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Figure 1. Phylogenomic trees reconstructed using the concatenated nuclear (left) and plastid data (right) obtained using Hyb-Seq for 76 samples of the Tamus clade of Dioscorea . Samples included are representative of its distribution range across the Mediterranean region. Filled circles represent branches with support values over 90%, while lower values are shown on branches. Colours represent the main clades found in the nuclear tree, see Results (D. orientalis violet, DC1 blue, DC2 green, DC3 red), and roman numbers identifying the subclades in D. communis in the plastid tree (I, II, III; subclades within each clade were indicated with lowercase letters a and b). Dashed lines connect the same samples in the nuclear and plastid trees.
Figure 2. Admixture proportions for K = 3 genetic groups obtained from genetic structure analysis of nuclear data of Mediterranean Dioscorea communis samples through ten replicates in STRUCTURE (see text for details). Each sample is shown by a vertical bar partitioned according to its membership to one of the Kclusters, represented in red, green and blue. The samples follow the same order as in the nuclear phylogenetic tree (Figure 1) and organized by clades (DC2 and DC3). The plastid clades (I, II and III, Figure 1) were labelled next to the sample codes. An asterisk (*) was used to represent the only sample of D. communis (R32) that was resolved as part of clade DC1 based on nuclear data, and in a different clade with plastid data (see Figure 1).
Figure 3. Environmental niche models (ENM) constructed using a current climate envelop and occurrence data for the samples of the Tamus clade of Dioscorea analysed in this study. ENMs were estimated for each of the four lineages identified in the Tamus clade with background maps adjusted to reflect their estimated potential distributions: DC3 clade of D. communis ; DC2 clade of D. communis ; the Macaronesian DC1 lineage of D. communis ; andD. orientalis . A 10% threshold cropping was applied for each distribution range model (see Results). The legend represents the prediction of probability of occurrence.
Figure 4. Principal Component Analysis (PCA) conducted with 19 bioclimatic variables for samples of the Tamus clade of Dioscoreaacross the Mediterranean region separated into the four main lineages (see Results): Macaronesian DC1 clade of D. communis in light blue; D. communis clade DC2 in green; D. communis DC3 clade in red; and D. orientalis in purple.
Figure 5. Phylogenetic tree reconstructed using the concatenated nuclear data obtained using Hyb-Seq for 76 samples of the Tamus clade of Dioscorea . Morphological, ploidy and geographic distribution trait variation is represented with circles for each sample. Leaf: filled circle, trilobed; empty circle, cordate; ploidy level: filled circle, allelic ratio >2 (estimated as polyploid); empty circle, allelic ratio <2 (estimated as diploid; see Results); geographic distribution: filled circle, W and C Mediterranean; empty circle, E Mediterranean; inflorescence: filled circle, sessile solitary; empty circle, pedunculated fascicule.
Figure 6. Geographic distribution of the 76 samples of the Tamus clade of Dioscorea coded according to their respective lineage in the phylogenetic tree based on concatenated nuclear data (Figure 1), D. cretica (DC2) in green, and subclade; and pink, orange, and red for western European, central Mediterranean and eastern Mediterranean clades in D. communis s.s. (DC3), respectively. ForD. orientalis , in purple, codes in the map indicate their phylogenetic position named “Leb” (Lebanon) and “S23”. For D. edulis (DC1), in light blue, codes in the map indicate their phylogenetic position named “Mad” (Madeira), “Ten” (Tenerife) and “GC” (Gran Canaria). Roman numbers in the mapped dot samples represent their respective plastid tree lineage (Figure 1). Asterisks indicate cultivated samples in Botanic Gardens of unknown geographic origin.