As an immediate response to the selection of certain organisms and new habitats, evolution changes rapidly. An environment's overall conditions may be impacted by such changes. Parallel evolution occurs when identical features respond to identical population pressures and mutations, and this eventually results in changes to an organism's phenotype, or outward appearance. Changes in allele frequency may also be connected to parallel adaptation. However, it is still unclear what impact allelic frequency has had on the evolution of wild populations.
Finding specific genomic areas that are subject to natural selection is the main objective of evolutionary genetics. This is important in order to effectively comprehend the foundation of adaptation on a genetic scale. Nonetheless, the underlying concern of such researches is the complexity of behavioral traits and the effect of environmental and genetic factors on it. This particularly happens with traits having numerous behavioral and phenotypic effects. Furthermore, the fact that an allele provides adaptive benefits in a certain environment cannot be easily verified through the linking of phenotypes with genotypes.
Since animal migration is the most common topic in evolutionary genetic researches, it has been known that there is a genetic basis for the physical differences in migratory traits. Such traits are regarded as threshold traits since their expression greatly relies on environmental factors, growth and development as well as the genetic makeup of organisms.
This particular study shall deal with Onchorhyncus mykiss, a salmonid that is known to be widely distributed in fisheries for commercial production. This is because O. mykiss has displayed specific variations in terms of its life history and migration. Its characteristic transformation from being a freshwater rainbow trout to becoming an anadromous steelhead accounts for its selection as the organism of interest in this study.
Anadromous and resident O. mykiss situated in the same watershed are regarded as close relatives. With consideration of behavioral traits related to migration, a process called smoltification, which refers to the structural and physiological changes that occur in the anadromous O. mykiss, is deemed significant specifically for adaptation to seawater. In contrast, resident O. mykiss are highly adaptive in freshwater, and their reproductive capacity develops only in one year.
Genetic research has been done previously regarding O. mykiss populations. Based on results obtained from previous studies, the hypothesis is that chromosome Omy5 possesses a genomic region that has a strong linkage with the expression of life histories in this species. This region will eventually be subjected to divergent natural selection in numerous populations.
The loci subset situated on Omy5 is characterized by a unique pattern of deviation on habitats of resident and anadromous species. Such pattern is a consequence of parallel natural selection that acts upon traits affected by single or multiple genes. The assumption is that the transformation of O. mykiss from being a resident to an anadromous species is based on a specific genetic mechanism that greatly influences its adaptation with the environment.
In addition, it can be hypothesized that the anadromous and resident populations of O. mykiss display the same divergence of life history. The evidence of gene linkage in these populations is that the isolated upstream populations have the same freshwater phenotypes while all downstream populations have the same migratory lifestyles.
Materials and Methods
Population Samples
Samples were obtained from 21 populations of anadromous fish species situated below or above artificial dams and waterfalls in five watersheds located in California and the southern part of Oregon. Samples were also acquired from three hatchery strains of rainbow trout in California. All samples that were selected have different life histories and included juvenile and adult stages, aside from winter and summer steelhead ecotypes. The populations situated above the water barriers were a combination of coastal steelheads and inland trout populations.
Marker Development, Genotyping and Analysis
In a previous study, a total of 344 single nucleotide polymorphisms (SNPs) were determined for mapping to chromosome Omy5 along with Restriction-site Aided DNA (RAD) sequencing. From these SNPs, 55 SNPtype assays were performed through the alignment of sequences with each SNP acquired from BAC Swanson (Sw) clones. Additional assays were also performed for the chromosome Omy5 loci identified by other researchers.
A group of assays were done for 32 SNP loci situated on 17 of the 28 O. mykiss groups. Genotyping of the loci was performed through the 96.6 SNP Genotyping Arrays on an EP1 system, which included two controls per array. Selected genotypes were run through the Genotyping Analysis Software. The parameters determined were primer sequences, map positions, summary statistics and specific genotypes for all loci.
Genepop was utilized to test for Hardy-Weinberg (H-W) equilibrium and LD. Those with p-values less than Bonferoni-corrected critical values are regarded as statistically significant. The quantity of paired linkages which were more than the critical value was also determined. These were eventually compared with the Scott Creek anadromous O. mykiss as reference due to its massive sample size and polymorphic characteristic. To determine the relationship between the species’ life history and the Omy5 alleles, the allele frequency differences for all populations were compared with the Scott Creek O. mykiss.
Results and Analysis
Genetic Data
From the 95 SNPs that were analyzed, eight SNPs did not increase in value and were not able to exhibit polymorphism. They were also found to be inconsistent with Mendelian segregation. Along with the removal of these loci, the 87 loci which were retained during the experiment had 55 markers situated on chromosome Omy5. About 32 loci were found in other linkage sets. In addition, four loci exhibited significant differences from the H-W equilibrium.
Population Structure
Consistency with previous studies on non-Omy5 loci was found for genetic divergence determined through FST and phylogenetic network analysis. There was a significant relationship found between populations above and below the waterfalls and dams in a watershed. Increasing divergence was observed to be proportional with distance along the coastline of California. On the other hand, high divergence was observed for loci on Omy5 between populations above and below water barriers.
