Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus

Abstract

Background Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-sized shallow-sea fish, Collichthys lucidus plays a vital role in the structure and functioning of marine ecosystem processes. C. lucidus has been shown to have an obvious population structure. Therefore, it is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure. Results A total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified and applied to elucidate the fine-scale genetic structure and local thermal adaptation of 8 C. lucidus populations. Population structure analysis based on all SNPs indicated that the northern group and southern group of C. lucidus have a strong differentiation. Moreover, 314 SNPs were found to be significantly associated with temperature variation, and annotations of genes containing temperature-related SNPs suggested that genes were involved in material (protein, lipid, and carbohydrate) metabolism and immune responses. Conclusion The high genetic differentiation of 8 C. lucidus populations may have been caused by long-term geographic isolation during the glacial period. Moreover, we suspected that variation in these genes associated with material (protein, lipid, and carbohydrate) metabolism and immune responses was critical for adaptation to spatially heterogeneous temperatures in natural C. lucidus populations. In conclusion, this study could help us determine how C. lucidus populations will respond to future ocean temperature rising.

Molecular population genetics and phylogeographic studies of Ligia exotica and Ligia cinerascens in East Asia

“…Second, two genetic lineages of L. exotica exhibited general allopatric distribution, which appears to be more evident in China along the coastline than in Japan. Similarly, such allopatric distribution patterns have been reported in many diverse marine taxa such as Collichthys lucidus (Richardson, 1844), Cyclina sinensis (Gmelin, 1791), Eriocheir De Haan, 1835, Monodonta labio (Linnaeus, 1758), Oratosquilla oratoria (De Haan, 1844), and Tubaca arcuate (De Haan, 1835) (Xu et al, 2009;Ni et al, 2012;Cheng and Sha, 2017;Zhao et al, 2017;Zhao et al, 2021;Hwang et al, 2022;Shih et al, 2022). Such studies suggested that the allopatric distribution observed in the coastline of China is caused by sea level fluctuations in the Pleistocene (Xu et al, 2009;Ni et al, 2014).…”

Systematic headwater sampling of white‐spotted charr reveals stream capture events across dynamic topography

“…In addition, a novel genetic cluster comprising populations in the Lake Biwa drainage was identified, likely due to the time resolution of the methods employed for the investigation of genetic structures and sample sites. NGS‐based genome‐wide SNP analyses generally have finer resolution than conventional haplotype analyses for mitochondrial DNA (Hirai, 2020; Zhao et al, 2021). In addition, genome‐wide analyses avoid accidental biases, such as mitochondrial replacement or selective sweeps (Christie & Beekman, 2017).…”

Comparative transcriptome analysis reveals sex bias in expression patterns of genes related to sex steroids and immunity in the skin of spinyhead croaker Collichthys lucidus

“…Spinyhead croaker, Collichthys lucidus , is a small shallow‐water fish with a short‐distance migratory habit, mainly distributed in the west coast of the Pacific Ocean, from Japan to the Philippines (Zhao et al ., 2021). It is a potential cultured species being exploited due to its delicious taste and high economic value.…”