Coyne, J. A., Orr, H. A. Speciation (Sinauer, Sunderland, MA, 2004).
Rosenthal, G. G. Mate Choice (Princeton University Press, 2017).
Mayr, E. Animal Species and Evolution (Harvard University Press, 1963).
Arguello, J. R. & Benton, R. Open questions: tackling Darwin’s “instincts”: the genetic basis of behavioural evolution. BMC Biol. 15, 8–10 (2017).
Bay, R. A. et al. Genetic coupling of female mate choice with polygenic ecological divergence facilitates stickleback speciation. Curr. Biol. 27, 3344–3349 (2017).
Shahandeh, M. P., Pischedda, A., Rodriguez, J. M. & Turner, T. L. The genetics of male pheromone preference difference between Drosophila melanogaster and Drosophila simulans. G3 Genes Genomes Genet. 10, 401–415 (2020).
Gould, F. et al. Sexual isolation of male moths explained by a single pheromone response QTL containing four receptor genes. Proc. Natl Acad. Sci. USA. 107, 8660–8665 (2010).
Leary, G. P. et al. Single mutation to a sex pheromone receptor provides adaptive specificity between closely related moth species. Proc. Natl Acad. Sci. USA 109, 14081–14086 (2012).
Fan, P. et al. Genetic and neural mechanisms that inhibit Drosophila from mating with other species. Cell 154, 89–102 (2013).
Brand, P. et al. The evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees. Nat. Commun. 11, 1–11 (2020).
Xu, M. & Shaw, K. L. Genetic coupling of signal and preference facilitates sexual isolation during rapid speciation. Proc. R. Soc. B 286, 20191607 (2019).
Seehausen, O. et al. Speciation through sensory drive in cichlid fish. Nature 455, 620–626 (2008).
Hench, K., Vargas, M., Höppner, M. P., McMillan, W. O. & Puebla, O. Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence. Nat. Ecol. Evol. 3, 657–667 (2019).
Merrill, R. M. et al. Disruptive ecological selection on a mating cue. Proc. R. Soc. B Biol. Sci. 279, 4907–4913 (2012).
Jiggins, C. D., Naisbit, R. E., Coe, R. L. & Mallet, J. Reproductive isolation caused by colour pattern mimicry. Nature 411, 302–305 (2001).
Servedio, M. R., Van Doorn, G. S., Kopp, M., Frame, A. M. & Nosil, P. Magic traits in speciation: ‘magic’ but not rare? Trends Ecol. Evol. 26, 389–397 (2011).
Jiggins, C. D. Ecological speciation in mimetic butterflies. Bioscience 58, 541–548 (2008).
Jiggins, C. D., Estrada, C. & Rodrigues, A. Mimicry and the evolution of premating isolation in Heliconius melpomene Linnaeus. J. Evol. Biol. 17, 680–691 (2004).
Merrill, R. M. et al. Genetic dissection of assortative mating behaviour. PLoS Biol. 17, e2005902 (2018).
Reed, R. D. et al. Optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science 333, 1137–1141 (2011).
Martin, A. et al. Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand. Proc. Natl Acad. Sci. USA 109, 12632–12637 (2012).
Nadeau, N. J. et al. The gene cortex controls mimicry and crypsis in butterflies and moths. Nature 534, 106–110 (2016).
Felsenstein, J. Skepticism Towards Santa Rosalia, or why are there so few kinds of animals? Evolution 35, 124–138 (1981).
Massey, J. H., Chung, D., Siwanowicz, I., Stern, D. L. & Wittkopp, P. J. The yellow gene influences Drosophila male mating success through sex comb melanization. Elife 8, 1–20 (2019).
Merrill, R. M., Van Schooten, B., Scott, J. A. & Jiggins, C. D. Pervasive genetic associations between traits causing reproductive isolation in Heliconius butterflies. Proc. R. Soc. B Biol. Sci. 278, 511–518 (2011).
