R code from: Evidence for widespread inter-basin vicariance of fishes associated with quiescent geologic features in the southeastern United States

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).