Alterations in Mc1r gene expression are associated with regressive pigmentation in Astyanax cavefish

Abstract

Diverse changes in coloration across distant taxa are mediated through alterations in certain highly conserved pigmentation genes. Among these genes, Mc1r is a frequent target for mutation, and many documented alterations involve coding sequence changes. We investigated whether regulatory mutations in Mc1r may also contribute to pigmentation loss in the blind Mexican cavefish, Astyanax mexicanus. This species comprises multiple independent cave populations that have evolved reduced (or absent) melanic pigmentation as a consequence of living in darkness for millions of generations. Among the most salient cave-associated traits, complete absence (albinism) or reduced levels of pigmentation (brown), have long been the focus of degenerative pigmentation research in Astyanax. These two Mendelian traits have been linked to specific coding mutations in Oca2 (albinism) and Mc1r (brown). However, four of the seven caves harboring the brown phenotype exhibit unaffected coding sequences compared to surface fish. Thus, diverse genetic changes involving the same genes likely impact reduced pigmentation among cavefish populations. Using both sequence and expression analyses, we show that certain cave-dwelling populations harboring the brown mutation have substantial alterations to the putative Mc1r cis-regulatory region. Several of these sequence mutations in the Mc1r 5′ region were present across multiple, independent cave populations. This study suggests that pigmentation reduction in Astyanax cavefish evolves through a combination of both coding and cis-regulatory mutations. Moreover, this study represents one of the first attempts to identify regulatory alterations linked to regressive changes in cave-dwelling populations of Astyanax mexicanus.

Asymmetric Facial Bone Fragmentation Mirrors Asymmetric Distribution of Cranial Neuromasts in Blind Mexican Cavefish

“…Although this population is part of the “El Abra” complex, it likely colonized the subterranean environment at a different time in the geologic past than Pachón [9]. Evidence to support this includes the fact that, unlike Pachón, Tinaja cavefish harbor some (albeit reduced) melanic pigmentation [12]. Further, although Tinaja cavefish demonstrate regressed vision, they lose their eyes at a slower pace compared to Pachón.…”

Flickers of speciation: Sympatric colour morphs of the arc‐eye hawkfish,Paracirrhites arcatus, reveal key elements of divergence with gene flow

“…Noncoding flanking regions of the Mc1r gene regulate gene expression. For example, Stahl and Gross () recently reported that cave‐dwelling fishes (genus Astyanax ) with no coding sequence variation in Mc1r still demonstrate reduced expression due to mutations in the 5′ regulatory region. Similarly, mutations in regulatory elements of two other pigment genes, yellow in Drosophila (Jeong, Rokas, & Carroll, ) and agouti in Peromyscus deer mice (Kingsley, Manceau, Wiley, & Hoekstra, ), can affect pigmentation via altered protein expression.…”

Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus

“…Furthermore, cis-regulatory changes can be more difficult to test functionally than coding mutations. Because of these challenges, most of the mutations and genes identified as causative for cave-related traits in the model system of Astyanax mexicanus have been coding mutations [39,40,[43][44][45][46][47] though there are some exceptions [48]. Allele-specific expression studies in hybrids are a powerful way of identifying cis-regulatory differences.…”