Smith et al. 2021 - Establishing conservation units to promote recovery of two threatened freshwater mussel species (Bivalvia: Unionida: Potamilus). Ecology and Evolution
Information about files:
- amponly_ind_assignments.csv - Designations to create the dataframe for P. amphichaenus only
- Pot_cov.csv - covfile to link metadata to genotype data
- Potamilus_RAD.R - R script used for data upload, filtering, and analyses. Datasets for external analyses were created using this script (e.g., fasta, structure)
- Report_DPota20-4942_SNP_2.csv - SNP calls from DArTSoft14 pipeline and associated metadata. This file contains 65,465 SNPs for 91 individuals (after exluding one poor sample) that were further filtered for analysis
- rm_PohiBra036.csv - Cull sample PohiBra036 due to poor genotyping
- stronly_ind_assignments.csv - Designations to create the dataframe for P. streckersoni only
- Potamilus_GBS_tree.tre - Phylogeny generated by BEAST from genotype by sequencing (DArT) data
- Potamilus_ND1_tree.tre - Phylogeny generated by BEAST from ND1 sequence data
Notes:
- Raw reads are deposited in the SRA (BioProject ID: PRJNA663379) and sample accession numbers can be found in Table 1 of Smith et al. 2021
- ND1 sequences used for mitochondrial data analysis are deposited on GenBank and accession numbers can be found in Table 1 of Smith et al. 2021
- Data for mapping has to be downloaded from public repositories (USGS, Natural Earth)