Additional file 3 of Molecular characterisation of Pinus sylvestris (L.) in Ireland at the western limit of the species distribution
Creators: name: Belton, Samuel
name: Cubry, Philippe
name: Roche, Jenni R.
name: Kelleher, Colin T.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Table S2. Chloroplast microsatellite (cpSSR) primers used to genotype Pinus sylvestris individuals in this work. Table S3. Nuclear microsatellite (nSSR) primers used to genotype Pinus sylvestris individuals in this work. Table S4a. Results of SAMOVA analysis, unconstrained by geographic data. Table S4b. Results of SAMOVA analysis, constrained by geographic data. Table S5. Estimates of haplotype genetic diversity (HCP) and expected heterozygosity (He) based on chloroplast (cpSSR) and nuclear (nSSR) SSR genotyping of Pinus sylvestris populations from various regions across its distribution range. Mean values are ± S.D. Table S6. Estimates of HCP based on cpSSR loci variation in Pinus sylvestris. In each case, He for Irish trees sampled in this work have been re-estimated according to the loci subsets indicated for different works. Figure S1. Mean Nei’s standard and Bruvo’s genetic distance between Scots pine individuals genotyped at cpSSR markers in each sampling population. Error bars are ± S.E. Figure S2. Pairwise FST comparisons between sampled populations. Estimates are based on variation in cpSSR allelic frequency according to Nei (1987). Values which are significantly different from zero are marked with asterisks (*p ≤ 0.05; **p ≤ 0.01; p*** ≤ 0.001; n = 348). Figure S3. Genetic diversity (He) and allelic richness (rarefaction down to 14 nSSR alleles) for each population. Error bars are 95% CIs derived from 1,000 bootstrap permutations of the data. Estimates in this case were calculated after removing the size loci (PtTX3116, SPAC11_6, psy117, PtTX3107, psy12 and psy125) displaying null allele frequencies above 10%. Figure S4. Pairwise RST comparisons between sampled populations. Estimates are based on variation of nSSR allele size differences. Values which are significantly different from zero are marked with asterisks (*p ≤ 0.05; **p ≤ 0.01; p*** ≤ 0.001; n = 344). Figure S5. Mean (a) Nei’s standard and (b) Bruvo’s genetic distance between Scots pine individuals genotyped at nSSR markers in each sampling population. Error bars are ± S.E. Figure S6. Distribution of r estimated under maximum likelihood using nSSR allele variation in sampled Scots pine (Pinus sylvestris) trees. Figure S7. Distribution of r estimated under maximum likelihood for each population (including the three and four genotypes from Norway and Scotland (Scottish (Coillte) were samples from a breeding population), respectively) based on nSSR variation in sampled Scots pine (Pinus sylvestris) trees. Figure S8. Frequency of different pedigree relationships inferred under ML for each population (including the three and four genotypes from Norway and Scotland (Scottish (Coillte)), respectively) based on nSSR variation in sampled Scots pine (Pinus sylvestris) trees. Figure S9. Principal Coordinates Analysis (PCoA) of the cpSSR allelic composition of each Scots pine (Pinus sylvestris) population. Shown are the first and second principal coordinates. Labels are coloured according to population separation in the SAMOVA analysis at K=2. Coloured shapes are also drawn around these points to assist in interpretation. Figure S10. Results of STRUCTURE analysis of Scots pine (Pinus sylvestris) nSSR data. In this case, six loci (PtTX3116, SPAC11_6, psy117, PtTX3107, psy12 and psy125) displaying null allele frequencies above 10% were removed prior to STRUCTURE runs. (a) (i) Mean posterior probability values of K (L(K)), error bars are ± S.D. (ii) Delta K values used to infer the main structure of the data. (b) Frequency of K groups within each sampling population including those located in Spain, France and Norway (inset). (c) Bar plots of admixture coefficients for each sampled individual. Figure S11. Principal Coordinates Analysis (PCoA) of the nSSR allelic composition of each Scots pine (Pinus sylvestris) population. Shown are the first and second principal coordinates. Labels are coloured according to the null allele-adjusted STRUCTURE group (K=2) which is most frequent in each population. Coloured shapes are also drawn around these points to assist in interpretation. Loci (PtTX3116, SPAC11_6, psy117, PtTX3107, psy12 and psy125) which displayed null allele frequencies above 10% were removed prior to analysis. Figure S13. Results of an analysis of genotype groups (K) using TESS3. (a) Given are the cross-validation (CV) scores based on the root-mean squared errors between the genotypic frequencies predicted from a training set to those computed from a test set (i.e., genotype likelihood) for each locus. (b) The frequency of K groups within each population are given, including (inset) populations from Spain, France and Norway (for Norway only three individual are used). (c) Individual K ancestral proportions for each individual. Figure S14. Estimates of expected heterozygosity (He) for Pinus sylvestris from three different regions based on 18 nSSR loci (grey) and a reduced set of 12 loci (white). The latter remained after removing six loci (PtTX3116, SPAC11_6, psy117, PtTX3107, psy12 and psy12) which displayed null allele frequencies above 10%. Error bars are 95% CI values derived from 1,000 bootstrap permutations of the data.