Adaptation and convergence in circadian‐related genes in Iberian freshwater fish

Abstract

Background The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock – positive loop) and repress expression (cryptochrome (cry) and period (per) – negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type. Results We identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes. Conclusions Our results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.

Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species

“…In particular, increasing temperatures and propensity for seasonal drought from north to south (the latter leading to isolation of fish in deeper water sections during summer, when large portions of the riverbed dry out) (Gasith and Resh 1999;Magalhães et al 2003;Jesus et al 2017) might impose strong selective pressures. This is consistent with previous studies that found (i) signatures of positive selection based on dN/dS on circadian genes likely associated with thermal adaptation in Squalius species (Moreno et al 2021), and (ii) differences in gene expression between species inhabiting Atlantic (S. carolitertii) and Mediterranean climates (S. torgalensis) when exposed to increasing temperatures (Jesus et al 2016(Jesus et al , 2017. Thus, its hybrid origin might confer some advantage to S. pyrenaicus North at intermediate environmental conditions, as described in other organisms.…”

Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species

“…In particular, increasing temperatures and propensity for seasonal drought from north to south (the latter leading to isolation of the fish in the deeper water sections during the summer, when large portions of the riverbed dry out) (Gasith and Resh, 1999;Magalhães et al, 2003;Jesus et al, 2017) might impose strong selective pressures. This is consistent with previous studies that found (i) signatures of positive selection based on dN/dS on circadian genes likely associated with thermal adaptation in Squalius species (Moreno et al, 2021), and (ii) differences in gene expression between species inhabiting Atlantic (S. carolitertii) and Mediterranean climates (S. torgalensis) when exposed to increasing temperatures (Jesus et al, 2016(Jesus et al, , 2017. Thus, its hybrid origin might confer some advantage to S. pyrenaicus North at intermediate environmental conditions, as described in other organisms.…”

Circadian clock and temperature-associated genes vary along climate gradients in lichenized fungi

“…Given this fundamental role of the circadian clock in environmental adaptation, it is not surprising that biological rhythms vary along latitudinal as well as elevation gradients (Hut et al, 2013). Signals of adaptation along environmental gradients, in particular latitudinal gradients, have been observed in the circadian clock components of a variety of lineages, from insects (Helfrich-Förster et al, 2020, Lindestad et al 2022) and other animals (Moreno et al, 2021) to plants (Yerushalmi et al, 2011) and fungi (Ellison et al, 2011).…”

“…Many dN/dS approaches are used to analyze evolutionary patterns across species, rather than within species (Moreno et al, 2021), although some work has been done on intraspecific adaptation levels of viruses and other fast-evolving life forms (Pond et al, 2006). We were able to observe some evidence of selection across circadian-associated genes (Table S6), similar to that of the temperature-associated genes we analyzed (Table S7).…”