

doi: 10.2307/51051
[18]

Salehialavi Y, Fritzsche K, Arnqvist G. 2011. The cost of mating and mutual mate choice in 2 role–reversed honey locust beetles. Behavioral Ecology 22(5):1104−13

doi: 10.1093/beheco/arr097
[19]

Hu F, Zhang GN, Wang JJ. 2009. Scanning electron microscopy studies of antennal sensilla of bruchid beetles, Callosobruchus chinensis (L.) and Callosobruchus maculatus (F.) (Coleoptera: Bruchidae). Micron 40:320−26

doi: 10.1016/j.micron.2008.11.001
[20]

Hotzy C, Polak M, Rönn JL, Arnqvist G. 2012. Phenotypic engineering unveils the function of genital morphology. Current Biology 22:2258−61

doi: 10.1016/j.cub.2012.10.009
[21]

Berger D, Martinossi-Allibert I, Grieshop K, Lind MI, Maklakov AA, et al. 2016. Intralocus sexual conflict and the tragedy of the commons in seed beetles. The American Naturalist 188(4):E98−E112

doi: 10.1086/687963
[22]

Immonen E, Sayadi A, Stojković B, Savković U, Đorđević M, et al. 2023. Experimental life history evolution results in sex-specific evolution of gene expression in seed beetles. Genome Biology and Evolution 15:evac177

doi: 10.1093/gbe/evac177
[23]

Lu HR, Mao CY, Zhang LJ, He JW, Wang XS, et al. 2024. High-quality reference genome of cowpea beetle Callosobruchus maculatus. Scientific Data 11:799

doi: 10.1038/s41597-024-03638-w
[24]

Arnqvist G, Westerberg I, Galbraith J, Sayadi A, Scofield DG, et al. 2024. A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements. G3 Genes Genom Genet 14:jkad266

doi: 10.1093/g3journal/jkad266
[25]

Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114−20

doi: 10.1093/bioinformatics/btu170
[26]

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37(8):907−15

doi: 10.1038/s41587-019-0201-4
[27]

Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7):923−30

doi: 10.1093/bioinformatics/btt656
[28]

Pereira V, Waxman D, Eyre-Walker A. 2009. A problem with the correlation coefficient as a measure of gene expression divergence. Genetics 183(4):1597−600

doi: 10.1534/genetics.109.110247
[29]

Hu J, Wang Z, Sun Z, Hu B, Ayoola AO, et al. 2024. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biology 25:107

doi: 10.1186/s13059-024-03252-4
[30]

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963

doi: 10.1371/journal.pone.0112963
[31]

Roach MJ, Schmidt SA, Borneman AR. 2018. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics 19:460

doi: 10.1186/s12859-018-2485-7
[32]

Zhang X, Zhang S, Zhao Q, Ming R, Tang H. 2019. Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nature Plants 5(8):833−45

doi: 10.1038/s41477-019-0487-8
[33]

Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, et al. 2016. Juicebox provides a visualization system for hi-C contact maps with unlimited zoom. Cell Systems 3:99−101

doi: 10.1016/j.cels.2015.07.012
[34]

Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, et al. 2020. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences of the United States of America 117:9451−57

doi: 10.1073/pnas.1921046117
[35]

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, et al. 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Research 34:W435−W439

doi: 10.1093/nar/gkl200
[36]

Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. 2016. BRAKER1: unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32(5):767−69

doi: 10.1093/bioinformatics/btv661
[37]

Li H. 2023. Protein-to-genome alignment with miniprot. Bioinformatics 39:btad014

doi: 10.1093/bioinformatics/btad014
[38]

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, et al. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33(3):290−95

doi: 10.1038/nbt.3122
[39]

Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, et al. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9:R7

doi: 10.1186/gb-2008-9-1-r7
[40]

Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238

doi: 10.1186/s13059-019-1832-y
[41]

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30(4):772−80

doi: 10.1093/molbev/mst010
[42]

Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17(4):540−52

doi: 10.1093/oxfordjournals.molbev.a026334
[43]

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32:268−74

doi: 10.1093/molbev/msu300
[44]

Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24(8):1586−91

doi: 10.1093/molbev/msm088
[45]

Wang Y, Tang H, DeBarry JD, Tan X, Li J, et al. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research 40:e49

doi: 10.1093/nar/gkr1293
[46]

Van Dam MH, Cabras AA, Henderson JB, Rominger AJ, Pérez Estrada C, et al. 2021. The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution. PLoS Genetics 17:e1009745

doi: 10.1371/journal.pgen.1009745
[47]

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, et al. 2018. MUMmer4: a fast and versatile genome alignment system. PLoS Computational Biology 14:e1005944

doi: 10.1371/journal.pcbi.1005944
[48]

