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 (...