Premise: The genetic structure of hybrid zones provides insight into the potential for gene flow to occur between plant taxa. Four closely related European orchid species (Orchis anthropophora, O. militaris, O. purpurea, and O. simia) hybridize when they co-occur. We aimed to characterize patterns of hybridization in O. militaris–O. purpurea, O. purpurea–O. simia, and O. anthropophora–O. simia hybrid zones using molecular and morphological data. Methods: We used 11 newly isolated nuclear microsatellites to genotype 695 individuals collected from seven hybrid zones and six allopatric parental populations in France. Geometric morphometric analysis was conducted using 15 labellum landmarks to capture the main aspects of petal shape. Results: Backcrossing was asymmetric toward O. militaris in multiple O. militaris–O. purpurea hybrid zones. Hybrids in O. purpurea–O. simia and O. anthropophora–O. simia hybrid zones were largely limited to F1 and F2 generations, but further admixture had occurred. These patterns were reflected in labellum geometric morphometric data, which correlated strongly with nuclear microsatellite data in all three species combinations. Conclusions: The coexistence of parental and admixed individuals in these Orchis hybrid zones implies they are likely to be tension zones being maintained by a balance between gene flow into the hybrid zone and selection acting against admixed individuals. The pattern of admixture in the three species combinations suggests intrinsic selection acting on the hybrids is weaker in more closely related taxa. ; This work was supported by NERC, the Bentham-Moxon Trust, the Systematics Research Fund, the Botanical Research Fund, and the OSU-OREME.
Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life. ; Alberta Ministry of Advanced Education; Alberta Innovates AITF/iCORE Strategic Chair [RES0010334]; Musea Ventures; National Key Research and Development Program of China [2016YFE0122000]; Ministry of Science and Technology of the People's Republic of ChinaMinistry of Science and Technology, China [2015BAD04B01/2015BAD04B03]; State Key Laboratory of Agricultural Genomics [2011DQ782025]; Guangdong Provincial Key Laboratory of core collection of crop genetic resources research and application [2011A091000047]; Shenzhen Municipal Government of China [CXZZ20140421112021913/JCYJ20150529150409546/JCYJ20150529150505656]; National Science FoundationNational Science Foundation (NSF) [DBI-1265383, IOS 0922742, IOS-1339156, DEB 0830009, EF-0629817, EF-1550838, DEB 0733029, DBI 1062335, 1461364]; National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [1R01DA025197]; Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [Qu 141/5-1, Qu 141/6-1, GR 3526/7-1, GR 3526/8-1]; Natural Sciences and Engineering Research Council of CanadaNatural Sciences and Engineering Research Council of Canada ; The 1KP initiative was funded by the Alberta Ministry of Advanced Education and Alberta Innovates AITF/iCORE Strategic Chair (RES0010334) to G.K.-S.W., Musea Ventures, The National Key Research and Development Program of China (2016YFE0122000), The Ministry of Science and Technology of the People's Republic of China (2015BAD04B01/2015BAD04B03), the State Key Laboratory of Agricultural Genomics (2011DQ782025) and the Guangdong Provincial Key Laboratory of core collection of crop genetic resources research and application (2011A091000047). Sequencing activities at BGI were also supported by the Shenzhen Municipal Government of China (CXZZ20140421112021913/JCYJ20150529150409546/JCYJ20150529150505656). Computation support was provided by the China National GeneBank (CNGB), the Texas Advanced Computing Center (TACC), WestGrid and Compute Canada; considerable support, including personnel, computational resources and data hosting, was also provided by the iPlant Collaborative (CyVerse) funded by the National Science Foundation (DBI-1265383), National Science Foundation grants IOS 0922742 (to C.W.d., P.S.S., D.E.S. and J.H.L.-M.), IOS-1339156 (to M.S.B.), DEB 0830009 (to J.H.L.-M., C.W.d., S.W.G. and D.W.S.), EF-0629817 (to S.W.G. and D.W.S.), EF-1550838 (to M.S.B.), DEB 0733029 (to T.W. and J.H.L.-M.), and DBI 1062335 and 1461364 (to T.W.), a National Institutes of Health Grant 1R01DA025197 (to T.M.K., C.W.d. and J.H.L.-M.), Deutsche Forschungsgemeinschaft grants Qu 141/5-1, Qu 141/6-1, GR 3526/7-1, GR 3526/8-1 (to M.Q. and I.G.) and a Natural Sciences and Engineering Research Council of Canada Discovery grant (to S.W.G.). We thank all national, state, provincial and regional resource management authorities, including those of province Nord and province Sud of New Caledonia, for permitting collections of material for this research. ; Public domain authored by a U.S. government employee