Limited hybridization and introgression despite stocking among endemic Interior Highlands black basses (Centrarchidae: Micropterus)

Aim Smallmouth Bass (Micropterus dolomieu; SMB) are globally popular among anglers and have been widely introduced (i.e., stocked) for population management and sportfishing. Importantly, stocking was prevalent before cryptic diversity within the SMB complex was known, which now includes three newly elevated species: Neosho Bass (M. velox; NB), Little River Bass (M. sp. cf. dolomieu Little River; LRB), and Ouachita Bass (M. sp. cf. dolomieu Ouachita River; OB). We sought to quantify population structure and hybridization and introgression in these three recently described species. Location Species-level diversity, particularly in the basin-restricted LRB and OB in the Ouachita Mountains within the Central Interior Highlands (CIH), North America, suggests the presence of distinct genetic variation that could be eroded by introgression.  Methods We estimated interspecific introgression and intraspecific population differentiation in the Smallmouth Bass species complex (SMB-C) using 472 s..., Individual fish were captured by hook-and-line angling or boat electrofishing. Small clips (~12–15mg) of fin tissue were excised from the upper caudal fin of the fish and placed in 95% ethanol buffer solution, and fish were immediately released. Genomic DNA was extracted from fin clips using DNeasy Blood and Tissue Extraction Kits (QIAGEN), and samples were processed at the Center for Aquaculture Technology (CAT; San Diego, CA, USA)., We recommend the raw .vcf file be processed using standard software on a high-efficieny computing cluster. , # Reproduce analyses for the Central Interior Highlands Hybridization project \[Gunn et al. 2023] Follow the steps listed below in the Analyses section to reproduce analyses for this study. Each step below gives a summary of the analysis and directs you to a general code file (e.g., snolh_structure_analysis.Rmd below in Analysis 1) which then works through the analysis step-by-step. This general file will usually point you to other Rmd code, bash shell scripts, or python scripts. # Project: Central Interior Highlands Hybridization: Spotted, Smallmouth, Neosho, Ouachita, and Little River Bass (SNOLH) Investigating hybridization and population structure among and within the black basses (genus Micropterus) in the Central Interior Highlands (CIH) ecoregion, including natural and anthropogenic hybridization between Spotted Bass (SPB; Micropterus punctulatus) and species within the Smallmouth Bass species complex (SMBC): Smallmouth Bass (SMB; M. dolomieu), the newly elevated Neosho Bass (...## 研究目标 小口黑鲈（Smallmouth Bass, SMB，学名*Micropterus dolomieu*）在全球范围内深受垂钓爱好者青睐，且为开展种群管理与休闲垂钓活动，已被广泛引种（即放流）。值得注意的是，在小口黑鲈复合群的隐存多样性被探明之前，放流活动就已极为普遍；如今该复合群已被新划定为三个物种：尼舒黑鲈（Neosho Bass, NB，*M. velox*）、利特尔河黑鲈（Little River Bass, LRB，*M. sp. cf. dolomieu Little River*）以及沃希托黑鲈（Ouachita Bass, OB，*M. sp. cf. dolomieu Ouachita River*）。本研究旨在量化这三个新近定名物种的种群结构、杂交情况与基因渐渗现象。 ## 研究区域 该区域的物种多样性，尤其是分布于北美中部内陆高地（Central Interior Highlands, CIH）沃希托山脉、仅局限于特定流域的LRB与OB，提示其存在独特的遗传变异，而这类变异可能因基因渐渗而丢失。 ## 研究方法 本研究采用472个[原文此处内容存在截断]位点，对小口黑鲈复合群（SMB-C）的种间基因渐渗与种内种群分化情况进行评估。研究人员通过手竿垂钓或船载电捕的方式捕获实验个体，从鱼的尾鳍上缘剪下约12~15毫克的鳍组织样本，将其置于95%乙醇缓冲液中保存，随后立即将鱼只放归自然。使用DNeasy血液与组织提取试剂盒（QIAGEN）从鳍组织样本中提取基因组DNA，样本处理工作在美国加利福尼亚州圣地亚哥的水产养殖技术中心（Center for Aquaculture Technology, CAT）完成。建议使用高性能计算集群上的标准软件对原始.vcf文件进行处理。 # 重现中部内陆高地杂交项目分析（Gunn等，2023） 请按照下述分析部分列出的步骤重现本研究的分析流程。下述每个步骤均会对分析内容进行概述，并指引至对应的通用代码文件（例如分析1中的`snolh_structure_analysis.Rmd`），该文件将逐步完成整个分析流程。此类通用文件通常会指向其他R Markdown（Rmd）代码文件、Bash Shell脚本或Python脚本。 # 研究项目：中部内陆高地杂交：斑黑鲈、小口黑鲈、尼舒黑鲈、沃希托黑鲈与利特尔河黑鲈（SNOLH） 本研究旨在探究中部内陆高地（CIH）生态区内黑鲈属（*Micropterus*）物种种间及种内的杂交与种群结构，包括斑黑鲈（Spotted Bass, SPB，*Micropterus punctulatus*）与小口黑鲈复合群（SMBC）各物种——小口黑鲈（SMB，*M. dolomieu*）以及新近定名的尼舒黑鲈等——之间的自然杂交与人为杂交现象。