DOI: 10.5061/dryad.573n5tbnb
title: R code from: Evidence for widespread inter-basin vicariance of fishes associated with quiescent geologic features in the southeastern United States

description: Stream captures are implicated as drivers of speciation in many groups of
 lotic fishes. In the southeastern United States, numerous stream-dwelling
 animals possess restricted trans-divide populations at localities where
 quiescent geologic features intersect drainage divides, suggesting
 potential evidence for inter-basin vicariance via stream capture. However,
 there has not yet been a comprehensive quantitative biogeographical
 analysis of these patterns. In the associated paper, we present evidence
 for widespread patterns of evolutionarily recent inter-basin vicariant
 events across major geologic structures that have been tectonically
 dormant for many millions of years. We used Kriging spatial interpolation
 analysis on a dataset of 5434 sample sites (~188,000 species-specific
 distribution records) that included ~375 fish species to visualize
 patterns of aberrant fish distribution records across highland
 physiographic regions of Alabama, Georgia, Tennessee, and the Carolinas
 (USA). These patterns were further explored with a comprehensive synthesis
 of published fish distribution maps and museum records. We collected
 cytochrome-b sequence data from 337 individual fish of 14 representative
 “transferred” species (20 intraspecies population pairs) from ~11 paired
 localities across the Brevard Fault, Allatoona Fault, and Blue Ridge
 Escarpment implicated in inter-basin captures to estimate coarse timing of
 vicariant events and to infer distributional artefacts caused by
 anthropogenic introduction. A heatmap generated from Kriging analysis
 shows a concentration of aberrant distributional records of fishes around
 the Brevard Fault Zone and the Blue Ridge Escarpment and other more minor
 quiescent geologic features. Our synthesis of museum records and fish
 distribution literature revealed documented evidence of a total of 115
 species-transfer incidences (52 taxa) that exhibit inter-basin transfer
 along these features. Of the 20 intraspecies population pairs examined for
 genetic diversity, measures of phi-ST and associated AMOVA p-values
 indicate significant levels of genetic divergence for 13. Large-scale,
 quiescent geologic structures appear to drive localized vicariant events
 via stream capture through fostering differential erosional rates of
 captor and victim tributaries. Stream capture emerges as a prevalent
 process underlying inter-basin range-expansion and diversification of
 aquatic animals in upland regions. This repository includes R
 code used for geospatial analyses, as well as R code used for population
 genetic analyses. All genetic data is available for download and future
 use through NCBI GenBank. Fish assemblage data can be obtained through the
 relevant state agencies (see paper's data availability statement).
description: # R code from: Evidence for widespread inter-basin vicariance of fishes
 associated with quiescent geologic features in the southeastern United
 States Dataset DOI:
 [10.5061/dryad.573n5tbnb](https://doi.org/10.5061/dryad.573n5tbnb) ##
 Description of the data and file structure These files include R scripts
 for geospatial Ordinary Kriging analysis and analyses of genetic
 divergence, each stored as a separate downloadable R-markdown script. In
 addition to .Rmd scripts, the geospatial analyses are also included as a
 knitted PDF with embedded outputs and visuals. ### Files and variables
 #### File: Updated_code_for_BFZ_genetic_analyses.Rmd
 **Description:** Genetic analysis R code, in .Rmd format. **File:
 Brevard_Fault_Spatial_Analysis_Code_Dryad.pdf**  **Description:** Spatial
 analysis R code, in knit PDF format with embedded outputs and visuals
 **File: Brevard_Fault_Spatial_Analysis_Dryad.Rmd**
 **Description:** Spatial analysis R code, in .Rmd format. ## Code/software
 Needed programs: R version 4.3.2, including the following packages: dplyr,
 data.table, gstat, adegenet, poppr, and ade4. Other useful packages (but
 not essential for core analyses) include mapview, sf, lattice, stars,
 terra, and ggplot2. Working directory and input file information will need
 to be changed to accommodate the user's own input file path. ##
 Access information Other publicly accessible locations of the data: * NCBI
 GenBank repository (see related paper's Appendix S1, Supporting
 information) *
 [https://www.deq.nc.gov/about/divisions/water-resources/water-sciences-section/biological-assessment-branch/fish-community-assessment-data](https://www.deq.nc.gov/about/divisions/water-resources/water-sciences-section/biological-assessment-branch/fish-community-assessment-data)