Van Schooten, B. et al. Divergence of chemosensing during the early stages of speciation. Proc. Natl. Acad. Sci. USA 117, 16348–16447 (2020).
Seeholzer, L. F., Seppo, M., Stern, D. L. & Ruta, V. Evolution of a central neural circuit underlies Drosophila mate preferences. Nature 559, 564–569 (2018).
Martin, S. H. et al. Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Res. 23, 1817–1828 (2013).
Davey, J. et al. Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution. G3 6, 695–708 (2015).
Darragh, K. et al. A novel terpene synthase produces an anti-aphrodisiac pheromone in the butterfly Heliconius melpomene. Preprint at https://www.biorxiv.org/content/10.1101/779678v1 (2019).
Pinharanda, A. et al. Sexually dimorphic gene expression and transcriptome evolution provide mixed evidence for a fast-Z effect in Heliconius. J. Evol. Biol. 32, 194–204 (2019).
Roberts, A., Pimentel, H., Trapnell, C. & Pachter, L. Identification of novel transcripts in annotated genomes using RNA-seq. Bioinformatics 27, 2325–2329 (2011).
Wittkopp, P. J., Haerum, B. K. & Clark, A. G. Evolutionary changes in cis and trans gene regulation. Nature 430, 85–88 (2004).
Thomas, P. D. et al. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 34, 645–650 (2006).
Choi, Y., Sims, G. E., Murphy, S., Miller, J. R. & Chan, A. P. Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 7, e46688 (2012).
Martin, S. H., Davey, J. W. & Jiggins, C. D. Evaluating the use of ABBA-BABA statistics to locate introgressed loci. Mol. Biol. Evol. 32, 244–257 (2015).
Martin, S. H., Davey, J. W., Salazar, C. & Jiggins, C. D. Recombination rate variation shapes barriers to introgression across butterfly genomes. PLoS Biol. 17, 1–28 (2019).
Nosil, P. Ecological Speciation (Oxford University Press, 2012).
Kopp, M. et al. Mechanisms of assortative mating in speciation with gene flow: connecting theory and empirical research. Am. Nat. 191, 1–20 (2018).
Butlin, R. K. & Smadja, C. M. Coupling, reinforcement, and speciation. Am. Nat. 191, 155–172 (2018).
Westerman, E. L. et al. Aristaless controls butterfly wing color variation used in mimicry and mate choice. Curr. Biol. 28, 3469–3474 (2018).
Kronfrost, M. R. et al. Linkage of butterfly mate preference and wing color preference cue at the genomic location of wingless. Proc. Natl Acad. Sci. USA 103, 6575–6580 (2006).
Chamberlain, N. L., Hill, R. I., Kapan, D. D., Gilbert, L. E. & Kronforst, M. R. Polymorphic butterfly reveals the missing link in ecological speciation. Science 326, 847–850 (2009).
McCulloch, K. J. et al. Sexual dimorphism and retinal mosaic diversification following the evolution of a violet receptor in butterflies. Mol. Biol. Evol. 34, 2271–2284 (2017).
Zaccardi, G., Kelber, A., Sison-Mangus, M. P. & Briscoe, A. D. Colour discrimination in the red range with only one long-wavelength sensitive opsin. J. Exp. Biol. 209, 1944–1955 (2006).
Monteiro, A. Gene regulatory networks reused to build novel traits. BioEssays 34, 181–186 (2012).
Martin, A. et al. Multiple recent co-options of optix associated with novel traits in adaptive butterfly wing radiations. Evodevo 5, 7 (2014).
Kandel, E. R., Schwartz, J. H., Jessell, T. M., Siegelbaum, S. A. & Hudspeth. A. J. Principles of Neural Science, 2012th edn. (McGraw Hill, New York, 2000).
Ramsey, M. E., Vu, W. & Cummings, M. E. Testing synaptic plasticity in dynamic mate choice decisions: N-methyl d-aspartate receptor blockade disrupts female preference. Proc. R. Soc. B Biol. Sci. 281, 20140047 (2014).