Linkage Disequilibrium
Of the 495 pairwise linkage experiments for LD among 32 non-Omy5 loci, values were not significantly different with the Bonferroni-corrected critical values performed for multiple tests. There was also no significant difference observed in pairs situated on the same chromosome. On the other hand, significant differences were found for 602 of the 1430 pairwise experiments among 55 Omy-5 loci. This confirms the hypothesis that there is a strong linkage of such SNPs to the Omy5 loci. The fact that there are concordant patterns displayed for LD and allele frequency differences across O. mykiss populations proves the existence of a phenotypic linkage in this particular species.
Allele frequency and haplotype variation among populations
There was a consistency found between allele frequency differences and LD analysis. Allele frequencies of loci on Omy5 are highly associated with the above and below water barriers for each fish population. A single, linked haplotype was described for the 30 SNP loci with the greatest average pairwise r2 values (including those with r2 values higher than 0.50). These specific loci were found to be almost identical in terms of allele frequencies that have strong connections with the life history of these populations.
Resident and anadromous haplotypes were considered in this particular study. Populations situated above water barriers were found to have lower average allele frequencies for the anadromous haplotype compared to those located below water barriers. The highest average frequency of the anadromous haplotype was seen among the four populations below the water barrier. One example would be that of the adult steelhead.
Comparison of resident trout species with current species above the water barrier was also done. It was found that four out of five resident trout populations were constant for the resident haplotype as compared with the current species which retained its polymorphism. Resident trout populations were observed to have significantly lower average allele frequency for the anadromous haplotype.
Discussion
Results obtained clearly support the idea that evolutionary changes happen at a rapid rate in natural populations, along with adaptive divergence. This is deemed as a population’s way of reacting to specific selections done in a short period of time. The outcomes of the experiment also support the idea that artificial selection has a greater impact compared to natural selection. The manner of how selection influences the genetic makeup of an organism as well as the assumption that parallel trait evolution has a close association with parallel genetic evolution somehow remains vague.
In the tests done for this study, evidence was found regarding the influence of parallel evolution on the genomic region of Omy5 in O. mykiss populations. Such evidence was further explained by the fact that parallel natural selection contradicts the life history of anadromous trout populations above the water barriers. Furthermore, non-random linkages with life history were found in allele frequencies of SNPs situated on Omy5. This supports the evidence that there is a strong selection in one area of Omy5 and a series of repetitive parallel modifications in the allele frequency of the haplotype as a form of reaction to specific environments.
The evidence of parallel evolution at a genetic level is consistent with previous studies on stickleback populations migrating from marine to freshwater ecosystems. It is also consistent with findings on the parallel evolution of vertebrate pigmentation.
Results obtained strengthen the findings of prior studies on O. mykiss populations in terms of the genetic makeup of traits linked with its migration and life history. The data obtained in this study also supports the hypothesis that the genomic region on Omy5 serves as a control region which affects the individual life history of O. mykiss populations as either resident or anadromous.
There are areas of decreased recombination which may come from different mechanisms and are generally present in the genomes of several species. Nonetheless, the chromosome Omy5 is excluded from the universal recombination patterns observed in O. mykiss chromosomes. Adaptation can be attributed from chromosomal inversions since the reduction or removal of recombination in such areas prevents the separation of co-adapted alleles at numerous loci to form larger haplotypes.
Results in this study also indicated that there are no precise locations for the genes that influence the differences between anadromous and resident life histories in the O. mykiss, but through the consideration of the lack of recombination across generations, one could tell that these genes were relatively close together.
Conservation Implications
The study of evolutionary genetics plays an important role on environmental conservation. This study with regard to populations of O. mykiss serves as a steppingstone for conservationists to exert effort in the preservation of such species along with other related organisms.
It has been found that California steelhead populations are under the protection of the 1973 U.S. Endangered Species Act (ESA). Nevertheless, this protection is only limited to naturally-grown anadromous O. mykiss populations below water barriers. Fish species situated above natural and artificial water barriers are not included in the ESA protection. This is regardless of the finding that O. mykiss populations either situated above or below water barriers share a common origin. It also does not take into account the evidence that resident and anadromous O. mykiss populations exhibit alternate phenotypes.
Consequently, there are certain populations with allele frequencies that contradict with the consistency of the relationship between life history and the chromosome Omy5. Such allele frequency patterns though have an implication with regard to the reproduction of O. mykiss populations.
With regard to the findings on haplotypes, there may have been a certain duration required for strong selection to counteract the life history of O. mykiss populations. This is for the purpose of eliminating the anadromous (AD) haplotype, which was found to be of lower allele frequency in O. mykiss populations above water barriers compared to current species.
The results obtained in this study clearly provide ample evidence regarding the evolutionary and migratory changes of a certain population. It also provides an effective mechanism which utilizes genomic data to determine the life history of specific organisms over a period of time.
Work Cited
Pearse, Devon E., Miller, Michael R., Abadia-Cardoso, Alicia, & Garza, John Carlos. “Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout.” Proceedings of the Royal Society B., vol. 281, no. 20140012, 2014. pp. 1-9. http://dx.doi.org/10.1098/rspb.2014.0012
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