West-Eberhard, M. J. Developmental plasticity and evolution. (Oxford University Press. 2003).
G. de Jong. Evolution in phenotypic Plasticity: Patterns of plasticity and the Emergence of Ecotypes. N. Phytologist 166, 101118 (2005).
Ezard, T. H. G., Prizak, R. & Hoyle, R. B. The fitness cost of adaptation via phenotypic and maternal plasticity. Funct. Ecol. 28, 693701 (2014).
Williams, C. M. et al. An introduction to the symposium on Understanding the evolutionary impacts of seasonality. Integr. Comp. Biol. 57, 921933 (2017).
Murren, C. J. et al. Limitations on the evolution of phenotypic phenotypicplasticity: costs and limits of phenotypes and plasticity Heredity 115, 293301 (2015).
Sommer, R. J. Phenotypic Plasticity: From theory and genetics to current challenges and future opportunities. Genetics 215, 113 (2020).
Beldade, P., Mateus, A. R. A. Keller, R.A. Evolution and molecular mechanisms for adaptive developmental plasticity. Mol. Ecol. 20, 13471363 (2011).
E. Lafuente & P. Beldade. Genomics and developmental plasticity in animal embryos. Front. Genet. 10, (2019).
Marden J. H. Quantitative & evolutionary biology of alternative transcription: how changing the mix between alternative transcripts affects both phenotypic plasticity, and reaction norms. Heredity 100, 111120 (2008).
CAS
PubMed
Google Scholar
Baralle, F. E. & Giudice, J. Alternative splicing is a regulator of tissue identity and development. Nat. Rev. Mol. Cell Biol. 18, 437451 (2017).
Bush, S. J., Chen, L., Tovar-Corona, J. M. & Urrutia, A. O. Alternative splicing and evolution of phenotypic novelty. Philos. Trans. R. Soc. B: Biol. Sci. 372, 20150474 (2017).
Marden, J. H. & Cobb J. R. Territorial success and mating success for dragonflies that differ in muscle power output and presence gregarine gut parasites. Anim. Behav. 68, 857865 (2004).
Kijimoto, T., Moczek, A. P. & Andrews, J. Diversification of doublesex functions underlies morph- and sex-specific development beetlehorns. Proc. Natl Acad. Sci. USA 109, 2052620531 (2012).
Bear, A.; Prudic, K. L. & Monteiro A. The latent effect of steroid hormone signaling during the development of the butterfly’s adult male sexual behavior is known as “steroid hormone signaling”. Bicyclus anynana. PLoS ONE 12, e0174403 (2017).
Martin Anduaga, A. et al. Thermosensitive alternative to splicing senses, and mediates temperature adaption in Drosophila. eLife 8, e44642 (2019).
Deshmukh R., Lakhe D. & Kunte K. Tissue-specific development regulation and isoform use underlie doublesex’s role in sex differentiation. Papilio swallowtails. R. Soc. Open Sci. 7, 200792 (2020).
Grantham, M. E. & Brisson, J. A. A large amount of differential splicing is responsible for phenotypically plastic Aphid morphs. Mol. Biol. Evol. 35, 19341946 (2018).
Price, J. et al. Alternative splicing in the bumblebee is associated with phenotypic flexibility Bombus terrestris. Mol. Ecol. 27, 10361043 (2018).
CAS
PubMed
Google Scholar
Lees, J. G., Ranea, J. A. C. A. Orengo, C. A. Identification and characterisation of key alternative splicing events Drosophila development. BMC Genomics 16, 608 (2015).
Jaki, A. M. and Schltterer C. The effect of temperature and genotype in patterns of alternative splicing. Genetics 204, 315325 (2016).
Healy, T. M. & Schulte P. M. Patterns for alternative splicing as a response to cold acclimation of fish. J. Exp. Biol. 222, jeb193516 (2019).
S. Signor & S. Nuzhdin. Acute alcohol exposure is mediated by dynamic changes in gene expression and alternative splicing. Drosophila melanogaster. Heredity 121, 342360 (2018).
Lang, A. S.; Austin, S. H.; Harris, R. M. and Calisi, R. M. & MacManes M. D. Stress-mediated convergence in splicing landscapes among male and female rock doves. BMC Genomics 21, 251 (2020).
Suresh, S., Crease, T. J., Cristescu, M. E. & Chain, F. J. J. There are many options for splicing. Daphnia pulexLineages in response to acute exposure to copper BMC Genomics 21, 433 (2020).
Thorstensen M. J., Baerwald M. R., & Jeffries K. M. RNA sequencing describes the population structure and plasticity-selection dynamics of a non-model fish. BMC Genomics 22, 273 (2021).
