Population structure and signals of local adaptation in Eugenia uniflora L. (Myrtaceae), a widely distributed species in the Atlantic Forest

Nicole Moreira Vetö**, Dragos Postolache**, Frank L. Guzman Escudero, Elia Vajana, Ricardo Burgo Braga, Fabiano Salgueiro, Rogério Margisi, Giovanni G. Vendramin, Andreia C. Turchetto-Zolet

** Equally contributing authors.

The folders LD analysis.zip, LEA analysis.zip and LFMM analysis.zip contain all input data and scripts used to run quality control (QC), linkage disequilibrium (LD), LEA and LFMM analyses in Vetö, Postolache et al. (2022).

LD analysis.zip

• analysis.R/genomics.R: R scripts used to run QC and LD analysis.
• Eugenia.bed/bim/fam/ped/map: raw molecular file (85 individuals, 523 SNPs).
• Eugenia_qced.bed/bim/fam: QC-ed molecular file (80 individuals, 395 SNPs).
• c1.txt/c2.txt/c3.txt: individuals belonging to genetic cluster one (c1; 27 individuals), two (c2; 27 individuals) and three (c3; 26 individuals) as defined by discriminant analysis of principal components.
• Eugenia_qced_c1/c2/c3.bed/bim/fam: molecular files corresponding to genetic cluster one, two and three; input for the within-group LD analyses.
• ldrm_c1/c2/c3_alpha0.01.txt: SNPs showing statistical evidence of LD in genetic cluster one, two and three (59, 202 and 181 SNPs, respectively; p-value<0.01 after Bonferroni correction).
• ldrm_shared_0.01.txt: SNPs showing statistical evidence of LD in all genetic clusters (18 SNPs shared).
• leq_c1/c2/c3_alpha0.01.txt: p-values for the non-significant pairwise correlation tests among SNPs in genetic cluster one, two and three (p-value>0.01 after Bonferroni correction); these files contain the identifiers of the SNPs showing linkage equilibrium in the genetic clusters.
• Eugenia_qced_ldpruned.bed/bim/fam/ped/map: QC-ed molecular file with SNPs in LD excluded (80 individuals, 372 SNPs).

LEA analysis.zip

• LEA.R: R script used to run LEA.
• LEA-Eugenia-LD-pruned-2021-Bonf0.01.html: report on the analysis with results included.
• 2021_Eugenia_qced_ldpruned_372snp_80ind: input file for the LEA.R script.
• str.geno: inut file for sNMF analysis.
• snps_list: SNPs inluded into analysis.
• LEA_Eugenia_Pvalues 2021.txt: one-column data frame reporting the p-values derived by LEA analysis (one SNP per line).
• LEA-outliers-bonf-alpha0.01.txt: data frame reporting outliers from LEA analysis after Bonferroni correction.

LFMM analysis.zip

• LFMM.R: R script used to run LFMM.
• LFMM_Eugenia_LD-pruned-Bonf0.01.html: report on the analysis with results included.
• 361SNPs_Structure_Eugenia.str: input file for the sNMF analysis (unlinked loci with LEA outliers excluded).
• 361snps_list.csv: SNPs undergoing sNMF analysis.
• Coord_Eugenia_80Indiv_LDpruned.csv: IDs, FIDs and geographical coordinates of the individuals undergoing LFMM analysis.
• synthetic_6_PCAVariables_ordered.csv: population-based environmental characterization for LFMM analysis.
• snps_list.csv: the 372 unlinked SNPs undergoing LFMM analysis.
• lfmm-k3-outliers.txt & lfmm-k4-outliers: outliers from LFMM analysis after correcting for three (k3) and four (k4) latent factors, respectively.
• lfmm-outliers.txt: LFMM results as defined by the shared outliers between the k3 and k4 runs (see main text).
• shared-outliers.txt: shared outliers between LFMM analysis (lfmm-outliers.txt) and LEA analysis (LEA-outliers-bonf-alpha0.01.txt).