Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila

Abstract

In insects and crustaceans, the Down syndrome cell adhesion molecule (Dscam) occurs in many different isoforms. These are produced by mutually exclusive alternative splicing of dozens of tandem duplicated exons coding for parts or whole immunoglobulin (Ig) domains of the Dscam protein. This diversity plays a role in the development of the nervous system and also in the immune system. Structural analysis of the protein suggested candidate epitopes where binding to pathogens could occur. These epitopes are coded by regions of the duplicated exons and are therefore diverse within individuals. Here we apply molecular population genetics and molecular evolution analyses using Daphnia magna and several Drosophila species to investigate the potential role of natural selection in the divergence between orthologs of these duplicated exons among species, as well as between paralogous exons within species. We found no evidence for a role of positive selection in the divergence of these paralogous exons. However, the power of this test was low, and the fact that no signs of gene conversion between paralogous exons were found suggests that paralog diversity may nonetheless be maintained by selection. The analysis of orthologous exons in Drosophila and in Daphnia revealed an excess of non-synonymous polymorphisms in the epitopes putatively involved in pathogen binding. This may be a sign of balancing selection. Indeed, in Dr. melanogaster the same derived non-synonymous alleles segregate in several populations around the world. Yet other hallmarks of balancing selection were not found. Hence, we cannot rule out that the excess of non-synonymous polymorphisms is caused by segregating slightly deleterious alleles, thus potentially indicating reduced selective constraints in the putative pathogen binding epitopes of Dscam.

Figure 1. Dscam of Daphnia magna.

A) Protein domains; Ig-immunoglobulin domains; FNIII- fibronectin III domains. The grey and black boxes represent the transmembrane and cytoplasmic domains. B) mRNA, each box corresponds to a constitutive exon and the colored boxes 4, 6 and 11, correspond to exons that are the result of mutual exclusive alternative splicing of arrays of duplicated exons, as indicated in C) * Dscam exons of Daphnia sampled in the present study.

Figure 2. Dscam horse-shoe structure outline and detailed epitope II.

A) Outline of the Dscam horse-shoe structure formed by the first four Ig domains (D1–D4). B & C) Detail of Epitope II, formed by the two interstrand loops C′-D of exon 4 and A′-B of exon 6, respectively. Each strand is indicated by an encircled letter. The Drosophila aminoacid residues corresponding to the actual structures are in black uppercase initials (exon 4.1 and 6.34 of Dr. melanogaster). Da. magna residues have been positioned in function of the known homology of the molecule in the region coded by exon 4 and 6 (BRITES et al. 2008) and are represented by red lowercase initials. Polymorphic sites at exons 6 for Da. magna and Dr. melanogaster are represented by lowercase initials, each color corresponds to positions on Epitope II coding regions in different paralogous exons 6.