Plethodon kentucki Range Limits

This GitHub repository is to accompany the following manuscript:
Emily F. Watts, Brian P. Waldron, and Shawn R. Kuchta. 2024. Hard edges, soft edges, and species range evolution: A genomic analysis of the Cumberland Plateau salamander

Methods

This repository is organized with scripts used to analyse the data used in this manuscript. These subtitles are in accordance with the subtitles used in the Materials and Methods in the manuscript.

Sampling, DNA Extraction, ddRAD, and Data Filtering

Ecological Niche Modeling

Includes the ODMAP protocol and the script we used to apply 'SDMTune' to parameterize our models.

Popultation Genetic Structure

Includes the script used to apply 'tess3r' and sNMF using 'LEA,' the script used to apply 'conStruct,' the DAPC script, and the script employing the R package 'poppr' to quantify genetic variation.

Isolation by Distance and Isolation by Environment

Contains the R scripts used to apply 'BEDASSLE' and apply the multiple matrix regression with randomization (MMRR).

Gene Flow and Effective Population Size

Contains the parm files for the east and west clusters and the scripts used to call MIGRATE-N.