Singh, A. A. Singh & Agrawal A. F. Sexual Dimorphism in Gene Expression: Coincidence and Population Genomics of Two Forms of Differential Expression in Drosophila melanogaster. bioRxiv (2021) https://doi.org/10.1101/2021.02.08.429268.
Rogers, T. F.; Palmer, D. H. & Wright A. E. The evolution of alternative splicing is driven by sex-specific selection in birds. Mol. Biol. Evolution 38, 519530 (2021).
CAS
Google Scholar
Fox, R. J.; Donelson J. M.; Schunter C., Ravasi T. & Gaitn Espiia J. D. Beyond purchasing time: The role of plasticity and phenotypic adaptations to rapid environmental changes. Philos. Trans. R. Soc. B: Biol. Sci. 374, 20180174 (2019).
Kelly, M. Climate change adaptation through genetic accommodation and assimilation phenotypes. Philos. Trans. R. Soc. B: Biol. Sci. 374, 20180176 (2019).
Oostra, V., Saastamoinen, M., Zwaan, B. J. & Wheat C. W. Strong phenotypic flexibility limits evolutionary responses to climate change. Nat. Commun. 9, 111 (2018).
CAS
Google Scholar
Wang, Y. et al. Mechanism of alternative splicing (Review) Biomed. Rep. 3, 152158 (2015).
CAS
PubMed
Google Scholar
Ule, J. & Blencowe, B. J. Alternative splicing regulatory systems: functions, mechanisms, evolution. Mol. Cell 76, 329345 (2019).
CAS
PubMed
Google Scholar
McManus, C. J., Coolon, J. D., Eipper-Mains, J., Wittkopp, P. J. & Graveley B.R. Evolution of splicing regulatory network in Drosophila. Genome Res. 24, 786796 (2014).
Gao, Q. Sun, W. Ballegeer M., Ballegeer C., Libert C. & Chen W. The predominant contribution of cis regulatory divergence to the evolution of mouse alternative siplicing. Mol. Syst. Biol. 11, 816 (2015).
Barbosa-Morais, N. L. et al. The evolutionary landscape for alternative splicing among vertebrate species Science 338, 15871593 (2012).
ADS
CAS
PubMed
Google Scholar
Wang, X. et al. Cis-regulated alternative silicing divergence: its potential contribution to environmental reactions Arabidopsis. Plant J. 97, 555570 (2019).
CAS
PubMed
Google Scholar
Huang, Y., Lack, J. B., Hoppel G. T. & Pool J. E. Parallel gene regulatory evolution in cold-adapted fly population. bioRxiv (2021) https://doi.org/10.1101/795716.
Lewis, J. J. Van Belleghem S. M. Papa R., Danko C. G. & Reed R. D. Numerous functionally connected loci encourage adaptive diversification along a neotropical mix zone. Sci. Adv. 6, eabb8617 (2020).
Lewis, J. J. R. D. Reed & Lewis, J. J. Genome-wide regulatory adaption shapes population-level genomic landscapes at Heliconius. Mol. Biol. Evol. 36, 159173 (2019).
CAS
PubMed
Google Scholar
Martin, S. H. et al. Natural selection and genetic diversity in the butterfly Heliconius melpomene. Genetics 203, 525541 (2016).
Brakefield, P. M., Beldade, P. & Zwaan, B. J. The African Butterfly Bicyclus anynana: A model for evolutionary genetics, and evolutionary developmental biology. Cold Spring Harb. Protoc. 2009, pdb.emo122 (2009).
Mateus, A. R. A. et al. Adaptive developmental Plasticity: The ability to respond to external cues and internal signals separately to create phenotypic flexibility. BMC Biol. 12, 97 (2014).
Oostra, V. et al. Ecdysteroid hormones link the seasonal insect’s juvenile environment to other adult life histories. Am. Naturalist 184, E79E92 (2014).
van Bergen, E. et al. Conserved patterns in integrated developmental plasticity among a group of polyphenic, tropical butterflies. BMC Evolut. Biol. 17, 59 (2017).
Singh, P. et al. Complex multi-trait responses in a seasonal butterfly to multivariate environmental cues. Evol. Ecol. (2020) https://doi.org/10.1007/s10682-020-10062-0.
Prudic K. L., Jeon C., Cao H. & Monteiro A. Developmental plasticity drives mutual sexual ornamentation in butterfly species’ sexual roles. Science 331, 7375 (2011).
ADS
CAS
PubMed
Google Scholar
Chen, L., Bush, S. J., Tovar-Corona, J. M., Castillo-Morales, A. & Urrutia A. O. Correcting differential transcript coverage reveals a strong correlation between alternative splicing & organism complexity. Mol. Biol. Evol. 31, 14021413 (2014).
