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Background  Despite the growing interest in the female side of copulatory interactions, the roles played by differential expression and alternative splicing mechanisms of  pre-RNA  on tissues outside of the reproductive tract have remained largely unknown. Here we addressed these questions in the context of con- vs heterospecific matings between  Drosophila mojavensis  and its sister species,  D. arizonae . We analyzed transcriptional responses in female heads using an integrated investigation of genome-wide patterns of gene expression, including differential expression ( DE ), alternative splicing ( AS ) and intron retention ( IR ).    Results  Our results indicated that early transcriptional responses were largely congruent between con- and heterospecific matings but are substantially perturbed over time. Conspecific matings induced functional pathways related to amino acid balance previously associated with the brain’s physiology and female postmating behavior. Heterospecific matings often failed to activate regulation of some of these genes and induced expression of additional genes when compared with those of conspecifically-mated females. These mechanisms showed functional specializations with  DE  genes mostly linked to pathways of proteolysis and nutrient homeostasis, while  AS  genes were more related to photoreception and muscle assembly pathways.  IR  seems to play a more general role in  DE  regulation during the female postmating response.    Conclusions  We provide evidence showing that  AS  genes substantially perturbed by heterospecific matings in female heads evolve at slower evolutionary rates than the genome background. However,  DE  genes evolve at evolutionary rates similar, or even higher, than those of male reproductive genes, which highlights their potential role in sexual selection and the evolution of reproductive barriers.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07669-0.

Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation