A Fish Tale: Tracing the Divergence of a Species
What does it take for one species to evolve into another?
Scientists in Japan are getting a glimpse of speciation in action, by studying three strains of medaka fish (Oryzias latipes).
Called the Japanese rice fish because of its presence in rice paddies, the small (up to about 3.5 cm) native of East Asia can also be found in marshes, ponds, slow-moving streams, tide pools, and aquariums. The medaka has been a popular pet since the 17th century because of its hardiness and pleasant coloration, which varies from creamy-white to yellowish in the wild to white, creamy-yellow, or orange in aquarium-bred individuals.
Scientists are more interested in its genetics, but earlier attempts to sequence the fish’s 800 Mb genome were not the best quality, and had 97,933 gaps in the sequences.
So researchers at the University of Tokyo started from scratch, using Single Molecule, Real-Time (SMRT) Sequencing. This advanced technology allowed them to study difficult-to-detect centromeres and changes in DNA structure that were missing in the previous genome assemblies.
In a paper published in Nature Communications, senior authors Hiroyuki Takeda and Shinich Morishita described some of the differences they found in the genomes of three medaka species from different geographic regions of Japan and Korea.
Originally considered a single species since they can mate and produce healthy offspring under laboratory conditions, the strains have accumulated genetic mutations and phenotypic diversity over a long period of geographical separation.
Many of these changes seem to center around the centromeres. Centromeres are the points where the “arms” of chromosomes meet, the assembly site for proteins as the spindle prepares for cell division.
Typically depicted as Xs, chromosomes actually come in a variety of shapes, depending on where the centromeres are located. The X-shaped chromosomes, with the centromere in the middle so that the two arms of the chromosomes are almost equal, are called metacentric. If the arms’ lengths are unequal, forming an L shape, the chromosome is said to be submetacentric. If the chromosome’s centromere is located closer to its end than to its center, it may be described as subtelocentric. If the short arm is so short that it is hard to observe, but still present, then the chromosome is acrocentric.
The scientists discovered that the pace of evolution in each of the medaka strains differed depending on the shape and sequence of their centromeres, with acrocentric chromosomes evolving more slowly.
Fissions, fusions, and translocations are also shaping the medaka genome, but the chromosomal rearrangement has had to happen on a large scale before affecting the position of the fish’s centromeres, the scientists found.
Studying epigenetic activity — changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself — the researchers found divergent methylation patterns among the strains, suggesting that centromeres accumulate epigenetic diversity as well as sequence diversity during speciation.
They observed that each local strain has independently experienced thousands of mid-sized (1–50 kbp) insertion events — not enough to cause reproductive isolation, but possibly enough to participate in the regulation of genes and contribute to phenotypic variations.
All of these are important clues to what may cause or contribute to the speciation of vertebrates, including humans.
