Fig 1.
A. Coffea ambongensis in its natural environment during the dry season. B. Coffea ambongensis in its natural environment during the wet season. C. Coffea bissetiae, fruits. D. Coffea boinensis, fruits. Pictures: Rickarlos Bezandry.
Fig 2.
Maximum likelihood tree of 57 full-length chloroplast genomes of the genus Coffea.
Major clades (MC1-MC4) are color-coded in a manner similar to the publication in Charr et al., 2020. Only bootstrap values greater than 85 are shown here. Bootstrap value = 100.
Fig 3.
Maximum likelihood tree with 28,800 concatenated nuclear SNP markers for 47 species.
Only bootstrap values above 85 are shown in the tree. Bootstrap value = 100.
Fig 4.
Baracoffea genetic diversity assessed using 9,665 variant SNPs.
A. Genetic distance of Coffea species from Madagascar. B. PCA analysis. C. Geographic position of species used in the analysis.
Fig 5.
Principal component analysis with eight quantitative variables (climate, geography and genomics), botanical series (including Baracoffea) and Malagasy Coffea species (species codes are explained in S1 File).
AnnPrecip: Annual precipitation, TempSeas: Temperature seasonality, MeanTemp: Mean temperature, X2C: Genome size (2C, pg), Alt: Altitude, WatDeficit: Water deficit, DryMonths: number of dry months. A. Scree plot. B. Variables of PCA. C. Biplot.
Fig 6.
Principal component analysis with seven quantitative variables (climate, geography and genomics) and the five principal components from biallelic SNP.
Botanical series and Coffea species are shown (species codes details in S1 File). AnnPrecip: Annual precipitation, TempSeas: Temperature seasonality, MeanTemp: Mean temperature, X2C: Genome size (2C, pg), Alt: Altitude, WatDeficit: Water deficit, DryMonths: number of dry months. A. Scree plot. B. Variables of PCA. C. Biplot.