Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil.
Genome Biol Evol. 2024 Sep 3;16(9). doi: 10.1093/gbe/evae194.
Understanding the combined effects of environmental heterogeneity and evolutionary processes on marine populations is a primary goal of seascape genomic approaches. Here, we utilized genomic approaches to identify local adaptation signatures in Littoraria flava, a widely distributed marine gastropod in the tropical West Atlantic population. We also performed molecular evolution analyses to investigate potential selective signals across the genome. After obtaining 6,298 and 16,137 single nucleotide polymorphisms derived from genotyping-by-sequencing and RNA sequencing, respectively, 69 from genotyping-by-sequencing (85 specimens) and four from RNA sequencing (40 specimens) candidate single nucleotide polymorphisms were selected and further evaluated. The correlation analyses support different evolutionary pressures over transcribed and non-transcribed regions. Thus, single nucleotide polymorphisms within transcribed regions could account for the genotypic and possibly phenotypic divergences in periwinkles. Our molecular evolution tests based on synonymous and non-synonymous ratio (kN/kS) showed that genotype divergences containing putative adaptive single nucleotide polymorphisms arose mainly from synonymous and/or UTR substitutions rather than polymorphic proteins. The distribution of genotypes across different localities seems to be influenced by marine currents, pH, and temperature variations, suggesting that these factors may impact the species dispersion. The combination of RNA sequencing and genotyping-by-sequencing derived datasets provides a deeper understanding of the molecular mechanisms underlying selective forces responses on distinct genomic regions and could guide further investigations on seascape genomics for non-model species.
了解环境异质性和进化过程对海洋种群的综合影响是景观基因组学方法的主要目标。在这里，我们利用基因组学方法来识别热带西大西洋种群中广泛分布的海洋腹足类动物——Littoraria flava 的局部适应特征。我们还进行了分子进化分析，以研究整个基因组中潜在的选择信号。在分别从测序和 RNA 测序获得 6,298 和 16,137 个单核苷酸多态性后，从测序中获得 69 个（85 个样本）和从 RNA 测序中获得 4 个（40 个样本）候选单核苷酸多态性被选择并进一步评估。相关性分析支持转录和非转录区域的不同进化压力。因此，转录区域内的单核苷酸多态性可能解释了近海螺的基因型和表型差异。我们基于同义与非同义比值（kN/kS）的分子进化测试表明，包含假定适应性单核苷酸多态性的基因型差异主要源于同义或 UTR 替换，而不是多态性蛋白。不同地理位置的基因型分布似乎受到海洋流、pH 值和温度变化的影响，表明这些因素可能影响物种的扩散。RNA 测序和测序衍生数据集的组合提供了对不同基因组区域选择压力响应的分子机制的更深入理解，并可以指导对非模式物种的景观基因组学的进一步研究。