Hamid F. M. & Makeyev E.V. Emerging functions associated with nonsense-mediated decomposition. Biochem. Soc. Trans. 42, 11681173 (2014).
CAS
PubMed
Google Scholar
Tabrez, S. S., Sharma, R. D., Jain, V., Siddiqui, A. A. & Mukhopadhyay, A. Differential alternative splicing combined with nonsense-mediated decay mRNA of mRNA assures dietary restriction-induced longevity. Nat. Commun. 8, 306 (2017).
Uller T., Moczek A. P. Watson R. A., Brakefield P. M., & Laland K.N. Developmental biases and Evolution: A regulatory network perspective. Genetics 209, 949966 (2018).
Nijhout H. F. To plasticity, and back again eLife 4, e06995 (2015).
Helanter, H. & Uller T. Neutral and adaptive explanations of an association between caste-biased gene transcription and rate of sequence development. Front. Genet. 5, 297 (2014).
Pespeni M. H.; Ladner J. T.; & Moczek A. P. Selection signals in conditionally expressed gene in the diversification three horned Beetle species J. Evolut. Biol. 30, 16441657 (2017).
CAS
Google Scholar
Plass M. & Eyras E. Differentiated evolution rates in alternative exons. The implications for splicing regulation. BMC Evol. Biol. 6, 50 (2006).
Chen, F.-C., Pan, C.-L. & Lin, H.-Y. Independent effects of alternative Splicing and structural constraint in the evolution of mammalian Coding Exons. Mol. Biol. Evolution 29, 187193 (2012).
CAS
Google Scholar
C. Pea, S. Nylin, & N. Wahlberg. The radiation of Satyrini butterflies. (Nymphalidae, Satyrinae). A challenge for phylogenetic techniques. Zool. J. Linn. Soc. 161, 6487 (2011).
Bhardwaj, S. et al. Origin of phenotypic and morphological plasticity in satyrid butterflies eyespots. eLife 9, e49544 (2020).
Lewis, B. P. Green and S. E. Brenner provide evidence for the widespread use of alternative splicing in mRNA decay. PNAS 100, 189192 (2003).
ADS
CAS
PubMed
Google Scholar
Akerman, M. & Mandel-Gutfreund, Y. Alternative splicing regulation at tandem 3-splice sites. Nucleic Acids Res. 34, 2331 (2006).
Moran, N. A. Evolutionary maintenance of alternative phenotypes. Am. Naturalist 139, 971989 (1992).
Nijhout H. F. Development of adaptive polyphenisms. Evolution Dev. 5, 918 (2003).
Mank, J. E. Phenotypic dimorphism: The transcriptional architecture. Nat. Ecol. Evolution 1, 17 (2017).
Scheiner S. M., Barfield M., & Holt R. D. Genetics and phenotypic flexibility. XVII. Climate change response. Evolut. Appl. 13, 388399 (2020).
Osada N., Miyagi R., & Takahashi A. Cis-and trans-regulatory effect on gene expression in a naturally occurring population Drosophila melanogaster. Genetics 206, 21392148 (2017).
Cooper, R. D. & Shaffer H. B. Allele-specific gene regulation and gene expression help explain transgressive temperature tolerance in non-native hybrids (Endangered California Tiger Salamander)Ambystoma californiense). Mol. Ecol. 30, 9871004 (2021).
CAS
PubMed
Google Scholar
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 1521 (2013).
Baruzzo, G. et al. Simulation-based comprehensive benchmarking for RNA-seq alignmenters Nat. Methods 14, 135139 (2017).
CAS
PubMed
Google Scholar
Schuierer, S. et al. A comprehensive evaluation of RNA-seq protocol for low-quantity and degraded samples. BMC Genomics 18, 442 (2017).
Broad Institute. Picard toolkit. (2019).
Liao, Y.; Smyth, G. K. & Shi W. featureCounts is an efficient general-purpose program for assigning sequences to genomic features. Bioinformatics 30, 923930 (2014).
Liao, Y.; Smyth, G. K. & Shi. W. The R package Rsubread makes it easier, faster and more cost-effective to align and quantify RNA sequencing reads. Nucleic Acids Res 47, e47e47 (2019).
Chen, Y.; Lun, A. T. L. & Smyth. From reads and genes to pathways: differential expression analysis using Rsubread & the edgeR quasilikelihood pipeline. F1000Res 5, 1438 (2016).
R Core Team. R: A language and environment that allows for statistical computing. (R Foundation for Statistical Computing 2019).
Shen, L. GeneOverlap: Check and visualize gene overlaps. (2020).
