Cichlid Genome Consortium
In the lakes of East Africa, fishes of the family Cichlidae have undergone an extraordinarily rapid and extensive radiation. At least 1500 species of cichlid ('sick-lid') fish have evolved from a common ancestor in the last 10 million years. Within Lake Malawi over 700 species have arisen within just the last 2 MY
Our ultimate goal is to identify mechanisms responsible for speciation of these fishes. What evolutionary forces contribute to speciation? A number of factors are at work, including natural selection on the feeding apparatus, and sexual selection which has produced a riotous variety of male color patterns.
We have spent the last twenty years studying the genetic basis of phenotypic differences among closely related species of the rock-dwelling ‘mbuna’ lineage in Lake Malawi. We have performed QTL studies of the differences in jaw and tooth morphology to understand the genetic basis of trophic specialization. We have also mapped the genetic basis of differences in both male and female color patterns.
Labeotropheus trewavasae
Genetic maps
Several genetic linkage maps of cichlid fishes have been constructed. Our latest map, based on an interspecific F2 cross between O. niloticus and O. aureus has an average spacing of 3cM between microsatellite markers (Lee et al. 2005)(PDF).
We have also published a map for Lake Malawi cichlids, based on the F2 of an intergeneric cross of two Lake Malawi cichlids (Metriaclima zebra and Labeotropheus fuelleborni). Although this map has fewer markers, we were able to select markers from the tilapia map to fill in gaps. When we compare marker orders in these two maps, we find only two obvious rearrangements, indicating that gene order is largely conserved across this group of fishes.
RESEARCH AREAS
Sex Determination
Teleost fishes display a wonderful variety of mechanisms for sex determination. Both male heterogametic (XX-XY) and female heterogametic (ZW-ZZ) systems have been described, and many different genes have been implicated as controlling this fundamental developmental decision.
The sex chromosomes of African cichlids are still at an early stage of differentiation. There are no gross morphological differences in any chromosome pair, but molecular genetic analysis has identified XY and ZW systems on different chromosomes in a number of species. We suspect there may be as many as 40 independently evolved sex determiners segregating in the cichlids of East Africa.
We have characterized an XY system on linkage group 1 in the Nile tilapia (Oreochromis niloticus). In the blue tilapia, (O. aureus) we found the XY system on linkage group 1 and a second, ZW system on linkage group 3. A duplication of the anti-Mullerian hormone gene on linkage group 23 is responsible for another XY system in some strains of Nile tilapia.
Many Lake Malawi cichlids have an XY system on linkage group 7. A few species also segregate a ZW system on linkage group 5. An inversion on linkage group 5 links the ZW sex determiner to the orange-blotch color pattern which is found almost exclusively in females.
Our ultimate goals are to identify the genes underlying sex determination in this group of species, to reveal the molecular pathway of sex differentiation which they control, and to understand how the evolution of sex-determining mechanisms contributes to speciation.
B chromosomes
The genomes of eukaryotic species are typically organized into linear chromosomes, and each species has a characteristic number of chromosome pairs referred to as the A chromosomes (As). Thousands of eukaryotic species contain additional chromosomes commonly referred to as B chromosomes (Bs). These extra chromosomes are not essential and are found in some but not all individuals of a population. B chromosomes are thought to manipulate the normal mechanisms of cell division in order to increase their transmission to the next generation, a process known as drive.
We have identified supernumerary B chromosomes in many haplochromine cichlids. The B chromosomes of the Lake Victoria species Astatotilapia latifasciata contain thousands of short (200bp-200kbp) blocks of sequence duplicated from every chromosome in the ancestral karyotype.
We also found female-limited B chromosomes in seven Lake Malawi species . About 10% of females in these populations carry a single B chromosome, which they transmit to the vast majority (~100%) of their offspring. Because they are never found in males, we suspect the B chromosomes carry an epistatically-dominant female sex determiner. The B chromosome thus represents a novel genomic compartment for the accumulation of sexually antagonistic variation.
Genetics and Genomics
We have invested enormous effort over the last 25 years to develop genomic resources to support our research. We published the first linkage map for tilapia in 1998, and have since developed an extensive set of markers for genetic mapping in East African cichlids. We helped organize the first cichlid genome project, which resulted in the publication of draft genome sequences for 5 species in Science. We have since worked to improve the genome assemblies and annotations for both the Nile tilapia and the Lake Malawi zebra cichlid. These resources are described on our Genome Resources page.
Previous work
- Breeding behavior
- Trophic morphology
- Phylogenetics
- Population structure