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Genomic Study IDs Parallel Adaptations in Independent Stickleback Populations

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In a paper appearing online today in PLoS Genetics, University of Oregon researchers reported that they have detected evidence of parallel evolution in independently adapted freshwater fish populations.

"Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale," senior author William Cresko, a researcher with the UO's Center for Ecology and Evolutionary Biology, and colleagues wrote.

The team used a combination of restriction-site associated DNA, or RAD, sequence tags and high-throughput sequencing approaches to genotype 100 threespine stickleback from three Alaskan freshwater lakes and two ocean sites, gaining insights into genome adaptation and evolutionary patterns in the threespine stickleback, Gasterosteus aculeatus.

Threespine sticklebacks live in marine environments but have also adapted to estuarine and freshwater environments throughout Asia, Europe, and North America, the researchers noted, apparently through independent events in which the fish became isolated from their original ocean environment.

Once in freshwater, the fish tend to evolve quickly — in some cases leading to stickleback populations that are reproductively isolated from one another.

"Alaska has a lot of lakes that have been around only about 10,000 years, formed after glaciers receded," Cresko said in a statement. "Instead of dying out when they were cut off from saltwater, they evolved very rapidly and in a lot of ways, such as in their bones and armor, the shapes of their jaws, as well as coloration and behavior."

For the current study, the team used RAD-based sequencing to assess fish from five populations: three from Alaskan freshwater lakes and two from oceanic sites at Rabbit Slough and Resurrection Bay.

Researchers at UO developed the RAD approach, which is being used by the Eugene, Oregon-based UO spinoff company Floragenex. As GenomeWeb Daily News' sister publication BioArray News reported last month, Floragenex recently opened a subsidiary unit called Biota Sciences, which focuses on applying RAD to animal studies.

Using massively parallel Illumina sequencing of libraries created by RAD, the team generated sequences to align to a draft version of the stickleback reference genome. In the process, they pinned down 44,841 SNPs in the stickleback genomes, which were used to genotype the five fish populations.

Although the two ocean populations tested had the largest geographic distance between them, the researchers found less differentiation and genetic divergence between these two populations than between freshwater and ocean populations or within the freshwater populations — consistent with the notion that freshwater stickleback populations arose from oceanic populations independently of one another.

The researchers found similar genomic regions affected by balancing and divergent selection in populations from distinct populations suggesting parallel evolution has occurred in the fish.

In particular, the genomic analyses revealed that linkage groups with high and low nucleotide diversity and heterozygosity tend to overlap in the freshwater stickleback populations. Among the genes in these frequently affected regions were those involved in innate immune response, pathogen detection, and inflammatory genes.

"This pattern suggests independent, parallel evolution in the form of similar genomic regions responding to directional selection across freshwater populations," the researchers wrote. "[S]ome, but not all, of these peaks also appear in the overall oceanic-freshwater comparison."

When they narrowed in on the nine peaks that showed the most reliable differentiation peaks and did functional analyses of genes in these regions, the team turned up 31 candidate genes. Most corresponded to genes with roles in skeletal trait patterning or homeostasis, though several represented genes relating to osmotic stress or osmoregulatory organ development.

"Taken together our data support the biogeographic hypothesis that large populations of oceanic stickleback gave rise repeatedly to freshwater populations, which have become phenotypically differentiated on a background of minor neutral population divergence," the researchers wrote.

Those involved emphasized that while they used the stickleback reference genome for aligning the RAD tags in the current study, a similar approach comparing sequence reads to one another should be possible even in the absence of a sequenced genome.

As such, they say, the RAD-sequencing approach is expected to provide insights about other species as well, yielding information on everything from genes involved in speciation to clues about organizing genetic and physical genome maps.

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