Flashball
06-27-2024, 07:24 AM
Source: https://www.pnas.org/doi/10.1073/pnas.2406734121
SI12. Phenotypes
From the imputed samples, we extracted the genotype information at 116 SNPs (50, 51) involved in diet, disease and pigmentation phenotypes. More specifically, we analysed 25 SNPs involved in diet adaptation and metabolism, 50 in immunity response and 39 from the HlrisPlex-S (52) set for the prediction of eye, hair and skin colours (Table S14). For the pigmentation prediction, we prepared an input file for the HlrisPlex-S webtool (https://hirisplex.erasmusme.nl/) following its manual for formatting and results interpretation. Sample-by-sample phenotype prediction and genotypes (as counts of the effective alleles in the form 0, 1 or 2) are reported in Table S15, while sample-by-sample genotypes of the other markers are reported in Table S16.
We then grouped the ancient individuals in different cohorts: French Iron Age (FrenchIA; (35)), Koksijde main ancestry group, Koksijde outliers, Early Medieval English samples with a CNE ancestry (England_CNE; (34)) and estimated the allele frequency of the phenotypic markers. We then compared these groups and the two modern datasets (GoNL and MinE; (43–45)) performing an ANOVA test and applying a Bonferroni’s correction on an alpha value of 0.05 for the number of tested SNPs to set the significance threshold. For the significant variants, we performed a post-hoc Tukey test to identify the significantly different pairs of groups (Table S16). Also the allele frequency for the Wulpen site have been estimated and reported in Table S16, but it was excluded from the ANOVA analysis due to its small sample size.
We can therefore say that there have always been phenotypic variations among the Gauls as much as among the current ethnic French, so nothing surprising.
https://cdn.discordapp.com/attachments/998648108147822663/1255138270682153113/image_2024-06-25_14-28-13.png?ex=667e045b&is=667cb2db&hm=bf83f06923ec189b784f45310203aa1119a96be7e87f3a9 9cd426040827badce&
https://cdn.discordapp.com/attachments/998648108147822663/1255180837570478080/M5pI_Z1a.png?ex=667e2bff&is=667cda7f&hm=c66442d9cdeb97f006b910e22ff162b0aab47226059c6cc e6da8910e5d5f9ada&
Prediction of pigmentation for some modern ethnic French samples
https://cdn.discordapp.com/attachments/998648108147822663/1255152672005292063/FrenchPredictionTrait.png?ex=667e11c4&is=667cc044&hm=ae39ce9c1189a0b35f2defde66c0f933a9f67ae0697a00c 0ccecebe06534c52e&
https://cdn.discordapp.com/attachments/998648108147822663/1255152673397673984/FrenchPredictionTrait2.png?ex=667e11c4&is=667cc044&hm=335962ec120257a592efeb49fd69e5d969a2f5d07ef1281 bab48a115c2d41afe&
SI12. Phenotypes
From the imputed samples, we extracted the genotype information at 116 SNPs (50, 51) involved in diet, disease and pigmentation phenotypes. More specifically, we analysed 25 SNPs involved in diet adaptation and metabolism, 50 in immunity response and 39 from the HlrisPlex-S (52) set for the prediction of eye, hair and skin colours (Table S14). For the pigmentation prediction, we prepared an input file for the HlrisPlex-S webtool (https://hirisplex.erasmusme.nl/) following its manual for formatting and results interpretation. Sample-by-sample phenotype prediction and genotypes (as counts of the effective alleles in the form 0, 1 or 2) are reported in Table S15, while sample-by-sample genotypes of the other markers are reported in Table S16.
We then grouped the ancient individuals in different cohorts: French Iron Age (FrenchIA; (35)), Koksijde main ancestry group, Koksijde outliers, Early Medieval English samples with a CNE ancestry (England_CNE; (34)) and estimated the allele frequency of the phenotypic markers. We then compared these groups and the two modern datasets (GoNL and MinE; (43–45)) performing an ANOVA test and applying a Bonferroni’s correction on an alpha value of 0.05 for the number of tested SNPs to set the significance threshold. For the significant variants, we performed a post-hoc Tukey test to identify the significantly different pairs of groups (Table S16). Also the allele frequency for the Wulpen site have been estimated and reported in Table S16, but it was excluded from the ANOVA analysis due to its small sample size.
We can therefore say that there have always been phenotypic variations among the Gauls as much as among the current ethnic French, so nothing surprising.
https://cdn.discordapp.com/attachments/998648108147822663/1255138270682153113/image_2024-06-25_14-28-13.png?ex=667e045b&is=667cb2db&hm=bf83f06923ec189b784f45310203aa1119a96be7e87f3a9 9cd426040827badce&
https://cdn.discordapp.com/attachments/998648108147822663/1255180837570478080/M5pI_Z1a.png?ex=667e2bff&is=667cda7f&hm=c66442d9cdeb97f006b910e22ff162b0aab47226059c6cc e6da8910e5d5f9ada&
Prediction of pigmentation for some modern ethnic French samples
https://cdn.discordapp.com/attachments/998648108147822663/1255152672005292063/FrenchPredictionTrait.png?ex=667e11c4&is=667cc044&hm=ae39ce9c1189a0b35f2defde66c0f933a9f67ae0697a00c 0ccecebe06534c52e&
https://cdn.discordapp.com/attachments/998648108147822663/1255152673397673984/FrenchPredictionTrait2.png?ex=667e11c4&is=667cc044&hm=335962ec120257a592efeb49fd69e5d969a2f5d07ef1281 bab48a115c2d41afe&