DOI: 10.17617/3.z1vcpt
title: Data and code associated with "Reduced levels of relatedness indicate that great-tailed grackles disperse further at the edge of their range"

description: The files included in this repository contain the data and scripts required for the analyses presented in 
Lukas, Blackwell, Edrisi, Hardy, LeGrande, Marfori, McCune, Sevchik, Smith, Logan (2024)
"Reduced levels of relatedness indicate that great-tailed grackles disperse further at the edge of their range" 

Description of the files:
1) Lukas_GrackleDispersal_code.qmd
The manuscript and code for all analyses in the quarto format, for the open software R. The file can also be opened with any text editor. Contains all the scripts to load the relevant data (files 2-4), process it, generate the results and the figures.

2) Lukas_GrackleDispersal_data_genepop_Woodland.txt
Processed genotype data for individuals sampled in Woodland and Sacramento, California. It is in the genepop format: each row contains information for one individual; the first column has the identifier for the individual; the remaining columns contain the information on the alleles at each locus, with the numbers reflecting the four different bases, and two subsequent columns representing the alleles at one locus.

3) Lukas_GrackleDispersal_data_genepop_Tempe.txt
Processed genotype data for individuals sampled in Tempe, Arizona. It is in the genepop format: each row contains information for one individual; the first column has the identifier for the individual; the remaining columns contain the information on the alleles at each locus, with the numbers reflecting the four different bases, and two subsequent columns representing the alleles at one locus.

4) Lukas_GrackleDispersal_data_individualinfoforrelatedness.csv
Contains information for all individuals in the sample: their name, their unique identification, the coordinates at which they were trapped (latitude, longitude), the location at which they were first relocated (latitude, longitude), their sex (M=male, F=female), their age (A=adult, J=juvenile), the population in which they live, and the latitude and longitude we used as their location.

5) Lukas_GrackleDispersal_RawSequences_Indeces.txt
The index files linking the raw genetic sequences deposited at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658480/ to the respective individuals.

14185_3270_204492_HHTL7BGXT_Index_1 contains the information required to process the raw genotype file 14185_3270_204492_HHTL7BGXT_I1_ATCACG_R1.fastq.gz

14185_3270_204492_HHTL7BGXT_Index_2 contains the information required to process the raw genotype file 14185_3270_204493_HHTL7BGXT_I2_CGATGT_R1.fastq.gz

14185_3270_204492_HHTL7BGXT_Index_3 contains the information required to process the raw genotype file 14185_3270_204494_HHTL7BGXT_I3_TTAGGC_R1.fastq.gz

14185_3270_204492_HHTL7BGXT_Index_4 contains the information required to process the raw genotype file 14185_3270_204495_HHTL7BGXT_I4_Grackles_TGACCA_R1.fastq.gz

11076_3270_105008_H2HF7BGXC_Index_1 contains the information required to process the raw genotype file 11076_3270_105009_H2HF7BGXC_ASI2_CGATGT_R1.fastq.gz

11076_3270_105008_H2HF7BGXC_Index_2 contains the information required to process the raw genotype file 11076_3270_105009_H2HF7BGXC_ASI2_CGATGT_R1.fastq.gz

11076_3270_105008_H2HF7BGXC_Index_3 contains the information required to process the raw genotype file 11076_3270_105010_H2HF7BGXC_ASI3_TTAGGC_R1.fastq.gz

11076_3270_105008_H2HF7BGXC_Index_4 contains the information required to process the raw genotype file 11076_3270_105011_H2HF7BGXC_ASI4_TGACCA_R1.fastq.gz

11076_3270_105008_H2HF7BGXC_Index_5 contains the information required to process the raw genotype file 11076_3270_105012_H2HF7BGXC_LDMI5_ACAGTG_R1.fastq.gz
description: R, 4.3.3