README:

This dataset belongs to the thesis: McIntyre, J. 2020, 'Genetic Markers of Anthelmintic Resistance in Gastrointestinal Parasites of Ruminants'

Supervised by Prof. E. Devaney and Dr. R. Laing. External supervisors Dr. M. Vickers and Dr. L. King with the Agricultural and Horticultural Development Board Beef and Lamb.

Funders: BBSRC, AHDB and KTN.

Data is presented as appendices for the thesis. Filenames are descriptive and a short description of each file is below. Where futher explanation is of benefit, this is provided within the individual files. For example, Excel files contain a 'README' explanatory worksheet. In addition, a consent form used to gather material and data from farmers which was later used for Chapter 3 is provided.

Appendix 1 Arlequin parameters chosen.docx
The parameters selected for the microsatellite analysis.
Appendix 2 Bioinformatics Scripts.docx
The relevant bioinformatics scripts used. These will be uploaded onto GitHub in the future.
Appendix 3 ddRAD-Seq de-multiplexed summary statistics.docx
The Stacks process_radtags summary statistics for the Farm 2 individuals sequenced using ddRAD-Seq.
Appendix 4 ddRAD-Seq data (Farm 2).xlsx
The FST, F’ST and DEST results from the ddRAD-Seq analysis. Only those results greater than each threshold are included. 
Appendix 5 Pool-Seq High 10 kb windows identified on both Farms 2 and 3.xlsx
The 10 kb regions identified as genetically differentiated on both farms in the Pool-Seq analysis.
Appendix 6 Pool-Seq High 10 kb windows identified in the Farm 2 analysis.xlsx
Appendix 7 Pool-Seq High 10 kb windows identified in the Farm 3 analysis.xlsx
These contain the Pool-Seq data (FST, genes and predicted proteins) for each farm analysis. Only those 10 kb windows greater than the thresholds are included.
Appendix 8 Comparison of ddRAD-Seq Farm 2 SNPs with Pool-Seq Farm 2.xlsx
Appendix 9 Comparison of ddRAD-Seq Farm 2 SNPs with Pool-Seq Farm 3.xlsx
These contain the results after comparing the ddRAD-Seq Farm 2 data with the Pool-Seq data.
Appendix 10 Farm 2 GO analysis BIOMART output.xlsx
Appendix 11 Farm 3 GO analysis BIOMART output.xlsx
The information extracted using BIOMART is presented, with the four gene categories shown (neuronal, lipid, male and female related terms).
Appendix 12 Comparison of Pool-Seq with Choi et al 2017.xlsx
Includes the results of the analysis comparing the Pool-Seq data from each farm with the results presented by Choi et al., 2017. 
Appendix 13 Comparison of Pool-Seq with H. contortus data provided by Dr R Laing.xlsx
Includes the results of the analysis comparing the Pool-Seq data from each farm with the H. contortus MHco3(ISE)xMHco18(UGA) results provided by Dr R Laing (unpublished data). 
Appendix 14 Comparison of Pool-Seq with O. volvulus Doyle et al 2017.xlsx
Includes the results of the analysis comparing the Pool-Seq data from each farm with the results presented by Doyle et al., 2017. 
Appendix 15 CNV logfiles for pgp.docx
Includes additional information regarding the identification of the pgp-3 and pgp-9 Tci2 genes.
Appendix 16 Published paper (open access)
McIntyre, J., et al. (2018). "Hidden in plain sight - Multiple resistant species within a strongyle community." Vet Parasitol 258: 79-87. 
Note, this is not included in the electronic appendices on Enlighten, but can be found using the following DOI: https://doi.org/10.1016/j.vetpar.2018.06.012