Complex Craniofacial Changes in Blind Cave-Dwelling Fish Are Mediated by Genetically Symmetric and Asymmetric Loci

Abstract

The genetic regulators of regressive craniofacial morphologies are poorly understood. To shed light on this problem, we examined the freshwater fish Astyanax mexicanus, a species with surface-dwelling and multiple independent eyeless cave-dwelling forms. Changes affecting the skull in cavefish include morphological alterations to the intramembranous circumorbital bones encircling the eye. Many of these modifications, however, have evolved separately from eye loss, such as fragmentation of the third suborbital bone. To understand the genetic architecture of these eye-independent craniofacial alterations, we developed and scored 33 phenotypes in the context of an F 2 hybrid mapping pedigree bred from Pachón cavefish and surface fish. We discovered several individuals exhibiting dramatic left-right differences in bone formation, such as extensive fragmentation on the right side only. This observation, along with well-known eye size asymmetry in natural cave-dwelling animals, led us to further evaluate left-right genetic differences for the craniofacial complex. We discovered three phenotypes, inclusive of bone fragmentation and fusion, which demonstrated a directional heritable basis only on one side. Interestingly, the overall areas of affected bones were genetically symmetric. Phenotypic effect plots of these novel craniofacial QTL revealed that cave alleles are associated with abnormal conditions such as bony fusion and fragmentation. Moreover, many linked loci overlapped with other cave-associated traits, suggesting regressive craniofacial changes may evolve through linkage or as antagonistic pleiotropic consequences of cave-associated adaptations. These novel findings illuminate significant craniofacial changes accompanying evolution in complete darkness and reveal complex changes to the skull differentially influenced by genetic changes affecting the left and right sides.

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

“…This follows the observation that surface fish demonstrate near perfect cranial symmetry with respect to the facial bones that encircle the eye (the “circumorbital” series) [4]. In contrast, cave-dwelling populations harbor substantial asymmetry across the left-right axis for this bony complex at both the individual and population levels [4,7]. …”

“…These include a variety of fusions of the six dermal bones comprising the circumorbital series, as well as substantial “fragmentation” of the third suborbital bone. This latter (extreme) phenotype has only been observed in cavefish populations [7]. …”

“…These fish are also isolated, residing in “perched” pools within limestone caves distributed across the El Abra region (Figure 1) [9]. Further, Pachón cavefish comprised the genetic mapping population in a recent genetic study documenting genetic and morphological asymmetry in the cranial complex [7]. We subjected n = 30 individuals to our asymmetry protocol and discovered consistently lower values of symmetry compared to surface-dwelling fish (Figure 4).…”

“…Recent studies have demonstrated that patterns of fragmentation in cavefish are asymmetric [7]. Further, analyses in zebrafish reveal that the facial bone morphology is associated with distribution patterns of cranial neuromasts [8].…”

Dissection of the complex genetic basis of craniofacial anomalies using haploid genetics and interspecies hybrids in Nasonia wasps

“…Epistasis has been shown to play an important role in the degenerative craniofacial development of cavefish (Gross et al, 2014), and skull shape trait complexes in crosses between mouse strains (Wolf et al, 2005). …”