Supplementary information, PhD thesis "Bottleneck legacies and expansion consequences: the Italian wolf genomic make-up and the potential effect of anthropogenic hybridization on its evolutionary pathway"

Supplementary information regarding the chapters of my PhD thesis not published yet.

I uploaded only large Excel Tables which would negatively impact thesis readability.

Supplemental information for CHAPTER 3

Supplementary Table 1 – Whole-genome dataset. Yellow = related individual removed from the dataset; orange =  non-admixed Italian wolf; red = admixed Italian wolf; blue = non-admixed European wolf; purple = non-admixed dog; green = outgroup.

Supplementary Table 3 – List of genes associated with behavioral traits in dogs and captive wolves, tested using the ‘Behavioral genes shuffling’ approach.

Supplementary Table 5 – Gene ontology network results using STRING on genes within introgressed and validated regions in admixed Italian wolves (i.e., gene PREX2), and all the Italian wolves (the other genes). Green = functional enrichment for the candidate gene.

Supplemental information for CHAPTER 4

Supplementary Table 1 – The three datasets used in this study. DATASET1 = whole-genome data; DATASET2 = 170k SNPs data; DATASET3 = DNA samples analyzed for specific sociability loci. Yellow = dog whole-genomes intersected with 170k SNPs.

Supplementary Table 2 – Gene ontology network results using STRING on behavioral genes containing highly differentiated SNPs with effective (MOD-DEL and HIGH) or potential (MOD-NA) deleteriousness in DATASET1.

Supplementary Table 3 – Gene ontology network results using STRING on behavioral genes containing SNPs with significant FST differences between HYB and WIT in DATASET1.

Supplementary Table 4 – Table of sociability-related markers. Internal primers designed on ‘forward’ sequence are colored in green, while internal primers designed on ‘reverse’ sequence are colored in blue. ‘REF/ALT’ are the reference and alternative alleles, ‘Tm’ is the melting temperature, ‘GC%’ is the percentage of guanine and cytosine on the primer sequence.