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Cichlid Sequencing Reveals Possible Mechanisms Undergirding Their Evolution

NEW YORK (GenomeWeb) – A number of molecular mechanisms have shaped the genomes of East African cichlids and enabled the extensive diversity seen within the fishes' lineage, researchers from the Broad Institute and elsewhere reported in Nature today.

The researchers sequenced the genomes and transcriptomes of East African cichlid fishes, finding a number of distinctive features within the cichlids' genomes, as compared to an ancestral lineage, including increased gene duplications and a number of novel microRNAs.

"Our study reveals a spectrum of methods that nature uses to allow organisms to adapt to different environments," said co-senior author Kerstin Lindblad-Toh, scientific director of vertebrate genome biology at the Broad Institute and a professor at Uppsala University in Sweden, in a statement. "These mechanisms are likely also at work in humans and other vertebrates, and by focusing on the remarkably diverse cichlid fishes, we were able to study this process on a broad scale for the first time."

Cichlid fish, the researchers noted, are a prominent example of adaptive radiation, in which one lineage diversifies into a number of ecologically varied species in a short timespan. There are some 2,000 species of cichlid fish, most of which are found within just three African lakes. Lake Tanganyika has 250 cichlid species and was colonized between 10 million years and 12 million years ago and Lake Malawi has 500 cichlid species and was colonized less than 5 million years ago, while Lake Victoria, which was colonized some 15,000 years to 100,000 years ago, has 500 cichlid species.

For this study, the Broad-led team sequenced the genomes of five East African cichlid species: one from Lake Tanganyika, one from Lake Malawi, another from Lake Victoria, a fourth from a river near Lake Tanganyika, and, to represent the ancestral line, the Nile tilapia. They also sequenced the transcriptomes of 10 different tissues from the fish.

Through their subsequent analyses, the researchers found that the cichlid genomes harbor an abundance of gene duplications. For instance, the researchers found some 280 gene duplications in the lineage leading to the common ancestor of the lake cichlids and 148 duplications in the common ancestor of the haplochromines.

This, they noted, is a 4.5-fold to six-fold increase — after normalizing for branch lengths — in gene duplications as compared to older clades, and an even higher duplication rate in the common ancestor of just the haplochromines.
While the cichlid-specific gene duplications don't exhibit enrichment for any particular gene categories, the researchers found that a portion of them had increased gene expression or were newly expressed in certain tissues. Of the duplicates that lost or gained such tissue specificity, 43 percent gained expression in the testis.

The researchers also found that nearly 20 percent of the East African cichlid genomes are made up of transposable elements, mostly DNA transposons.

When inserted near the 5' untranslated regions, these transposons were significantly associated with increased gene expression, as compared to genes without such insertions. Similarly, transposons inserted in 3' untranslated regions were also significantly linked to increased gene expression, though not in brain or skeletal muscles.

These transposons, the researchers noted, follow an expected pattern of purifying selection, and intronic transposon insertion preferentially occurred in the antisense orientation of protein-coding genes. In intergenic regions, intronic DNA transposons and long interspersed nucleotide repetitive elements or long terminal repeats did not show any orientation preference. However, they noted that none of the cichlid genomes showed any deficit of sense-oriented LINE insertions.

This, they added, suggests that ancestral East African cichlids experienced a period of relaxed purifying selection during which transposon activity increased, but have recently begun to eliminate potentially harmful transposon insertions.

Cichlids also, the researchers reported, have a number of novel microRNAs. By deep sequencing small RNAs from the late embryo stage, the researchers uncovered 1,344 miRNA loci — between 250 and 270 per species.

By comparing these to other teleost miRNAs, they found 40 instances of de novo miRNA emergence and nine cases of miRNA loss. Further, they found four mature miRNA with mutations in the seed sequence, 92 miRNAs with mutations outside the seed sequenced, and some nine cases of arm switching.

These miRNAs, in turn, affect gene expression in the fish. For instance miR-10032, a de novo miRNA, affects the expression of the neurod2 gene, which is involved in brain development and neural differentiation while another de novo miRNA, miR-10029, affects the expression of the bmpr1b gene, which has been associated with the development and morphogenesis of organ systems.

"It's not one big change in the genome of this fish, but lots of different molecular mechanisms used to achieve this amazing adaptation and speciation," co-senior author Federica Di Palma, from the Genome Analysis Centre in the UK, said.

These and other findings suggested to the Broad-led group that the cichlid fish accumulated genetic variation through a number of different mechanisms during a time of relaxed purifying selection prior to their radiation into the African lakes. Then, upon colonizing the lakes, selection on a number of genomic regions allowed the fish to diversify into the current species.

"We conclude that neutral and adaptive processes both make important contributions to the genetic basis of cichlid radiations, but their roles are distinct and their relative importance has changed through time: neutral (and non-adaptive) processes seem to have been crucial to amassing genomic variation, whereas selection subsequently sorted some of this variation," the researchers said in their paper. "The interaction of both is likely to have been necessary for generating many and diverse new species in very short periods of time."

In a related editorial in Nature, Chris Jiggins from the University of Cambridge argued that accelerated evolution can result from either neutral evolution due to relaxed selection or from positive natural selection working through new selective pressures.

He added that the signatures described by the Broad team don't distinguish those two scenarios. Jiggins instead said it is likely that the retention of gene duplicates and rapid genetic divergence were driven by positive natural selection as the species adapted to the diverse ecological niches in the lakes. Extinction of early lineages, he added, could make it look as if there were a burst of rapid change on the branch leading to the living species.

"There may be no need to invoke a genetic revolution when plain old natural selection can explain the observed patterns," Jiggins said.