Panhuis TM, Butlin R, Zuk M, Tregenza T. Sexual selection and speciation. Trends Ecol Evol. 2001;16:364–71.
Article
PubMed
Google Scholar
Mendelson TC, Safran RJ. Speciation by sexual selection: 20 years of progress. Trends Ecol Evol. 2021;36:1153–63.
Article
PubMed
Google Scholar
Fisher RA. The genetical theory of natural selection. Oxford: Clarendon Press; 1930.
Book
Google Scholar
Lande R. Models of speciation by sexual selection on polygenic traits. Proc Natl Acad Sci U S A. 1981;78 6 I:3721–5.
Article
Google Scholar
Servedio MR, Boughman JW. The role of sexual selection in local adaptation and speciation. Annu Rev Ecol Evol Syst. 2017;48:85–109.
Article
Google Scholar
Eberhard WG. Sexual Selection and Animal Genitalia. Cambridge: Harvard University Press; 1985.
Langerhans RB, Anderson CM, Heinen-Kay JL. Causes and consequences of genital evolution. Integr Comp Biol. 2016;56:741–51.
Article
PubMed
Google Scholar
Brennan PLR, Prum RO. Mechanisms and evidence of genital coevolution: the roles of natural selection, mate choice, and sexual conflict. Cold Spring Harb Perspect Biol. 2015;7:1–21.
Article
Google Scholar
Simmons LW. Sexual selection and genital evolution. Austral Entomol. 2014;53:1–17.
Article
Google Scholar
Anderson CM, Langerhans RB. Origins of female genital diversity: predation risk and lock-and-key explain rapid divergence during an adaptive radiation. Evolution (N Y). 2015;69:2452–67.
Google Scholar
Sota T, Kubota K. Genital lock-and-key as a selective agent against hybridization. Evolution (N Y). 1998;52:1507–13.
Google Scholar
Arnqvist G, Rowe L. Correlated evolution of male and female morphologies in water striders. Evolution (N Y). 2002;56:936–47.
Google Scholar
Sota T, Nagata N. Diversification in a fluctuating island setting: rapid radiation of Ohomopterus ground beetles in the Japanese Islands. Philos Trans R Soc Lond B Biol Sci. 2008;363:3377–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sasabe M, Takami Y, Sota T. QTL for the species-specific male and female genital morphologies in Ohomopterus ground beetles. Mol Ecol. 2010;19:5231–9.
Article
PubMed
Google Scholar
Fujisawa T, Sasabe M, Nagata N, Takami Y, Sota T. Genetic basis of species-specific genitalia reveals role in species diversification. Sci Adv. 2019;5:eaav9939.
Article
PubMed
PubMed Central
Google Scholar
Takami Y. Mating behavior, insemination and sperm transfer in the ground beetle Carabus insulicola. Zoolog Sci. 2002;19:1067–73.
Article
PubMed
Google Scholar
Takami Y. Experimental analysis of the effect of genital morphology on insemination success in the ground beetle Carabus insulicola (Coleoptera Carabidae). Ethol Ecol Evol. 2003;15:51–61.
Article
Google Scholar
Kubota K, Miyazaki K, Ebihara S, Takami Y. Mechanical reproductive isolation via divergent genital morphology between Carabus insulicola and C. esakii with implications in species coexistence. Popul Ecol. 2013;55:35–42.
Nagata N, Kubota K, Yahiro K, Sota T. Mechanical barriers to introgressive hybridization revealed by mitochondrial introgression patterns in Ohomopterus ground beetle assemblages. Mol Ecol. 2007;16:4822–36.
Article
CAS
PubMed
Google Scholar
Sota T. Evolutionary biology of Carabus ground beetles. How species richness increases. Singapore: Springer Nature; 2022.
Okuzaki Y, Sota T. How the length of genital parts affects copulation performance in a carabid beetle: implications for correlated genital evolution between the sexes. J Evol Biol. 2014;27:565–74.
Article
CAS
PubMed
Google Scholar
Takami Y, Fukuhara T, Yokoyama J, Kawata M. Impact of sexually antagonistic genital morphologies on female reproduction and wild population demography. Evolution (N Y). 2018;72:2449–61.
Google Scholar
Sasabe M, Takami Y, Sota T. The genetic basis of interspecific differences in genital morphology of closely related carabid beetles. Heredity (Edinb). 2007;98:385–91.
Article
CAS
Google Scholar
Nomura S, Fujisawa T, Sota T. Role of sex-concordant gene expression in the coevolution of exaggerated male and female genitalia in a beetle group. Mol Biol Evol. 2021;38:3593–605.
Article
CAS
PubMed
PubMed Central
Google Scholar
Terada K, Nishimura T, Hirayama A, Takami Y. Heterochrony and growth rate variation mediate the development of divergent genital morphologies in closely related Ohomopterus ground beetles. Evol Dev. 2021;23:19–27.
