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Premise of the Study For the past one billion years, green plants (Viridiplantae) have dominated global ecosystems, yet many key branches in their evolutionary history remain poorly resolved. Using the largest analysis of Viridiplantae based on plastid genome sequences to date, we examined the phylogeny and implications for morphological evolution at key nodes. Methods We analyzed amino acid sequences from protein‐coding genes from complete (or nearly complete) plastomes for 1879 taxa, including representatives across all major clades of Viridiplantae. Much of the data used was derived from transcriptomes from the One Thousand Plants Project (1KP); other data were taken from GenBank. Key Results Our results largely agree with previous plastid‐based analyses. Noteworthy results include (1) the position of Zygnematophyceae as sister to land plants (Embryophyta), (2) a bryophyte clade (hornworts, mosses + liverworts), (3) Equisetum + Psilotaceae as sister to Marattiales + leptosporangiate ferns, (4) cycads + Ginkgo as sister to the remaining extant gymnosperms, within which Gnetophyta are placed within conifers as sister to non‐Pinaceae (Gne‐Cup hypothesis), and (5) Amborella, followed by water lilies (Nymphaeales), as successive sisters to all other extant angiosperms. Within angiosperms, there is support for Mesangiospermae, a clade that comprises magnoliids, Chloranthales, monocots, Ceratophyllum, and eudicots. The placements of Ceratophyllum and Dilleniaceae remain problematic. Within Pentapetalae, two major clades (superasterids and superrosids) are recovered. Conclusions This plastid data set provides an important resource for elucidating morphological evolution, dating divergence times in Viridiplantae, comparisons with emerging nuclear phylogenies, and analyses of molecular evolutionary patterns and dynamics of the plastid genome.

The Campanula pyramidalis complex is a group of closely related taxa with a distribution across the Balkans, from the Gulf of Trieste in the north to the Peloponnese Peninsula in the south, with small disjunct parts of the range in the south Apennines. Although 21 taxa were described within this complex, only three, C. pyramidalis, C. versicolor, and C. secundiflora, have been generally accepted in recent synoptical taxonomic treatments. Our molecular phylogenetic analyses based on sequences of three non‐coding chloroplast regions (psbA‐trnH, psbZ‐trnfM, trnG‐trnS) as well as of nuclear ribosomal internal transcribed spacers (nrITS), lend strong support to the recognition of several lineages which only partially correspond to generally accepted taxonomic concepts. Molecular data presented in this study showed that C. pyramidalis is a polyphyletic assemblage that segregates into three distinct lineages, one of which is described here as a new species, C. austroadriatica sp. nov. The lectotype of C. pyramidalis, redefined in a strict sense, is designated. Neither C. versicolor nor C. secundiflora were found to be strictly monophyletic, but their monophyly could not be rejected. Morphological and biogeographical implications are discussed.

While it is known that whole genome duplication (WGD) and reticulate evolution play important roles in plant evolution, the origins and evolutionary histories of most polyploid and reticulate groups are still poorly known. The North Temperate haplostemonous (NTH) Ludwigia L. (sections Isnardia (L.) W. L. Wagner & Hoch, Ludwigia, Microcarpium Munz, and Miquelia P. H. Raven) group, characterized by having 4-merous and haplostemonous flowers, pluriseriate and free seeds, glabrous and convex nectaries, and a north-temperate distribution, is a polyploid complex (2×, 4×, 6×, and 8×) of 24 species with frequent reports of inter- and intrasectional hybridization. Although earlier biosystematics studies postulated some evolutionary scenarios and recent molecular phylogenetic studies have partially tested these propositions, the full history of their reticulate evolution remains puzzling. In this study, we sequenced four chloroplast regions (rpL16, rpoB-trnC, trnL-trnF, and ycf6-psbM) and conducted extensive molecular cloning of the biparentally inherited single-copy nuclear PgiC gene (376 clones in total), sampling 23 of the 24 NTH Ludwigia species whose chromosome numbers and ploidy levels were confirmed. Both the chloroplast and PgiC trees include strongly supported sister clades of section Ludwigia (four diploid species) and the “Microcarpium complex” (composed of sections Isnardia, Microcarpium, and Miquelia), which together are sister to the rest of Ludwigia. In the PgiC tree, eight clades are identified within the Microcarpium complex, with four clades including no extant diploid species. Neither sections Isnardia nor Microcarpium are monophyletic, while the monospecific section Miquelia has a hybrid origin. By integrating our phylogenetic trees with previous cytological hypotheses, the reticulate evolution of NTH Ludwigia is disentangled and four to eight extinct diploid species are inferred. Ancestral area reconstruction supports a North American origin of L. ovalis whose current East Asian distribution reflects a relict of the Arcto-Tertiary Geoflora. Based on our results, we propose to synonymize sections Microcarpium and Miquelia under the expanded section Isnardia.

Chusquea is a diverse genus of American woody bamboos, accounting for almost half of the woody bamboo species in the Neotropics. Previous analyses of molecular data have recovered four major lineages within Chusquea, but morphological synapomorphies have been identified only for subgenus Rettbergia. This study estimates a chloroplast phylogeny of Chusquea with a focus on relationships within the large and intractable Euchusquea clade. Phylogenetic analyses were conducted on 40% of the described species in Chusquea, with data from five chloroplast regions and a preliminary survey of the nuclear internal transcribed spacer complex. Several results from previous studies were corroborated, including the presence of two clades formerly comprising the genus Neurolepis and monophyly of subgenus Rettbergia. The clades formerly in Neurolepis are named as Chusquea subgenus Platonia and Chusquea subgenus Magnifoliae based on molecular support and potential morphological synapomorphies. We recovered two strongly supported and five weakly supported clades within Euchusquea, but relationships among these lineages were not resolved and species composition of the clades conflicts strongly with current taxonomic groupings based on morphology. Low resolution of the chloroplast phylogeny estimation, low variability in nuclear data, character conflict, and geographical distribution of chloroplast lineages all suggest a recent radiation of the Euchusquea clade. Given the present weak molecular support for relationships within Euchusquea and the lack of synapomorphic morphological characters to define clades, we recommend the use of the current morphology-based taxonomy as a practical means of assessing and describing diversity in the Euchusquea clade.

