Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times beyond. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptation to aquatic environments by including 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptation, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as ((Tofieldiaceae, Araceae), core Alismatids). There is phylogenetic conflict among the backbone of the three main clades that could be due to incomplete lineage sorting and introgression. We identified 18 putative WGD events. One of them had occurred at the most recent common ancestor of core Alismatids, and four occurred at seagrass lineages. Other events are distributed in terrestrial, emergent, and submersed life-forms and seagrasses across Alismatales. We also found that lineage and life-form were each important for different evolutionary patterns for the genes related to freshwater/marine adaptation. For example, some light or ethylene-related genes were lost in the seagrass Zosteraceae, but present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments, phylogeny, and whole-genome duplication of Alismatales.

ABSTRACT. The endangered marsh herb, Caldesia grandis, is native to China. We investigated the spatial structure of the genetic variation of three populations of C. grandis using RAPD markers and spatial autocorrelation analysis, based on the method of equal distance interval. A total of 157 individuals were sampled from four patches collected from the region of Hunan and Yunnan Provinces, China. Among the polymorphic bands generated by seven selective primers, polymorphic bands with frequencies ranging from 20 to 80% were used to calculate Moran's I spatial autocorrelation coefficient for each patch. We found significant spatial structure of genetic variation in the three patches in Bei Hai (BH) (patches BH-1 and BH-2) and Guai Hu (GH) (patch GH-1) populations of C. grandis (with significant positive autocorrelation within the short distance class). In contrast, the genetic variation in ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 11 (3): 2412-2421 (2012) Spatial genetic structure of Caldesia grandis 2413the Lang Pan Hu (LPH) population (patch LPH-1) was found to be randomly distributed. The different spatial distribution patterns may be attributed to environment differences. These results have implications for the conservation and management of this species, especially for sampling strategies for ex situ conservation.