Figure 1. Evolutionary analysis of kep1 family.

(A) Origination events of the newly originated kep1 gene family. The phylogeny of the Drosophila species and the divergence time are indicated [18]. On the phylogenetic tree, the blue box represents the parental gene kep1, and green and grey boxes represent the intact new genes and pseudogenes of the kep1 family, respectively. The approximate starting point of the origination of the kep1 family is depicted as a red circle. (B) Multiple alignments for protein sequences of kep1 family genes in D. melanogaster. The asterisks denote the positions of identical amino acids. The blue line under the alignment shows the KH RNA-binding domain. (C) Distribution of dN/dS throughout the kep1-nsr pair. With 120-bp windows and 6-bp slides, dN/dS ratios were estimated using the maximum likelihood method [53] and plotted. Blue and red spots represent dN/dS ratios that are statistically significantly lower and higher than the neutral expectation (p-value <0.05, two-tailed Fisher's exact test), respectively. Regions embedded in the KH domain, as depicted by the grey block, are enriched with signals of purifying selection. (D) Likelihood values of nucleotide substitutions for nsr in Drosophila lineages. Numbers of nonsynonymous and synonymous substitutions for the entire coding sequences are labeled above the lineages, and ω values (dN/dS) are labeled beneath the lineages. A ω value representing the lineage that shows significant evidence of positive selection is highlighted in red. Abbreviations: D. melanogaster (mel); D. simulans (sim); D. sechellia (sec); D. yakuba (yak); D. erecta (ere), and D. ananassae (ana).