Adaptive mechanisms for cold temperature
A good understanding of how ecological variants of fishes can affect their population structure will provide more comprehensive implications for conservation management and decision-making (Li, Xue, Zhang, & Liu, 2018). Water temperature is one of the most important abiotic factors that influence the phenotypes and habitats of aquatic organisms (Chen, Farrell, Matala, Hoffman, & Narum, 2018). As an important environmental stressor, low and high temperatures have broad biological effects on marine organisms. These thermal effects generate intense selective pressures on several genes and genome regions.
In this study, selective sweep was conducted to identify the thermally affected genes between the northern and southern populations of S. japonica . The strategy of combining alternative statistical approaches in detecting selective signatures can provide sound results by decreasing false-positive rates. We evaluated the genetic attributes of the candidate genes relative to the genomic background. We scanned the genome-wide variations using F ST and π ratio values. The cold- and high-temperature adaptation conditions shared only two candidate genes.
A total of 81 candidate genes shared by both the π ratio andF ST analysis in the RS population were recognized as potentially affected genes related to cold adaptation. Cold adaptation and acclimatization studies suggested that more than one mechanism is involved in the biological response to cold stress (White, Alton, & Frappell, 2012; Liu et al., 2018). Consistent with our expectations from the biological complexity of cold adaptation, several different processes, rather than one particular term or pathway, were highlighted by our selection tests. Low temperatures may influence energy metabolism. Nine selection genes (low-density lipoprotein receptor [LDLR ], ZBTB20 ,PICALM , and nup35 ) were related to lipid metabolic process. Lipids are the main components of cytomembrane (Meer, Voelker, & Feigenson, 2008). A common cold adaptation mechanism for the cell is to manipulate the membrane lipid composition to maintain membrane fluidity and, correspondingly, proper membrane permeability and function of membrane protein complexes (e.g., transporters) (Russell &Nichols, 1999).
Previous studies showed that the permeability of cell membranes considerably changes under long-term low temperature conditions and damages the integrity and stability of cell membranes. The LDLRgene is one important candidate gene for cold adaptation. LDLR , a glycoprotein located on the surface of cells, mediates the endocytic uptake of LDL cholesterol in the liver, which is a key regulator of the metabolism of plasma low-density lipoprotein cholesterol. LDLR  is the most powerful determinant of variation in total cholesterol and LDL cholesterol levels (Hansen et al., 1997). This gene plays an essential role in protecting cell membrane integrity under cold stress. The strong selection pressure on this gene is useful in adapting to low temperatures. A similar result was also observed in the low-density lipoprotein receptor-related protein 5 (LRP5 ) gene, another gene member of low-density lipoprotein receptor of humans (Cardona et al., 2014). LRP5 shows strong signals of selection in indigenous Siberian human populations. LRP5 has a high expression in the liver of humans and plays a role in cholesterol metabolism. Natural selection of the LRP5 gene helps Siberian persons to cope with the cold climate. The TPO gene is involved in thyroid metabolism (Leonard, Snodgrass, & Sorensen, 2005). The thyroid determines the basal metabolic rate of the body. Natural selection of the TPO gene in the RS population may maintain the basal metabolic rate and stabilize lipid levels in the serum.
We also detected substantial adaptive evidence concerning ion exchange and transportation, which are processes that affect the fluidity and permeability of the cell membrane and directly and indirectly linked to thermal regulation. We identified a considerable number of genes that encode transporters (the MFS transportersSLC22A5 , SLC7A2 , and SLC25A5 ) and ion channels (e.g., the voltage-gated sodium channel SCN4B ) in the genome regions of the RS population under selective sweeps. For example,SLC22A5 is a specific transporter that exists in the membranes of cells and mitochondria involved in the uptake or release of carnitine. Four copies of SLC22A5 in the genome of S. japonicaindicated gene expansion. Carnitine is a carrier for long-fatty acids and facilitates their transport into the mitochondria for lipid oxidation. Defective SLC22A5 causes systemic carnitine deficiency, resulting in metabolic decompensation. SLC7A2functions as a permease involved in transporting cationic amino acids across the plasma membrane. These transporter and ion channel genes are crucial for transmembrane transport to maintain a stable balance between the internal and external environments of cells under cold temperature. Therefore, the genes that encode transcellular ion transporters and channel proteins are reshaped by natural selection under cold stress environment.
Smooth muscle contraction, which includes vasoconstriction and vasodilation, is another process implicated in cold adaptation. Two genes involved in this process that showed evidence of strong signals of selection are CPI17 (protein phosphatase 1 regulatory subunit 14A) and CACNB4 . CPI17 is the inhibitor of PPP1CA. It has more than 1000-fold inhibitory activity when phosphorylated, creating a molecular switch for regulating the phosphorylation status of PPP1CA substrates and smooth muscle contraction in the absence of increased intracellular Ca2+ concentration (Li et al., 2001). The CACNB4  gene encodes a calcium channel subunit expressed in the heart and increases peak calcium current that is important for cardiac muscle contraction under cold stress (Rouhiainen et al., 2016). Although no data on the heart rate of the populations are available, cold exposure is known to increase cardiac pressure. Thus, this efficient cardiovascular regulation might be a possible cold adaptive mechanism in the RS population. These genetic changes might facilitate the adaptation and survival of S. japonica in low-temperature areas.
Cell repair and clear necrotic organelles are also important processes of cold adaptation in the RS population. Interferon regulatory factor 1 (IRF1 ) is a transcriptional regulator that displays a remarkable functional diversity in regulating cellular responses (Oshima et al., 2004). Under cold stress, IRF1 causes cells to suspend proliferation to survive in adverse environmental conditions and also decisively triggers apoptosis when cell damage becomes irreparable, thereby preventing harmful cells from harming other normal cells. DnaJ homolog subfamily C member 10 is involved in the correct folding of proteins and the degradation of misfolded proteins (Oka, Pringle, Schopp, Braakman, & Bulleid, 2013). It promotes the apoptotic signaling pathway in response to endoplasmic reticulum stress.
The enrichment tests provided 50 significant GO terms and one KEGG pathway after FDR adjustment. The enrichment GO categories and KEGG pathways were primarily associated with cell apart, transmembrane transporter activity, tissue homeostasis, lipid metabolism, apoptosis, and vascular smooth muscle contraction. These functional clusters are biologically relevant to cold adaptations and essential in regulating mechanisms for fish to respond to a cold environment.