The subfamily Polygonoideae has a world-wide distribution and is an important component of many countries' floras. In this study we present the most comprehensive sampling available to date, including data from three chloroplast genes (matK, ndhF, rbcL) for 82 species in Polygonaceae (54 from Polygonoideae). Based on our results, we propose a new taxonomic classification for Polygonoideae that includes five well-supported tribes: Calligoneae, Fagopyreae, Persicarieae, Polygoneae, and Rumiceae. Overall, the results from molecular data represent significant progress in understanding the evolutionary relationships of major groups within the family. This classification also provides an assessment of diagnostic morphological characters for the tribes. The present work will promote reevaluation of morphological characters within this diverse group, especially synapomorphies for Polygonoideae, and for tribes with a particularly complex history such as Fagopyreae, Persicarieae, and Polygoneae. A new combination, Fagopyrum tibeticum, is proposed.

While it is known that whole genome duplication (WGD) and reticulate evolution play important roles in plant evolution, the origins and evolutionary histories of most polyploid and reticulate groups are still poorly known. The North Temperate haplostemonous (NTH) Ludwigia L. (sections Isnardia (L.) W. L. Wagner & Hoch, Ludwigia, Microcarpium Munz, and Miquelia P. H. Raven) group, characterized by having 4-merous and haplostemonous flowers, pluriseriate and free seeds, glabrous and convex nectaries, and a north-temperate distribution, is a polyploid complex (2×, 4×, 6×, and 8×) of 24 species with frequent reports of inter- and intrasectional hybridization. Although earlier biosystematics studies postulated some evolutionary scenarios and recent molecular phylogenetic studies have partially tested these propositions, the full history of their reticulate evolution remains puzzling. In this study, we sequenced four chloroplast regions (rpL16, rpoB-trnC, trnL-trnF, and ycf6-psbM) and conducted extensive molecular cloning of the biparentally inherited single-copy nuclear PgiC gene (376 clones in total), sampling 23 of the 24 NTH Ludwigia species whose chromosome numbers and ploidy levels were confirmed. Both the chloroplast and PgiC trees include strongly supported sister clades of section Ludwigia (four diploid species) and the \"Microcarpium complex\" (composed of sections Isnardia, Microcarpium, and Miquelia), which together are sister to the rest of Ludwigia. In the PgiC tree, eight clades are identified within the Microcarpium complex, with four clades including no extant diploid species. Neither sections Isnardia nor Microcarpium are monophyletic, while the monospecific section Miquelia has a hybrid origin. By integrating our phylogenetic trees with previous cytological hypotheses, the reticulate evolution of NTH Ludwigia is disentangled and four to eight extinct diploid species are inferred. Ancestral area reconstruction supports a North American origin of L. ovalis whose current East Asian distribution reflects a relict of the Arcto-Tertiary Geoflora. Based on our results, we propose to synonymize sections Microcarpium and Miquelia under the expanded section Isnardia.

Both the origin of domesticated apple and the overall phylogeny of the genus Malus are still not completely resolved. Having this as a target, we built a 134,553-position-long alignment including two previously published chloroplast DNAs (cpDNAs) and 45 de novo sequenced, fully colinear chloroplast genomes from cultivated apple varieties and wild apple species. The data produced are free from compositional heterogeneity and from substitutional saturation, which can adversely affect phylogeny reconstruction. Phylogenetic analyses based on this alignment recovered a branch, having the maximum bootstrap support, subtending a large group of the cultivated apple sorts together with all analyzed European wild apple (Malus sylvestris) accessions. One apple cultivar was embedded in a monophylum comprising wild M. sieversii accessions and other Asian apple species. The data demonstrate that M. sylvestris has contributed chloroplast genome to a substantial fraction of domesticated apple varieties, supporting the conclusion that different wild species should have contributed the organelle and nuclear genomes to the domesticated apple.

The Greater Cape Floristic Region (GCFR) of southern Africa is characterised by large, endemic radiations of flowering plants, the so-called 'Cape Clades', but it is unknown whether such radiations are also found in non-angiosperms. We hypothesise that GCFR-endemic lineages exist in the xeric adapted cheilanthoid ferns. To test this hypothesis with special emphasis on the alternative hypothesis of frequent colonization, the phylogenetic relations, divergence times, and ancestral areas of the cheilanthoid ferns of the GCFR and adjacent regions are investigated. The dataset includes 22 cheilanthoid fern species occurring in the GCFR. With two exceptions, all GCFR-endemics are part of two clades that diversified in the Afro-Madagascan region. The GCFR-endemics are further concentrated in three high-endemism subclades that did not originate simultaneously, but within the timeframe of angiosperm Cape Clades diversification. According to ancestral area reconstructions the ancestors of the two larger Afro-Madagascan clades were likely GCFR-endemic, and a substantial part of the diversification history of these clades took place in the GCFR. The high diversity of cheilanthoids in the GCFR appears to stem primarily from in situ diversification, not from immigration. This pattern resembles the numerous radiations of angiosperm clades in the GCFR, and may be caused by the same factors. We did not find evidence for rapid, synchronised radiations as documented for some, albeit not all, angiosperm Cape Clades. High diversification within and dispersal out of the GCFR has likely enriched cheilanthoid diversity in the Afro-Madagascan region.