Genetic mapping files

High-throughput genetic mapping (Folder “Genetic mapping files”) The datasets in items 1 to 3 relate to high-throughput genotyping, supplemented with microsatellite genotyping to ascertain parentage of progeny with more than a single sire and/or dam, and to map the microsatellite markers. Initial bioinformatic processing is described in the “Data_description” file provided, and was followed by formatting for genetic mapping analysis using LepMap3 software (Rastas 2017). Rastas, P., 2017 Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics 33: 3726-3732. doi: 10.1093/bioinformatics/btx494 https://sourceforge.net/p/lep-map3/wiki/LM3 Home/ Most files are Excel files of genotypes and allele counts, or genotypes in the format required by LepMap3, or text files. 1. Microsatellite sequences found in the guppy female and male genome assemblies using the PERF software v0.4.5 (Avvaru et al., 2018). Excel files: Guppy_genes_and_microsats_on_femaleLG12_malechr12_KK07July2021 Guppy_genes_and_microsats_on_unplaced_scaffolds_updated3rdNov2020 Avvaru, A. K., D. Sowpati and R. Mishra, 2018 PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences Bioinformatics 34: 943–948. doi: 10.1093/bioinformatics/btx721 2. Excel file with information about genes on the guppy sex chromosome in the male and female assemblies, and on the homologous chromosome (Xm8) in the platyfish, Xiphophorus maculatus: “Guppy_female_Gene_positions_on_Guppy_male_and_Platyfish” 3. Genetic map input and results files a. Folder “Files for all individual families” contains sparse maps, estimated mostly with microsatellite markers (including some families not analysed in detail, and therefore not listed in Supplementary Table 1 of the associated manuscript: AHPGrp3) b. ALP2_B2_LAH_QLP1_BI_QHPGrp5_mappings_2021: microsatellite marker genotypes, showing assignments of parentage for individual progeny in the ALP2B2 family. HIGH-THROUGHPUT GENOTYPING EXPERIMENTS (3 folders): The list below shows the contents of the folders for each experiment. c. EXPERIMENT 2 (NGS1242. LAH, QHPG5 and ALP2B2 families, plus guppy natural population samples) i. NGS_1242_DNA-samples_for.review.Deborah.190212 ii. SNPs targeted: File “probeStats_high-specificity_ST5041G_1_1781.xlsx” iii. hiseq_platelayouts_Dec2018 iv. Genotypes_targeted_Bowtie2-Genome_Freebayes-ploidy2-min-count-8_NGS1242_2019-05-20 (genotyping results with allele counts) d. EXPERIMENT 3 (NGS2589. QHPG5 family plus Micropoecilia picta, parae and bifurca) i. NGS2589_sample_form_sn_211222 ii. probe_ST5271G_1_3272_10k-selection iii. LGCG plates layout 1.2 Experiment 3 iv. Variants_all_GMCF8_QHPG5_NGS2589_2022-02-21 (genotypes, allele counts) v. Variants_all_GMCF8_picta_NGS2589_2022-02-21 (genotypes, allele counts) vi. Variants_all_GMCF8_parae_NGS2589_2022-02-21 (genotypes, allele counts) vii. Variants_all_GMCF8_bifurca_NGS2589_2022-02-21 (genotypes, allele counts) viii. “EX3_LG12_SNPs_coded_for_LepMap3.txt”: QHPG5 family genotypes for mapping e. EXPERIMENT 4 (NGS2945. QLP1B1 family plus Micropoecilia species as in Experiment 3, but with smaller sample sizes) i. LG12 and LG16 targets: file “probeStats_ST5271G_3_3633” ii. Names of samples and positions in the plates: File ‘NGS2589_sample_form v2’ iii. July 2022 plate layout for experiment 4-1 iv. Data_description.pdf: file with description of bioinformatic analysis by LGCG v. Genotypes_targeted_Bowtie2-Genome_all-min-count-8_NGS2945_2022-10-22 (Excel file with genotypes, allele counts) vi. LG16 for LepMap3: File “EX4_QLP1B_LG16_SIBSHIPs3,5,2_tabbed_for_LepMap3.xlsx” vii. LG12 for LepMap3: File “EX4_QLP1B_LG12_tabbed_for_LepMap3.txt”, and “EX4_QLP1B_LG12_SIBSHIPs3,5,2_tabbed_for_LepMap3.xlsx”