Identification of candidate gene associated with tree sparrow sperm evolution under environmental pollution
22 male individuals, a half from BY and the other from LJX, with an average coverage of ~11× (Table S2) were sequenced. As the genome-wide differentiation between the two populations is low (F ST = 0.0058; Figure 1A; Figure S1), the BY population shows reduced nucleotide diversity and more compactly clustered in biplot of principal component analysis (Figure 1B; Figure S2), possibly reflecting some genomic regions are under strong recent selection in BY population. We search for genome-wide signatures of selection related to sperm variation in BY tree sparrows through pairwise genetic differentiation (F ST) and differences in nucleotide diversity (π) between BY and LJX populations in 50 kb sliding windows with 10 kb steps. We define the 1% most differentiated regions as outliers for BY population (Figure 2C; Figure S3). A total of 45 outlier regions distributed across 17 chromosomes are detected and the genes contained in these regions are defined as positively selected genes (PSGs) (Table S4).
We subsequently compare gene expression levels of testis between BY (n = 7) and LJX (n = 7) tree sparrows (Table S5) and find there are only 2 genes differentially expressed between the two populations (Figure S4; Table S6). Although so few differentially expressed genes (DEGs) are detected, one of the two DEGs, the gene encoding serine/threonine protein kinase PIM1, do overlap with the PSGs (Figure 1C and 1D). At the same time, we find 5 PIM1 genes encoded PIM1 are centered in the outlier regions spread across 4 chromosomes (chromosome 25, 27, 30 and 35) (Table S4), 2 of which have complete kinase domain (Figure 1C). Signatures of selection in multiple PIM1 genes coupled with upregulated PIM1 gene expression in testis indicate thatPIM1 may play an important role in the sperm evolution of BY tree sparrows.