Bloch, N. I. et al. Early neurogenomic response associated with variation in guppy female mate preference. Nat. Ecol. Evol. 2, 1772–1781 (2018).
Delclos, P. J., Forero, S. A. & Rosenthal, G. G. Divergent neurogenomic responses shape social learning of both personality and mate preference. J. Evol. Biol. 223 (2020)
Yamaguchi, M. Role of regucalcin in brain calcium signaling. Integr. Biol. 4, 825–837 (2012).
Berridge, M. J. Neuronal calcium signaling. Neuron 21, 13–26 (1998).
Bashaw, G. J. & Klein, R. Signaling from axon guidance receptors. Cold Spring Harb. Perspect. Biol. 2, 1–17 (2010).
Prud’homme, B., Gompel, N. & Carroll, S. B. Emerging principles of regulatory evolution. Proc. Natl Acad. Sci. USA 104, 8605–8612 (2007).
Preger-Ben Noon, E. et al. Comprehensive analysis of a cis-regulatory region reveals pleiotropy in enhancer function. Cell Rep. 22, 3021–3031 (2018).
Lewis, J. et al. Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry. Proc. Natl Acad. Sci. USA. 116, 24174–24183 (2019).
Chouteau, M., Llaurens, V., Piron-Prunier, F. & Joron, M. Polymorphism at a mimicry supergene maintained by opposing frequency-dependent selection pressures. Proc. Natl Acad. Sci. USA 114, 8325–8329 (2017).
Southcott, L. & Kronforst, M. R. Female mate choice is a reproductive isolating barrier in Heliconius butterflies. Ethology 124, 862–869 (2018).
González-Rojas, M. F. et al. Chemical signals act as the main reproductive barrier between sister and mimetic Heliconius butterflies. Proc. R. Soc. B Biol. 287, 20200587 (2020).
Zhang, W. et al. Comparative transcriptomics provides insights into reticulate and adaptive evolution of a butterfly radiation. Genome Biol. Evol. 11, 2963–2975 (2019).
Weber, J. N., Peterson, B. K. & Hoekstra, H. E. Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice. Nature 493, 402–405 (2013).
Cande, J., Andolfatto, P., Prud’homme, B., Stern, D. L. & Gompel, N. Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship. PLoS ONE 7, 1–10 (2012).
McBride, C. S. et al. Evolution of mosquito preference for humans linked to an odorant receptor. Nature 515, 222–227 (2014).
Ding, Y., Berrocal, A., Morita, T., Longden, K. D. & Stern, D. L. Natural courtship song variation caused by an intronic retroelement in an ion channel gene. Nature 536, 329–332 (2016).
Bendesky, A. et al. The genetic basis of parental care evolution in monogamous mice. Nature 544, 434–439 (2017).
Auer, T. O. et al. Olfactory receptor and circuit evolution promote host specialization. Nature 579, 402–408 (2020).
Vehtari, A., Gelman, A. & Gabry, J. Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC. Stat. Comput. 27, 1413–1432 (2017).
Jiggins, C. D. The Ecology and Evolution of Heliconius Butterflies (Oxford University Press, 2016).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Anders, S., Pyl, P. T. & Huber, W. HTSeq- a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).
Montgomery, S. H. & Mank, J. E. Inferring regulatory change from gene expression: the confounding effects of tissue scaling. Mol. Ecol. 25, 5114–5128 (2016).
Montgomery, S. H., Rossi, M., McMillan, W. O. & Merrill, R. Neural divergence and hybrid disruption between ecologically isolated Heliconius butterflies. Preprint at https://www.biorxiv.org/content/10.1101/2020.07.01.182337v1 (2020)
McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Finn, R. D. et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 45, D190–D199 (2017).
York, R. A. et al. Behaviour-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes. Proc. Natl Acad. Sci. USA 115, 1081–1090 (2018).
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).
Source: Ecology - nature.com
