Geographic variation in opsin expression does not align with opsin genotype in Lake Victoria cichlid populations

Abstract

Sensory adaptation to the local environment can contribute to speciation. Aquatic environments are well suited for studying this process: The natural attenuation of light through water results in heterogeneous light environments, to which vision-dependent species must adapt for communication and survival. Here, we study visual adaptation in sympatric Pundamilia cichlids from southeastern Lake Victoria. Species with blue or red male nuptial coloration co-occur at many rocky islands but tend to be depth-differentiated, entailing different visual habitats, more strongly at some islands than others. Divergent visual adaptation to these environments has been implicated as a major factor in the divergence of P. pundamilia and P. nyererei, as they show consistent differentiation in the long-wavelength-sensitive visual pigment gene sequence (LWS opsin). In addition to sequence variation, variation in the opsin gene expression levels may contribute to visual adaptation. We characterized opsin gene expression and LWS genotype across Pundamilia populations inhabiting turbid and clear waters, to examine how different mechanisms of visual tuning contribute to visual adaptation. As predicted, the short-wavelength-sensitive opsin (SWS2b) was expressed exclusively in a population from clear water. Contrary to prediction however, expression levels of the other opsins were species- and island-dependent and did not align with species differences in LWS genotype. Specifically, in two locations with turbid water, the shallow-water dwelling blue species expressed more LWS and less RH2A than the deeper-dwelling red species, while the opposite pattern occurred in the two locations with clear water. Visual modeling suggests that the observed distribution of opsin expression profiles and LWS genotypes does not maximize visual performance, implying the involvement of additional visual tuning mechanisms and/or incomplete adaptation.

Open research badge: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://hdl.handle.net/10411/I1IUUQ.

Keywords: LWS; ecological speciation; haplochromine; sensory drive.

Figure 1

Sampling locations. (a) Blue and red Pundamilia males were sampled from five island locations in southeastern Lake Victoria. (b) Irradiance spectra at four of the sampling locations (irradiance was not measured at Anchor Island). Vertical lines indicate the spectral midpoint at 1 m depth: The wavelength at which the total light intensity of shorter wavelengths is equal to that of longer wavelengths

Figure 2

Depth distribution of sampled fish. (a) Mean capture depth (± standard deviation) of fish used in this study compared to the (b) depth distributions reported by Seehausen et al. (2008; Anchor Island depth distributions are from unpublished field data collected by OS in 1991/1992). Sample sizes are indicated above each bar

Figure 3

Light environments at the study locations. Orange ratio (OR) increases with depth at all islands; Luanso, the most turbid location (Secchi disk: ~50 cm), has the highest OR. Irradiance spectra for Anchor Island were unavailable, so OR values were estimated as the median of the OR values at Makobe and Python Islands. At Luanso Island, spectra were only available to 4 m depth, thus linear regression (gray dashed line) was used to estimate OR for fish captured at 5 m

Figure 4

Geographic variation in opsin expression. The blue and red species expressed SWS2b at clear water Makobe Island only (blue: p < 0.01; red: p < 0.001). SWS2a expression was influenced only by the individual effect of island (χ ²(4) = 12.42, p = 0.014); for all fish (both species combined), expression at Makobe was higher than at Python (Z = 2.91, p = 0.028) and slightly higher than at Luanso (Z = 2.57, p = 0.074). RH2A: there was a significant island by species interaction (χ ²(4) = 39.96, p < 0.001). Tukey Post hoc revealed higher RH2A expression in Makobe blue phenotypes compared to Python, Kissenda, and Luanso (p < 0.029); Anchor and Makobe did not differ (p = 0.29). Makobe red phenotypes expressed less RH2A than red phenotypes at Python (Z = −3.50, p = 0.018) and slightly less than those at Kissenda (Z = −2.99, p = 0.090). RH2A expression in Anchor Island red types was lower than both Python and Kissenda (p < 0.01) but did not differ from Makobe (p = 0.9). LWS: again, there was a significant interaction between island and species (χ ²(4) = 21.62, p = 0.0002). Post hoc revealed lower LWS expression in Makobe blue phenotypes compared to all other locations (p < 0.038). For the red phenotypes, LWS expression was higher at Anchor (Anchor vs. Python: Z = 3.48, p = 0.02; Anchor vs. Kissenda: Z = 3.72, p < 0.01; Anchor vs. Makobe: Z = 3.18, p = 0.052). Sample sizes are indicated above each bar and error bars represent ± standard error. ***indicates p < 0.001, **indicates p < 0.01, *indicates p < 0.05, • indicates p < 0.1.

Figure 5

Island‐ and species‐specific opsin expression and LWS genotype. (a) Species differences in opsin expression varied across islands. Makobe Island: LWS expression did not differ between Pundamilia pundamilia and Pundamilia nyererei (p = 0.3) but RH2A expression was higher in P. pundamilia (Z = 3.02, p = 0.016). SWS2a did not differ (p > 0.9) and SWS2b was slightly higher in P. nyererei (Z = 2.63, p = 0.055). Anchor Island: all comparisons were nonsignificant (p > 0.86). Python Island: P. sp. “pundamilia‐like” expressed more LWS than P. sp. “nyererei‐like” (Z = 3.68, p < 0.01), while P. sp. “nyererei‐like” expressed more RH2A than P. sp. “pundamilia‐like” (Z = 5.00, p < 0.001). SWS2a or SWS2b expression did not differ (p > 0.83). Kissenda Island: LWS expression was slightly higher in P. sp. “pundamilia‐like” (Z = 2.64, p = 0.053) while P. sp. “nyererei‐like” expressed significantly more RH2A (Z = 3.32, p < 0.01). SWS2a and SWS2b expression did not differ (p > 0.9). Luanso Island: there were no differences in opsin expression (p > 0.9). Sample sizes are indicated above each bar and error bars represent ± standard error. ***indicates p < 0.001, **indicates p < 0.01, *indicates p < 0.05, • indicates p < 0.1. (b) Consistent with previously reported patterns (Seehausen et al., 2008), the blue species were generally “PP” genotypes and the red species were “HH” genotypes. Anchor Island had not been previously investigated: the “H” allele was absent, but the “M3” allele was present in the red phenotypes. All fish at Luanso Island were “PP” genotypes

Figure 6

Relationship between LWS genotype and opsin expression differs between islands. Opsin expression is both genotype‐ and location‐dependent, as evidenced by the significant interaction of LWS genotype and island for RH2A (χ ²(5) = 41.24, p < 0.001) and LWS expression (χ ²(5) = 27.53, p < 0.001). In turbid waters (Python and Kissenda), individuals with LWS genotype “PP” had (a) lower RH2A expression and (b) higher LWS expression than individuals with “HH” genotypes. This pattern was reversed in clear waters (Makobe). All fish at Luanso Island were “PP” genotypes. Error bars represent ± 95% C.I

Figure 7

Similar visual performance despite different opsin expression profiles. For both the (a) blue and (b) red species, total Q_c of the resident fish did not systematically differ from hypothetical immigrants. Here, all blue fish are “PP” genotypes and all red fish are “HH” genotypes. For Q_c values of the individual opsins, see Figure S5. Sample sizes are indicated above each bar and error bars represent ±standard error. **indicates p < 0.01, *indicates p < 0.05