Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids

Genomic insight into the nocturnal adaptation of the black-crowned night heron (Nycticorax nycticorax)

BACKGROUND

The black-crowned night heron (Nycticorax nycticorax) is an ardeid bird successfully adapted to the nocturnal environment. Previous studies had indicated that the eyes of the night herons have evolved several specialized morphological traits favoring nocturnal vision. However, the molecular mechanisms of the nocturnal vision adaptation of night herons remained inattentions. In this study, the whole genome of N. nycticorax was sequenced and comparative analyses were performed on the vision-related and olfactory receptor (OR) genes to understand the molecular mechanisms of the visual and olfactory adaptation of night herons.

RESULTS

The results indicated that a number of vision genes were under positive or relaxed selection in N. nycticorax, whereas a number of other vision genes were under relaxed or intensified selection in the boat-billed heron (Cochlearius cochlearius), which suggested that the two species adapt to nocturnality with different genetic mechanisms. The different selections acting on vision genes are probably associated with the enlargement of eye size and the enhancement of visual sensitivity in night herons. The analyses on olfactory receptor (OR) genes indicated that the total number of OR genes in the genomes of N. nycticorax and C. cochlearius were about half those in the little egret (Egretta garzetta), whereas the diversity of their OR genes was not remarkably different. Additionally, the number of expressed OR genes in the transcriptomes of N. nycticorax was also fewer than that in E. garzetta. These results suggest a reduced olfactory capability in night herons compared with E. garzetta.

CONCLUSIONS

Our results provided evidence that several vision genes of the night herons were subjected to different natural selections, which can contribute to a better understanding of the genetic mechanisms of visual adaptions of the night heron. In addition, the finding of the reduced number of total and expressed OR genes in night herons may reflect a trade-off between olfaction and vision.

Repeated Genetic Targets of Natural Selection Underlying Adaptation of Fishes to Changing Salinity

Ecological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis on the osmoregulatory system. Given the complex, integrated and polygenic nature of this system, we expected that signatures of natural selection would span numerous genes across functional levels of osmoregulation, especially salinity sensing, hormonal control, and cellular ion exchange mechanisms. We find support for this prediction: genes coding for V-type, Ca2+, and Na+/K+-ATPases, which are key cellular ion exchange enzymes, are especially common targets of selection in species from six orders of fishes. This indicates that while polygenic selection contributes to adaptation across salinity boundaries, changes in ATPase enzymes may be of particular importance in supporting such transitions.

Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish

Understanding the contribution of different molecular processes to evolution and development is crucial for identifying the mechanisms of adaptation. Here, we used RNA-sequencing data to test the importance of alternative splicing and differential gene expression in a case of parallel adaptive evolution, the replicated postglacial divergence of the salmonid fish Arctic charr (Salvelinus alpinus) into sympatric benthic and pelagic ecotypes across multiple independent lakes. We found that genes differentially spliced between ecotypes were mostly not differentially expressed (<6% overlap) and were involved in different biological processes. Differentially spliced genes were primarily enriched for muscle development and functioning, while differentially expressed genes were involved in metabolism, immunity and growth. Furthermore, alternative splicing and gene expression were mostly controlled by independent cis-regulatory quantitative trait loci (<3.4% overlap). Cis-regulatory regions were associated with the parallel divergence in splicing (16.5% of intron clusters) and expression (6.7%-10.1% of differentially expressed genes), indicating shared regulatory variation across ecotype pairs. Contrary to theoretical expectation, we found that differentially spliced genes tended to be highly central in regulatory networks ("hub genes") and were annotated to significantly more gene ontology terms compared to nondifferentially spliced genes, consistent with a higher level of pleiotropy. Together, our results suggest that the concerted regulation of alternative splicing and differential gene expression through different regulatory regions leads to the divergence of complementary processes important for local adaptation. This provides novel insights into the importance of contrasting but putatively complementary molecular processes in rapid parallel adaptive evolution.

Rapid adaptation through genomic and epigenomic responses following translocations in an endangered salmonid

Identifying the molecular mechanisms facilitating adaptation to new environments is a key question in evolutionary biology, especially in the face of current rapid and human-induced changes. Translocations have become an important tool for species conservation, but the attendant small population sizes and new ecological pressures might affect phenotypic and genotypic variation and trajectories dramatically and in unknown ways. In Scotland, the European whitefish (Coregonus lavaretus) is native to only two lakes and vulnerable to extirpation. Six new refuge populations were established over the last 30 years as a conservation measure. In this study, we examined whether there is a predictable ecological and evolutionary response of these fishes to translocation. We found eco-morphological differences, as functional traits relating to body shape differed between source and refuge populations. Dual isotopic analyses suggested some ecological release, with the diets in refuge populations being more diverse than in source populations. Analyses of up to 9117 genome-mapped SNPs showed that refuge populations had reduced genetic diversity and elevated inbreeding and relatedness relative to source populations, though genomic differentiation was low (F ST = 0.002-0.030). We identified 14 genomic SNPs that showed shared signals of a selective response to translocations, including some located near or within genes involved in the immune system, nervous system and hepatic functions. Analysis of up to 120,897 epigenomic loci identified a component of consistent differential methylation between source and refuge populations. We found that epigenomic variation and genomic variation were associated with morphological variation, but we were not able to infer an effect of population age because the patterns were also linked with the methodology of the translocations. These results show that conservation-driven translocations affect evolutionary potential by impacting eco-morphological, genomic and epigenomic components of diversity, shedding light on acclimation and adaptation process in these contexts.

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.