Fig. 3: Identification of candidates for adaptive splicing.
From: Alternative splicing and environmental adaptation in wild house mice
Lasp1 is a candidate for adaptive splicing among house mice in eastern North America. A Overlapping splicing 5’ and 3’ splice sites were used to identify clusters of alternatively spliced exons. The Lasp1 gene contains three differentially spliced clusters (arbitrarily named 29112, 29113, and 29114). B Differential splicing was assessed between the northernmost (New Hampshire/Vermont) and southernmost (Florida) populations on the latitudinal cline. Lasp1 had one cluster (29114) that exhibited differential splicing (FDR < 0.05). Cluster 29114 contained exons three, four, and five of Lasp1. Leafcutter measures differential splicing in terms of the change in percent-spliced in (ΔPSI) between populations. In Lasp1, exon 3 and 4 are spliced in at an average frequency of 0.34 and 0.17 between Florida and New Hampshire/Vermont populations, respectively and the ΔPSI for those exons is 0.17. C For each differentially spliced cluster between New Hampshire/Vermont and Florida, the splice-in frequency for the pair of exons with the highest ΔPSI was fitted to a linear model with latitude. The frequency of splicing between exon 3 and 4 of Lasp1 is correlated with latitude (p = 1.50 ×10−5, R2 = 0.32). D cis-sQTL for each clinally varying splicing event were identified with a linear-mixed model. Linkage disequilibrium between cis-sQTL (blue triangle) and LFMM outliers (asterisks) was calculated based on correlation.
