Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae)

Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which i. local adaptation and the early stages of speciation can be clearly identified and distinguished, ii. the amount of genetic divergence driven by the two processes is similar, and iii. comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly colored reef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome-wide levels of divergence that are comparable among allopatric populations (Fst estimate = 0.0042) and sympatric species (Fst estimate = 0.0038). Population genetic, clustering and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fract...局域适应与物种形成早期阶段背后的种群基因组模式是否具有相似性？要解答这一问题，需搭建满足以下三项条件的研究体系：其一，可清晰识别并区分局域适应与物种形成早期阶段；其二，两类过程所驱动的遗传分化程度相近；其三，既可从分类学维度（针对局域适应）、也可从地理学维度（针对物种形成）开展重复比较。本研究在加勒比海域广布的色彩艳丽的珊瑚礁鱼类——鮨鲈属（*Hypoplectrus* spp.，俗称哈姆雷特鱼）中，恰好发现了符合上述条件的研究体系。研究对3个重复种群中的3个同域共存物种的126个个体的近10万个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）位点进行了基因分型；其全基因组分化水平在异域种群（Fst估算值为0.0042）与同域物种间（Fst估算值为0.0038）基本相当。种群遗传学、聚类分析与系统发育分析结果显示，局域适应与物种形成过程呈现极为相似的基因组模式，二者均展现出大量的……