Scripts

Contains all the scripts used for data analysis in the paper

Supporting Information_Tables S2-S4_Figures S1-S5

Contains Supporting Tables S2-S4 and Supporting Figures S1-S

Supporting Figure S7

Supporting Figure S7: Frequencies of the three possible unrooted tree topologies (panel A) and the six possible internal species pairings (panel B) for all chromosomes

Data Files

Contains input files for different species tree analyses and phylogenetic trees

All data

This folder contains the information related to the analyses as well as the important results and scripts. Folders are described in individual README within the subfolders

Supporting Table S1

Supporting Table S1: List of all flycatcher samples used in the study

Supporting Figure S6

Supporting Figure S6: Distribution of nucleotide diversity (π, panel A), genealogical sorting index (gsi, panel B), depth of the lowest common ancestor of all four flycatcher species relative to the root depth (panel C), frequencies of all 15 possible rooted tree topologies (panel D), and topology diversity index (tdi, panel E) for all chromosomes

Raw read for No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon

MiSeq platform (Illumina) raw reads as described in Promerová et al (2016). "No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon". The data file consists on a compressed file divided in 6 folders. Each folder (named e.g. lib1) contains reads from one sequencing lain. Inside there are individual fasta files with reads from one individual. Each individuals is coded (file name) with three codes separated by underscore: "sample code" + "family code" + "offspring code". Codes are listed in supplementary information in files "README.csv" including also used barre code for sample identification inside within libraries

MHC-I genotypes and family information

The file includes three sheets: (i) MHC-I genotypes (columns: individual ID, individual coverage, allele name and allele coverage), (ii) family information for 130 families (columns: family ID, male name male, female name and juvenile name), (iii) family information for 40 families used to estimate genetic architecture (columns: family ID, individual ID, status, sex, allele name and the relative coverage for each allele)

Family information, MHC genotypes and MHC haplotypes

The file includes three sheets: (i) family information for 140 families (columns: ID_family, Status, ID_individual, Sex); (ii) MHC genotypes (columns: ID_individual and genotypes for each locus); (iii) MHC haplotypes (columns: ID_family, ID_parent, Sex, Haplotype