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Differential expression analysis between males and females in each taxon. (a) Histograms showing the number of differentially expressed genes (DEGs) in each taxon, including all sex-biased genes, male-biased genes, and female-biased genes. (b-d) Venn diagrams showing the number of all sex-biased genes (b), male-biased genes (c) and female-biased genes (d) across the four taxa. (eh) Hierarchical clustering and heatmaps showing expression patterns of hearing loss/deafness genes among DEGs in Rsi (e), Rpu (f), Rahi (g), and Raha (h), respectively. Rsi: R. sinicus, Rpu: R. pusillus, Rahi: R. affinis himalayanus, Raha: R. affinis hainanus.
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Phenotypic difference between males and females (sexual dimorphism) is widespread in animals. These sexual dimorphisms, in particular vocalizations and acoustic signals, have been shown to play important roles in mating choice and sexual selection. However, little is known about the molecular mechanisms underlying these phenotypic va...
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... on SVA-adjusted expression matrix, we performed DGE analysis between males and females in each taxon. In general, we found a higher number of DEGs in R. sinicus and R. affinis himalayanus (405 and 301 in the former and latter, respectively) than in R. pusillus and R. affinis hainanus (46 and 43 in the former and latter, respectively) (Figures 2a, S2, and Table S4). In addition, the number of female-biased genes was more than that of male-biased genes in all of the four taxa except for R. affinis himalayanus (Figure 2a). in R. pusillus and R. affinis hainanus (46 and 43 in the former and latter, respectively) (Fig- ures 2a, S2, and Table S4). ...
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... general, we found a higher number of DEGs in R. sinicus and R. affinis himalayanus (405 and 301 in the former and latter, respectively) than in R. pusillus and R. affinis hainanus (46 and 43 in the former and latter, respectively) (Figures 2a, S2, and Table S4). In addition, the number of female-biased genes was more than that of male-biased genes in all of the four taxa except for R. affinis himalayanus (Figure 2a). in R. pusillus and R. affinis hainanus (46 and 43 in the former and latter, respectively) (Fig- ures 2a, S2, and Table S4). ...
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... general, we found a higher number of DEGs in R. sinicus and R. affinis himalayanus (405 and 301 in the former and latter, respectively) than in R. pusillus and R. affinis hainanus (46 and 43 in the former and latter, respectively) (Figures 2a, S2, and Table S4). In addition, the number of female-biased genes was more than that of male-biased genes in all of the four taxa except for R. affinis himalayanus (Figure 2a). in R. pusillus and R. affinis hainanus (46 and 43 in the former and latter, respectively) (Fig- ures 2a, S2, and Table S4). In addition, the number of female-biased genes was more than that of male-biased genes in all of the four taxa except for R. affinis himalayanus (Figure 2a). ...
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... addition, the number of female-biased genes was more than that of male-biased genes in all of the four taxa except for R. affinis himalayanus (Figure 2a). in R. pusillus and R. affinis hainanus (46 and 43 in the former and latter, respectively) (Fig- ures 2a, S2, and Table S4). In addition, the number of female-biased genes was more than that of male-biased genes in all of the four taxa except for R. affinis himalayanus (Figure 2a). Specifically, in R. sinicus, we identified the largest number of DEGs with 136 malebiased and 269 female-biased genes ( Figure S2a). ...
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... addition, the number of female-biased genes was more than that of male-biased genes in all of the four taxa except for R. affinis himalayanus (Figure 2a). Specifically, in R. sinicus, we identified the largest number of DEGs with 136 malebiased and 269 female-biased genes ( Figure S2a). Functional enrichment analysis revealed that male-biased genes are enriched in GO terms related to ion transmembrane transport, Specifically, in R. sinicus, we identified the largest number of DEGs with 136 malebiased and 269 female-biased genes ( Figure S2a). ...
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... in R. sinicus, we identified the largest number of DEGs with 136 malebiased and 269 female-biased genes ( Figure S2a). Functional enrichment analysis revealed that male-biased genes are enriched in GO terms related to ion transmembrane transport, Specifically, in R. sinicus, we identified the largest number of DEGs with 136 malebiased and 269 female-biased genes ( Figure S2a). Functional enrichment analysis revealed that male-biased genes are enriched in GO terms related to ion transmembrane transport, muscle system process, central nervous system development, and cellular component morphogenesis, whereas female-biased genes are enriched in GO terms associated with cytoplasmic translation, mitotic cell cycle process, and mitochondrial ATP synthesis coupled electron transport ( Figure S4a,b and Table S5). ...
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... enrichment analysis revealed that male-biased genes are enriched in GO terms related to ion transmembrane transport, muscle system process, central nervous system development, and cellular component morphogenesis, whereas female-biased genes are enriched in GO terms associated with cytoplasmic translation, mitotic cell cycle process, and mitochondrial ATP synthesis coupled electron transport ( Figure S4a,b and Table S5). In R. pusillus, we identified 19 male-biased and 27 female-biased genes ( Figure S2b). These male-biased genes are enriched in GO terms related to carboxylic acid metabolic process, whereas female-biased genes are enriched in GO terms associated with ion transport, transmembrane transport, enteric nervous system development, and defense response to fungus and bacterium ( Figure S4c,d and Table S5). ...
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... in R. affinis himalayanus with no sexual differences of echolocation pulse frequencies, we also identified a large number of DEGs with 257 male-biased and 44 femalebiased genes ( Figure S2d). Only male-biased genes are functionally enriched in GO terms that are related to immune function and cytoskeleton organization ( Figure S4f and Table S5). ...
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... male-biased genes are functionally enriched in GO terms that are related to immune function and cytoskeleton organization ( Figure S4f and Table S5). In contrast, in another subspecies of R. affinis (R. affinis hainanus), we identified a small number of DEGs with 10 male-biased and 38 female-biased genes ( Figure S2c) and again only male-biased genes are enriched in GO terms that are related to elastic fiber assembly and the regulation of immune response ( Figure S4e and Table S5). ...
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... further identify genes whose expression changes are associated with sexual differences in the echolocation pulse frequency, we used a candidate gene approach by comparing the sex-biased DEGs identified in each taxon to the list of hearing loss or deafness genes obtained from the database of HMDC (The Human-Mouse: Disease Connection, accessed on 18 January in 2024). Although these candidate hearing loss or deafness genes are not enriched in these sex-biased DEGs in each taxon (all p > 0.05 in a hypergeometric test, Table S6), we still found multiple such hearing loss or deafness genes in the list of DEGs in each taxon, ranging from four in R. pusillus to 33 in R. sinicus (Figure 2e-h and Table S4). Specifically, in R. sinicus, POU1F1 shows the largest fold change except for two Y-linked genes (Table S4) and its protein is the first pituitary-specific transcription factor identified in the human and mouse with a restricted expression in the anterior pituitary lobe [52]. ...
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... investigate whether sex-biased gene expression is conserved across species, we compared the list of DEGs identified in each taxon with each other and found several overlapped DEGs between taxa (Figure 2b-d and Table S7). To further identify those genes which are male-biased in one taxon but female-biased in another taxon or the reverse, we compared the combined male-biased genes in all four taxa to those of female-biased genes and found 22 such genes including LRP2 (Table S7 and Figure S5). ...
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... this study, we found several overlapped sex-biased genes across the four taxa (Figure 2b), suggesting that sex-biased gene expression may be conserved in recently diverged taxa. Specifically, among female-biased genes across taxa, SLC6A2 overlapped between R. pusillus and R. sinicus, which is one of the ADHD risk genes in humans and has also been identified to have sexually dimorphic effects with a greater effect on females than on males [65]. ...
