Cichlid colors

I really can’t get over how much work went into the cichlid pigmentation paper that’s out in the current Science (Roberts et al. 2009). The paper examines the genetic basis for a “orange blotched (OB)” phenotype. It’s a simple kind of genetic question, and it hooks into a story that evolutionary biologists like – sex conflict in gene expression.

But wow how much work they did to iron out all the details. An example:

Pedigreed families from several species of the genera Labeotropheus and Metriaclima were genotyped for newly identified microsatellite markers on LG5 (46 families, 678 individuals, 349 OB individuals; table S1). Breakpoint analysis localized OB to an interval of less than 1 cM, corresponding to a region from 3.9 to 4.0 Mb on Tetraodon chromosome 11 (Fig. 2A). We then used association mapping in natural populations to pinpoint the causative locus. Single-nucleotide polymorphism (SNP) markers were developed spanning the region, including an intronic SNP marker for each annotated gene within the OB interval. We measured linkage disequilibrium (LD) between OB and SNPs within natural populations of Labeotropheus, Metriaclima, and Tropheops from the northern and southern parts of Lake Malawi (Fig. 2B). Within each population, a peak of LD was found in a region overlapping the interval defined by breakpoint analysis (Fig. 2, C to G). Given the shared pattern of association across study populations, we created a lake-wide mapping panel to increase the effective size of the mapping population. This lake-wide panel contains BB and OB individuals from 36 distinct populations of 12 species segregating OB (table S2). Analysis of marker data across these populations increased the resolution and statistical significance of LD beyond that available from any single population (Fig. 2H) (taxonomic names not italicized, because I'm in a Viennese cafe and too lazy right now, OK?).

This is the kind of stuff that a few years ago took multinational networks of cooperation; now it can be done in the context of a single lab with association mapping assisted by field biology.

It helps a lot that the trait is conspicuous and basically Mendelian. I would guess they had a strong presumption that it would be near the sex-determination locus, since the OB phenotype is very rare in males. They even end up concluding that the rare males who have it are probably products of some alternative sex-determining mechanism. So there were hints – and the hints went along with the idea of testing the hypothesis of sex conflict.

But you can see the potential here for widespread genomic work on cichlids. There are an endless number of questions, with hundreds of species in the three big African lakes. These are Lake Malawi cichlids in this paper (for the most part), but Victoria cichlids in particular are so young that you can figure most of their phenotypic differences will be genetically simple – it’s like postglacial stickleback evolution, but with hundreds of different switches. And each one is telling a story about the segregation of original genetic variations in rapidly speciating populations, the spread of new alleles under rapid selection, and the tectonics of the adaptive landscape that occur as genetic backgrounds quickly shift.

All this rich field biology, with the bonus that you can keep a bunch of inbred lines in fish tanks to test for Mendelian ratios and other classical genetic observations (as they did in this study).

Although Lake Victoria cichlids haven’t been around very long, their generations are a lot shorter than ours. So if you were thinking to compare the cichlid case with human timescales, like since the Last Glacial Maximum, think of what those fishes may have been like 1000 years after they reached the lake. They probably speciated fast, and we (of course) haven’t done so at all. Yet in other respects this may be an interesting comparison – and may be even more so as biologists move beyond the conspicuous pigmentation (and we of course do have many recent pigment variations…) and consider the genetics of habitat specializations and diet adaptations.


Roberts RB, Ser JR, Kocher TD. 2009. Sexual conflict resolved by invasion of a novel sex determiner in Lake Malawi cichlid fishes. Science 326:998-1001. doi:10.1126/science.1174705