Table 1: Genetic diversity and eco-genetic structure within diploid and allopolyploid Aegilops species. For each species, Ng individuals were genotyped at plastid and nuclear loci to estimate allelic richness (AR), observed heterozygosity (Ho), genetic diversity corrected for sample size (h ) and with ordered alleles (v ). The eco-genetic structure was assessed through (partial) Mantel tests associating genetic (G), climatic (E) and geographical (Geo) distances among individuals within each species and decomposed into significant isolation-by-distance (G ~ Geo) and isolation-by-environment (G ~ E | Geo). Range filling represents the fraction of suitable areas based on the climatic niche that is occupied by the species within the study area.
Genome composition of each species according to van Slageren (1994), with maternal progenitor underlined
Associations tested through 20000 permutations with p-values as *** < 0.001, ** < 0.01, * < 0.05 and ns for non-significant and confirmed through Redundancy Analysis whose significance is indicated in between brackets.
Fig. 1: Genetic and ecological additivity of diploid progenitors as a null hypothesis to analyze micro-evolution of allopolyploid species. Multilocus genotypes are shown for diploid (stars) and allopolyploid (diamonds) individuals over an adaptive landscape presenting fitness as grey isolines. On the left, ecological niches of diploid species are overlaid as shaded areas delimiting populations existing across the environmental space. Allopolyploids combine divergent suites of genes (shown as – or + between brackets) from diploid species (AoAo and BoBo) and are therefore expected to present genetic additivity (AeAeBeBe). Fixed heterozygosity for genes underlying the ecological niche of each diploid progenitor is expected to provide positive population growth over combined ranges of environmental conditions tolerated by progenitor species. As a null hypothesis, allopolyploid speciation therefore produces new species presenting the ecological additivity of their progenitors, with an observed niche (AoAoBoBo) similar to the expected niche (i.e. AeAeBeBe). On the right, main scenarios of possible ecological niche evolution during the establishment of allopolyploids are presented. Ecological niches of allopolyploids can retain the additivity of niches from their diploid progenitors. Significant deviation from such expected additivity is however characteristic of niche shifts in allopolyploids. Niche contraction occurs when allopolyploids do not outcompete diploid progenitors and occupy a subset of their niches. In contrast, niche expansion beyond the combined range of conditions tolerated by diploid progenitors is coherent with evolutionary novelties commonly postulated to promote allopolyploid establishment in face of their competition. Analyses relying on such expected additivity of diploids adequately test for multivariate niche conservatism vs shift in allopolyploids and, circumventing ambiguous pairwise comparisons with divergent progenitors, transcend diagnostics based on niche centroids (crosses) and/or niche breadths (braces along univariate ecological gradients). Verifiable conclusions are accordingly reached regarding niche conservatism vs novelty in allopolyploids responding to variable competition from diploids in space and time.
Figure 2: Evolution of Aegilops allopolyploid species following the merging of diploid progenitors. A. Phylogenetic relationships within and among four diploids species Ae. tauschii(DD), Ae. caudata (CC), Ae. umbellulata (UU) and Ae. comosa (MM), and four derived allopolyploid species Ae. cylindrica (DDCC), Ae. triuncialis (UUCC), Ae. geniculata(UUMM) and Ae. crassa (DDMM with tetraploids, 4x, and hexaploids, 6x). Origins of allopolyploid species were inferred through independent multi-labelled trees based on 30 nuclear loci anchored in the phylogeny of diploid wheats (Fig. S3). Divergence from maternal (plain line) and paternal (dashed line) progenitors are reported with corresponding dates. Tips present accessions from genetic clusters identified with the same loci, labelled according to Fig. 3. Maternal progenitor species of allopolyploids, identified using plastid loci, are underlined (Fig. S2).B. Nuclear genomic composition of the four allopolyploid species estimated as the proportion of conserved (blue), derived (orange) and lost (grey) haplotypes across loci as compared to those segregating within their diploid progenitors (Table S2).
Figure 3: Spatial genetic structure within four diploid and four derived allopolyploid Aegilops species. Genotyped accessions (circles) are assigned to genetic clusters inferred by STRUCTURE within each species, colored according to the stacked barplots underneath and approximately delimited across distribution ranges. Contact zones between genetic clusters showing admixed accessions are indicated by red stripes. Labels are otherwise as in Fig. 2.
Figure 4: Climatic niche dynamics of allopolyploidAegilops species. Climatic niche of each Aegilops species in the common climatic space (100% and 50% indicated as solid and dashed contour lines) along the first two principal components based on 20 bioclimatic factors shown in the central correlation circle (abbreviations in Fig. S6). The observed niche of each polyploid species is compared to the expected additivity of climatic niches modeled from both its diploid progenitors (blue + green). The fraction of the expected niche effectively occupied by the allopolyploid species characterizes niche stability (blue), whereas the unoccupied fraction is referred to as niche contraction (green). Climatic space occupied by the allopolyploids while not predicted by the additivity of diploid progenitors indicates niche expansion (red). For each allopolyploid, niche centroids of diploid progenitors are indicated as orange stars labelled with their genome composition. Labels are otherwise as in Fig. 2.