Gu, Z.Eils, R. and Schlesner M. Complex Heatmaps reveal patterns & correlations in multidimensional genomic information. Bioinformatics 32, 28472849 (2016).
CAS
Google Scholar
Huerta-Cepas, J. et al. eggNOG 5.0: A hierarchical, functionally, and phylogenetically annotated resource for orthology based on 5090 organisms & 2502 viruses. Nucleic Acids Res 47, D309D314 (2019).
CAS
PubMed
Google Scholar
Alexa, A. & Rahnenfuhrer, J. topGO: Enrichment analysis of Gene Ontology. (2016).
Larsson, J. et al. eulerr: Area-Proportional Euler, Venn Diagrams with Ellipses and Venn Diagrams with Euler. (2021).
Supek F., Bonjak M., kunca N. & muc T. REVIGO summarizes & visualizes long lists gene ontology terms. PLoS ONE 6, e21800 (2011).
Gu, Z. Gu, Z. & Hbschmann D. simplifyEnrichment is an R/Bioconductor package that allows for clustering and visualizing functional enrichment results. 2020.10.27.312116 (2020) https://doi.org/10.1101/2020.10.27.312116.
Gu, Z. simplifyEnrichment: Simplify Functional Enrichment Results. (Bioconductor version, Release (3.13), 202). https://doi.org/10.18129/B9.bioc.simplifyEnrichment.
Wahlberg N., Wahlberg M. A. & Zwaan B. J. Mitochondrial DNA signature to range-wide populations Bicyclus anynanaIt suggests a rapid expansion of the Refugia. PLoS ONE 6, e21385 (2011).
de Jong M. A., Collins S., Beldade P., Brakefield P. M. & Zwaan B. J. Footprints for selection in wild populations Bicyclus anynanaAlong with a latitudinal line. Mol. Ecol. 22, 341353 (2013).
Martin, M. Cutadapt Removes adapter sequences in high-throughput sequencing reads EMBnet. J. 17, 1012 (2011).
Joshi, N. & Fass, J. Sickle: A sliding-window adaptive, quality-based trimming device for FastQ files.
Li, H. Aligning sequence readings, clone Sequences, and Assembly Contigs with BWA–MEM. arXiv:1303.3997 [q-bio] (2013).
Korneliussen, T. S., Albrechtsen, A. R. ANGSD: Analysis of next-generation sequencing data. BMC Bioinforma. 15, 356 (2014).
Nowell, R. W. et al. A draft genome with high-coverage for the mycalesine butterflies Bicyclus anynana. GigaScience 6, (2017).
Xu, L. et al. OrthoVenn2: A web server for whole-genome analysis and annotation of orthologous groups across multiple species. Nucleic Acids Res. 47, W52W58 (2019).
Ranwez, V. Harispe S., Delsuc F. & Douzery E. J. P.: Multiple alignment of coding sequences accounting for frameshifts & stop codons. PLoS ONE 6, e22594 (2011).
Lucaci A. G. Wisotsky S. R. Shank S. D. Shank S. D. Weaver S. & Kosakovsky Pond S. L. Additional base hits: Widespread empirical support for instantaneous multiple nucleotide modifications PLoS One 16, e0248337 (2021).
Buerkner, P.-C. brms: An R Package for Bayesian Multilevel Models Using Stan. J. Stat. Softw. 80, 128 (2017).
Buerkner P.-C. Advanced Bayesian multilevel modelling with the R Package brms. R. J. 10, 395411 (2018).
Kassambara, A. rstatix – Pipe-Friendly Framework for Basic Statistical Tests. (2021).
Shen, S. et al. rMATS: Robust, flexible detection of differential alternative splicing using replicate RNA-Seq datasets. Proc. Natl Acad. Sci. USA 111, E5593E5601 (2014).
Alamancos G. P. and Pags A., Trincado J. L., Bellora N. & Eyras E. Leveraging transcript quantification to fast compute alternative splicing profiles RNA 21, 15211531 (2015).
Wang, Q. Rio, D. C. JUM is a method that allows for an exhaustive and non-annotated analysis to identify alternative pre-mRNA splicing pattern. Proc. Natl Acad. Sci. USA115, E8181E8190 (2018).
Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).
Kassambara, A. Publication-ready plots based on ggpubr and ggplot2. (2020).
Bivand, R. & Rundel, C. rgeos – Interface To Geometry Engine – Open Source GEOS. (2021).
South, A. afrilearndata – Small Africa Map Datasets For Learning. (2021).
Inkscape Project. Inkscape. (2021).
Steward, R. A., Oostra, V. & Wheat, C. W. B_anynana_differentialSplicing Github. zenodo.org https://zenodo.org/badge/latestdoi/255903232 (2021).