Goel M, Sun H, Jiao WB, Schneeberger K. 2019. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biology 20:277

doi: 10.1186/s13059-019-1911-0
[49]

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550

doi: 10.1186/s13059-014-0550-8
[50]

Zhang Z, Xiao J, Wu J, Zhang H, Liu G, et al. 2012. ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochemical and Biophysical Research Communications 419(4):779−81

doi: 10.1016/j.bbrc.2012.02.101
[51]

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20(9):1297−303

doi: 10.1101/gr.107524.110
[52]

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, et al. 2011. The variant call format and VCFtools. Bioinformatics 27(15):2156−58

doi: 10.1093/bioinformatics/btr330
[53]

Papachristos K, Sayadi A, Arnqvist G. 2024. Comparative genomic analysis of the pattern of evolution of male and female reproductive proteins in seed beetles. Genome Biology and Evolution 16:evae143

doi: 10.1093/gbe/evae143
[54]

Kim HS, Murphy T, Xia J, Caragea D, Park Y, et al. 2010. BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. Nucleic Acids Research 38:D437−D442

doi: 10.1093/nar/gkp807
[55]

Zhang L, Li S, Luo J, Du P, Wu L, et al. 2020. Chromosome-level genome assembly of the predator Propylea japonica to understand its tolerance to insecticides and high temperatures. Molecular Ecology Resources 20:292−307

doi: 10.1111/1755-0998.13100
[56]

Ando T, Matsuda T, Goto K, Hara K, Ito A, et al. 2018. Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles. Nature Communications 9:3843

doi: 10.1038/s41467-018-06116-1
[57]

Mathers TC, Wouters RHM, Mugford ST, Swarbreck D, van Oosterhout C, et al. 2021. Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome. Molecular Biology and Evolution 38(3):856−75

doi: 10.1093/molbev/msaa246
[58]

Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution 3(12):1632−41

doi: 10.1038/s41559-019-1050-8
[59]

Kaufmann P, Wolak ME, Husby A, Immonen E. 2021. Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance. Nature Ecology & Evolution 5(10):1394−402

doi: 10.1038/s41559-021-01530-z
[60]

Ellegren H, Parsch J. 2007. The evolution of sex-biased genes and sex-biased gene expression. Nature Reviews Genetics 8(9):689−98

doi: 10.1038/nrg2167
[61]

Garcia-Hughes G, Link N, Ghosh AB, Abrams JM. 2015. Hid arbitrates collective cell death in the Drosophila wing. Mechanisms of Development 138:349−55

doi: 10.1016/j.mod.2015.07.008
[62]

Deng S, Wang J, Ma E, Zhang J, Xing S. 2022. TDRD5 is required for spermatogenesis and oogenesis in Locusta migratoria. Insects 13(3):227

doi: 10.3390/insects13030227
[63]

Li X, Zhou J, Chen H, Wang F, Mei Q, et al. 2017. The association between the UBQLN1 polymorphism and Alzheimer's disease risk: a systematic review. Cellular and Molecular Biology 63(5):94−96

doi: 10.14715/cmb/2017.63.5.17
[64]

Blanc V, Riordan JD, Soleymanjahi S, Nadeau JH, Nalbantoglu I, et al. 2021. Apobec1 complementation factor overexpression promotes hepatic steatosis, fibrosis, and hepatocellular cancer. The Journal of Clinical Investigation 131:138699

doi: 10.1172/JCI138699
[65]

Arnqvist G, Rönn J, Watson C, Goenaga J, Immonen E. 2022. Concerted evolution of metabolic rate, economics of mating, ecology, and pace of life across seed beetles. Proceedings of the National Academy of Sciences of the United States of America 119:e2205564119

doi: 10.1073/pnas.2205564119
[66]

Tuda M, Rönn J, Buranapanichpan S, Wasano N, Arnqvist G. 2006. Evolutionary diversification of the bean beetle genus Callosobruchus (Coleoptera: Bruchidae): traits associated with stored-product pest status. Molecular Ecology 15(12):3541−51

doi: 10.1111/j.1365-294X.2006.03030.x
[67]

Dapper AL, Wade MJ. 2016. The evolution of sperm competition genes: The effect of mating system on levels of genetic variation within and between species. Evolution 70(2):502−11

doi: 10.1111/evo.12848
[68]

Parrett JM, Chmielewski S, Aydogdu E, Łukasiewicz A, Rombauts S, et al. 2022. Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load. Nature Ecology & Evolution 6(9):1330−42

doi: 10.1038/s41559-022-01816-w
[69]

Cīrulis A, Hansson B, Abbott JK. 2022. Sex-limited chromosomes and non-reproductive traits. BMC Biology 20:156

doi: 10.1186/s12915-022-01357-5