Complex signatures of selection and gene conversion in the duplicated globin genes of house mice

Abstract

Results of electrophoretic surveys have suggested that hemoglobin polymorphism may be maintained by balancing selection in natural populations of house mice, Mus musculus. Here we report a survey of nucleotide variation in the adult globin genes of house mice from South America. We surveyed nucleotide polymorphism in two closely linked alpha-globin paralogs and two closely linked beta-globin paralogs to test whether patterns of variation are consistent with a model of long-term balancing selection. Surprisingly high levels of nucleotide polymorphism at the two beta-globin paralogs were attributable to the segregation of two highly divergent haplotypes, Hbbs (which carries two identical beta-globin paralogs) and Hbbd (which carries two functionally divergent beta-globin paralogs). Interparalog gene conversion on the Hbbs haplotype has produced a highly unusual situation in which the two paralogs are more similar to one another than either one is to its allelic counterpart on the Hbbd haplotype. Levels of nucleotide polymorphism and linkage disequilibrium at the two beta-globin paralogs suggest a complex history of diversity-enhancing selection that may be responsible for long-term maintenance of alternative protein alleles. The alternative two-locus beta-globin haplotypes are associated with pronounced differences in intraerythrocyte glutathione and nitric oxide metabolism, suggesting a possible mechanism for selection on hemoglobin function.

Figure 1.—

Genomic structure of the α- and β-globin gene families of M. musculus. Location of the two adult α-globin paralogs, HBA-T1 and HBA-T2, on chromosome 11 (top). Location of the two adult β-globin paralogs, HBB-T1 and HBB-T2, on chromosome 7 (bottom).

Figure 2.—

Phylogenetic affinities of South American house mouse specimens (shown in bold) in relation to a global reference sample of M. musculus and congeneric species. (A) Neighbor-joining tree based on cytochrome b sequence variation (1144 bp). (B) Neighbor-joining tree based on mtDNA control region sequence variation (1063 bp). Bootstrap support values are given for select nodes on each tree.

Figure 3.—

Structural alignment of mammalian α- and β-globin sequences. For M. musculus, the alignment includes representative c- and d-type protein alleles from the two α-globin paralogs and representative s- and d-type protein alleles from the two β-globin paralogs. For the β-globin sequences, redox-active cysteine residues are shown in boxes.

Figure 4.—

Schematic illustration of allelic and nonallelic variation in the two house mouse β-globin paralogs, HBB-T1 and HBB-T2, on each of two haplotype backgrounds, Hbb^s and Hbb^d. Numbers refer to pairwise amino acid differences between alleles or paralogous genes. In the sample of South American mice, HBB-T1 and HBB-T2 are in nearly complete LD with each other such that chromosomes that carry a d-type allele at HBB-T1 typically carry a d-type allele at HBB-T2 (the Hbb^d haplotype), and likewise for s-type alleles (the Hbb^s haplotype).

Figure 5.—

Nucleotide polymorphism in the two β-globin paralogs of South American house mice, HBB-T1 and HBB-T2. For both genes, s-type alleles are shown in gray and d-type alleles are shown in white. Nonsynonymous polymorphisms are denoted by asterisks at the top of the alignments. In the HBB-T1 table of polymorphic sites (A), three interallelic gene conversion tracts are shown in boxes. In the HBB-T2 table of polymorphic sites (B), a dagger denotes the position of the localized cluster of insertion/deletion differences between the s- and d-type alleles (nucleotide positions 827–1277) that results in unalignable sequence between the two allele classes.

Figure 5.—

Nucleotide polymorphism in the two β-globin paralogs of South American house mice, HBB-T1 and HBB-T2. For both genes, s-type alleles are shown in gray and d-type alleles are shown in white. Nonsynonymous polymorphisms are denoted by asterisks at the top of the alignments. In the HBB-T1 table of polymorphic sites (A), three interallelic gene conversion tracts are shown in boxes. In the HBB-T2 table of polymorphic sites (B), a dagger denotes the position of the localized cluster of insertion/deletion differences between the s- and d-type alleles (nucleotide positions 827–1277) that results in unalignable sequence between the two allele classes.

Figure 6.—

Neighbor-joining phylogenies of s- and d-type alleles from each of the two β-globin paralogs, HBB-T1 (A) and HBB-T2 (B). In A, the three most basal branches in the clade of d-type alleles (specimen IDs shown in bold with an asterisk) represent sequences that have undergone interallelic gene conversion. ‘La Paz 021 HBB-T1 A’ and ‘Lima 138 HBB-T1 B’ are s-type alleles that have been partially converted by a d-type sequence, whereas ‘Lima 116 HBB-T1 A’ is a d-type allele that has been partially converted by an s-type sequence. See Figure 5A for details regarding the length and composition of the conversion tracts.

Figure 7.—

Alternative neighbor-joining phylogenies that illustrate the effects of concerted evolution between HBB-T1 and HBB-T2 on the Hbb^s haplotype. In A, the phylogeny based on 5′ flanking sequence recovers orthologous relationships among rodent HBB-T1 and HBB-T2 sequences. In B, by contrast, the phylogeny based on intronic sequence does not recover the true orthologous relationships due to conversion of HBB-T2 by HBB-T1 on the Hbb^s haplotype.

Figure 8.—

Sliding window plots of average nucleotide divergence between the two β-globin paralogs on the Hbb^s haplotype (A) and the Hbb^d haplotype (B). Window size, 50 bp; step size, 10 bp.

Figure 9.—

Sliding window plot showing variation in levels of silent site diversity within and between s- and d-type alleles of the HBB-T1 gene (window size = 50 bp, step size = 10 bp). Fixed replacement differences that distinguish the two allele classes are indicated by red arrows, and fixed differences at synonymous or noncoding sites are indicated by blue arrows. The three exons of HBB-T1 are shown as gray boxes.