Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora ( Cbp Cg ) and the other one from the selfing and genetically depauperate Capsella orientalis ( Cbp Co ). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size ( N e ), signatures of positive and negative selection, and gene expression patterns. In all three regions, N e of the two subgenomes decreased gradually over time and the Cbp Co subgenome accumulated more deleterious changes than Cbp Cg . There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris . Selective sweeps were more common on the Cbp Cg subgenome in Europe and the Middle East, and on the Cbp Co subgenome in Asia. In contrast, differences in expression were limited with the Cbp Cg subgenome slightly more expressed than Cbp Co in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions.
Berardia subacaulis Vill. is a monospecific genus that is endemic to the South-western Alps, where it grows on alpine screes, which are extreme habitats characterized by soil disturbance and limiting growth conditions. Root colonization by arbuscular mycorrhizal fungi (AMF) is presumably of great importance in these environments, because of its positive effect on plant nutrition and stress tolerance, as well as on structuring the soil. However, there is currently a lack of information on this topic. In this paper, we tested which soil characteristics and biotic factors could contribute to determining the abundance and community composition of AMF in the roots of B. subacaulis, which had previously been found to be mycorrhizal. For such a reason, the influence of soil properties and environmental factors on AMF abundance and community composition in the roots of B. subacaulis, sampled on three different scree slopes, were analysed through microscopic and molecular analysis. The results have shown that the AMF community of Berardia roots was dominated by Glomeraceae, and included a core of AMF taxa, common to all three scree slopes. The vegetation coverage and dark septate endophytes were not related to the AMF colonization percentage and plant community did not influence the root AMF composition. The abundance of AMF in the roots was related to some chemical (available extractable calcium and potassium) and physical (cation exchange capacity, electrical conductivity and field capacity) properties of the soil, thus suggesting an effect of AMF on improving the soil quality. The non-metric multidimensional scaling (NMDS) ordination of the AMF community composition showed that the diversity of AMF in the various sites was influenced not only by the soil quality, but also by the slope. Therefore, the slope-induced physical disturbance of alpine screes may contribute to the selection of disturbance-tolerant AMF taxa, which in turn may lead to different plant-fungus assemblages.
Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species and how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cg) and the other one from the selfing and genetically depauperate Capsella orientalis (Co). For each subgenome, we assessed its relationship with the diploid relatives, temporal change of effective population size Ne, signatures of positive and negative selection, and gene expression patterns. Introgression between C. bursa-pastoris and its diploid relatives was widespread and the two subgenomes were impacted differentially depending on geographic region. In all three regions, Ne of the two subgenomes decreased gradually and the Co subgenome accumulated more deleterious changes than Cg. Selective sweeps were more common on the Cg subgenome in Europe and the Middle East, and on the Co subgenome in Asia. In contrast, differences in expression were limited with the Cg subgenome slightly more expressed than Co in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy and were differentially affected by introgression and selection.
Primula allionii is endemic to a tiny area of the Maritime Alps and has one of the narrowest distribution ranges in this hotspot of biodiversity. Phylogeographical patterns in P. allionii were studied using plastid DNA markers and dominantly inherited markers (AFLP and ISSR) to verify any admixture between P. allionii and the sympatric P. marginata and to detect the phylogeographical history of the species. Morphometric measurements of flowers and admixture analysis support the hypothesis that hybridization occurs in nature. Species distribution models using two climate models (CCSM and MIROC) suggested a reduction in habitat suitability during cold periods. Phylogeographical analysis suggested an old allopatric divergence during the mid‐Pleistocene transition (about 0.8 Mya) without recolonization/contraction cycles. The Alps watershed does not act as a strong barrier between the two main areas of the distribution range, and moderate gene flow by pollen seems to create the admixture recorded among the stands. According to our results, the persistence of P. allionii throughout the Ice Age appears to be linked to the capacity of the Maritime Alps to provide a wide diversity of microhabitats consistent with the recent biogeographical pattern proposed for the Mediterranean Basin. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 637–653.
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