Article
PubMed
Google Scholar
Sánchez L, Guerrero I. The development of the Drosophila genital disc. BioEssays. 2001;23:698–707.
Article
PubMed
Google Scholar
Wang L, Evans J, Andrews HK, Beckstead RB, Thummel CS, Bashirullah A. A genetic screen identifies new regulators of steroid-triggered programmed cell death in Drosophila. Genetics. 2008;180:269–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petkau G, Wingen C, Jussen LCA, Radtke T, Behr M. Obstructor-A is required for epitheliale extracellular matrix dynamics, exoskeleton function, and tubulogenesis. J Biol Chem. 2012;287:21396–405.
Article
CAS
PubMed
PubMed Central
Google Scholar
Larkin A, Marygold SJ, Antonazzo G, Attrill H, dos Santos G, Garapati PV, et al. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res. 2021;49:D899–907.
Dobens L, Jaeger A, Peterson JS, Raftery LA. Bunched sets a boundary for Notch signaling to pattern anterior eggshell structures during Drosophila oogenesis. Dev Biol. 2005;287:425–37.
Article
CAS
PubMed
Google Scholar
Xia R, Jia H, Fan J, Liu Y, Jia J. USP8 promotes smoothened signaling by preventing its ubiquitination and changing its subcellular localization. PLOS Biol. 2012;10:e1001238.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schertel C, Albarca M, Rockel-Bauer C, Kelley NW, Bischof J, Hens K, et al. A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Genome Res. 2015;25:514–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anhezini L, Saita AP, Costa MSA, Ramos RGP, Simon CR. Fhos encodes a Drosophila Formin-Like Protein participating in autophagic programmed cell death. Genesis. 2012;50:672–84.
Article
CAS
PubMed
Google Scholar
Lammel U, Bechtold M, Risse B, Berh D, Fleige A, Bunse I, et al. The Drosophila FHOD1-like formin Knittrig acts through Rok to promote stress fiber formation and directed macrophage migration during the cellular immune response. Dev. 2014;141:1366–80.
Article
CAS
Google Scholar
Nishimura T, Nagata N, Terada K, Xia T, Kubota K, Sota T, et al. Reproductive character displacement in genital morphology in Ohomopterus ground beetles. Am Nat. 2022;199:E76–90.
Takami Y, Sota T. Rapid diversification of male genitalia and mating strategies in Ohomopterus ground beetles. J Evol Biol. 2007;20:1385–95.
Article
CAS
PubMed
Google Scholar
Nomura S, Fujisawa T, Sota T. Gene expression during genital morphogenesis in the ground beetle Carabus maiyasanus. Insect Sci. 2020;27:975–86.
Article
CAS
PubMed
Google Scholar
Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB. Direct determination of diploid genome sequences. Genome Res. 2017;27:757–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011;27:764–70.
Article
PubMed
PubMed Central
CAS
Google Scholar
Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, et al. GenomeScope: fast reference-free genome profiling from short reads. https://doi.org/10.1093/bioinformatics/btx153.
Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38:4647–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci. 2020;117:9451–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics. 2011;27:1691–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lomsadze A, Burns PD, Borodovsky M. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic Acids Res. 2014;42:e119–e119.
Article
PubMed
PubMed Central
CAS
Google Scholar
Stanke M, Schöffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinforma. 2006;7:1–11 2006 71.
Article
CAS
Google Scholar
Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008;24:637–44.
Article
CAS
PubMed
Google Scholar
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinformatics. 2016;32:767–9.
Article
CAS
PubMed
Google Scholar
Hoff KJ, Lomsadze A, Borodovsky M, Stanke M. Whole-genome annotation with BRAKER. Methods Mol Biol. 2019;1962:65–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brůna T, Hoff KJ, Lomsadze A, Stanke M, Borodovsky M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics Bioinforma. 2021;3(1):lqaa108.
Article
CAS
Google Scholar
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907–15 2019 378.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC. 2009;10:1–9 2009 101.
Google Scholar
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
Article
CAS
PubMed
Google Scholar
Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
Article
CAS
PubMed
Google Scholar
R Core Team. R Language Definition. Vienna: Austria R Found Stat Comput; 2000.
Google Scholar
Sun J, Nishiyama T, Shimizu K, Kadota K. TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics. 2013;14:219.
Article
PubMed
PubMed Central
Google Scholar
Hoffman GE, Schadt EE. variancePartition: Interpreting drivers of variation in complex gene expression studies. BMC Bioinformatics. 2016;17:483.
Article
PubMed
PubMed Central
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed
PubMed Central
CAS
Google Scholar
Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics. 2006;22:1540–2.
Article
CAS
PubMed
Google Scholar
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10:1–10.
CAS
Google Scholar
The UniProt Consortium. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021;49:D480–9.
Article
CAS
Google Scholar
Storey J, Bass A, Dabney A, Robinson D. qvalue: R package to estimate q-values and false discovery rate quantities. 2021. https://github.com/StoreyLab/qvalue. Accessed 11 Nov 2021.