Population Differentiation and Tajima’s D
We estimated genome-wide patterns of diversity (π), differentiation (FST ) and Tajima’s D of the pool-seq data using non-overlapping 10 kb sliding windows for northern and southern beetle populations. Average pairwise FST across the female genome was low at FST = 0.063 (SD = 0.038), with averages for individual chromosomes ranging from 0.053 (SD = 0.042) to 0.092 (SD = 0.062) (Fig. 4a, Tab. 2). Average Tajima’sD was negative for both northern (-0.859) and southern (-0.808) populations (Fig. 4b). Two regions exhibited elevated genetic differentiation. The first region was located at the terminal end of the neo-X chromosome between 47 and 64 Mb (Fig. 4c).FST for this region was significantly higher than the rest of the chromosome (average FST = 0.096 versus 0.038, unpaired t -test: t = 42.497, p -value = 5 x10-276). Average Tajima’s D in this genomic region was also significantly lower in the northern population compared to the rest of the chromosome (-1.294 versus -0.913, unpairedt -test: t = 20.771, p -value = 5.3 x10-88). This difference in Tajima’s D was not present in the southern population.
The second region of elevated genetic differentiation was on chromosome 4 between 2.7 and 6.7 Mb (average FST = 0.193 versus 0.061, unpaired t -test: t = 64.535, p -value = 5.1 x10-239) (Fig. 4d). This second region exhibited a significant difference in Tajima’s D between northern and southern populations (Tajima’s D = -0.615 versus 0.109, unpairedt -test: t = 27.756, p -value = 7.5 x10-118) and was located within the region of strong genetic linkage in female-aligned linkage group 4 (Fig. 3a). In the linkage map, this region was roughly 23 to 30 cM in size and contained 147 of the 515 SNPs (approximately 29%) in this linkage group. Upstream of this second region (start of chromosome to 2.7 Mb) we detected significantly lower levels of FST compared to the rest of the chromosome located downstream of this region (6.7 Mb to end of chromosome) (average FST = 0.045 versus 0.065, unpaired t -test: t = 19.043, p -value = 2.1x10-68). The Tajima’s D in this upstream region also showed a significant difference between northern and southern populations (Tajima’s D = 0.076 versus -0.155, unpairedt -test: t = 5.841, p -value = 8.76 x10-9). No differences between populations in Tajima’sD were apparent in the downstream region.
We characterized the gene composition of these two chromosomes using Gene Ontology (GO) annotation and KEGG pathway enrichment analysis. Overall, the neo-X chromosome contained genes significantly enriched in the Cellular Component GO terms: cell periphery (GO:0071944), plasma membrane (GO:0005886), and SWI/SNF complex (GO:0016514) (Supp. File 1). The 18 Mb region at the terminal end of the neo-X chromosome, containing 880 genes, was significantly enriched in genes with the Molecular Function GO term: catalytic activity, acting on a protein (GO:0140096); Biological Process GO terms: transport (GO:0006810) and establishment of localization (GO:0051234); and the Cellular Component GO terms: SWI/SNF complex (GO:0016514) and gap junction (GO:0005921). No KEGG pathway was significantly enriched in this region, or the neo-X chromosome overall.
On chromosome 4, neither the region of elevated differentiation between 2.7 and 6.7 Mb, nor the region downstream had any significantly enriched GO terms. However, the region upstream contained genes significantly enriched in the Molecular Function GO terms: alcohol-forming fatty acyl-CoA reductase activity (GO:0102965), fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019), oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620), and oxidoreductase activity, acting on the aldehyde or oxo group of donors (GO:0016903). No KEGG pathways were significantly enriched for chromosome 4.