Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop.

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Molecular phylogeny and morphology of Elatostema s.l. (Urticaceae): Implications for inter- and infrageneric classifications.

Elatostema s.s. (Urticaceae) comprises approximately 500 species of herbs and subshrubs distributed in tropical and subtropical Asia, Australasia, and Africa. The delimitation of Elatostema s.s. and the closely related genera Elatostematoides, Pellionia, and Procris has long been problematic because of the large number of taxa and presumed homoplasy among diagnostic morphological characters. In the present study, we refer to these four genera together as Elatostema s.l. To evaluate the circumscription of Elatostema s.l. and its generic and subgeneric classification, we conducted phylogenetic analyses of DNA sequence data from the internal transcribed spacer of the nuclear genome (nrITS) and two markers from the plastid genome (psbA-trnH and psbM-trnD) for 126 taxa, representing 88 species of Elatostema s.s., four of Elatostematoides, nine of Pellionia, and five of Procris. Ten selected morphological characters were investigated using ancestral state reconstructions. Our results show that Elatostema s.l. can be divided into three well-supported and morphologically distinct genera: Procris, Elatostematoides, and Elatostema sensu auct. The results of our molecular phylogeny suggest four strongly supported clades within this newly defined Elatostema s.a.: core Elatostema, Pellionia, Weddellia, and an as yet undescribed clade African Elatostema. Homoplasy among the morphological characters used in this study makes it impossible to circumscribe genera using synapomorphies, but combined suites of characters do enable the morphological diagnosis of Elatostema s.a., Elatostematoides, and Procris.

Molecular phylogeny of the nettle family (Urticaceae) inferred from multiple loci of three genomes and extensive generic sampling.

Urticaceae is one of the larger Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) to analyze the DNA sequence data from two nuclear (ITS and 18S), four chloroplast (matK, rbcL, rpll4-rps8-infA-rpl36, trnL-trnF) and one mitochondrial (matR) loci. We sampled 169 accessions representing 122 species, representing 47 of the 54 recognized genera within Urticaceae, including four of the six sometimes separated as Cecropiaceae. Major results included: (1) Urticaceae including Cecropiaceae was monophyletic; (2) Cecropiaceae was biphyletic, with both lineages nested within Urticaceae; (3) Urticaceae can be divided into four well-supported clades; (4) previously erected tribes or subfamilies were broadly supported, with some additions and alterations; (5) the monophyly of many genera was supported, whereas Boehmeria, Pellionia, Pouzolzia and Urera were clearly polyphyletic, while Urtica and Pilea each had a small genus nested within them; (6) relationships between genera were clarified, mostly with substantial support. These results clarify that some morphological characters have been overstated and others understated in previous classifications of the family, and provide a strong foundation for future studies on biogeography, character evolution, and circumscription of difficult genera.

Eight new species of Cestrum (Solanaceae) from Mesoamerica.

As part of the preparation of a taxonomic revision of Cestrum (Solanaceae) for Flora Mesoamericana eight hitherto undescribed species from Mexico, Guatemala, Costa Rica and Panama were identified. These eight new species are described and illustrated. Affinities of the species are discussed and Global Species Conservation Assessments presented.The new species are Cestrum amistadense A.K. Monro, sp. nov. (Vulnerable) which most closely resembles Cestrum longiflorum Ruiz & Pav., Cestrum contrerasianum A.K. Monro, sp. nov. (Vulnerable) which most closely resembles Cestrum formosum C.V.Morton, Cestrum darienense A.K. Monro, sp. nov. (Near Threatened) which most closely resembles Cestrum morae Hunz., Cestrum gilliae A.K. Monro, sp. nov. (Near Threatened) which most closely resembles Cestrum morae, Cestrum haberii A.K. Monro, sp. nov. (Vulnerable) which most closely resembles Cestrum poasanum Donn.Sm., Cestrum knappiae A.K. Monro, sp. nov. (Near Threatened) which most closely resembles Cestrum acuminatum Francey, Cestrum lentii A.K. Monro, sp. nov. (Near Threatened) which most closely resembles Cestrum johnniegentrianum D'Arcy and Cestrum talamancaense A.K. Monro (Least Concern) which most closely resembles Cestrum laxum Benth.

Three new species of Pilea (Urticaceae) from limestone karst in China.

Three hitherto undescribed species of Pilea (Urticaceae) from limestone karst in China are described and illustrated. Affinities of the species are discussed and Global Species Conservation Assessments presented. The new species are Pilea cavernicola A.K. Monro, C.J. Chen & Y.G. Wei, sp. nov. (Vulnerable) which most closely resembles Pilea scripta (Buch.-Ham. ex D.Don) Wedd. and Pilea gracilis Handel-Mazzetti, Pilea shizongensis A.K. Monro, C.J. Chen & Y.G. Wei, sp. nov. (Endangered) which is most similar to Pilea aquarum Dunn and Pilea guizhouensis A.K. Monro, C.J. Chen & Y.G. Wei, sp. nov. (Vulnerable) which resembles Pilea boniana Gagnep. and Pilea rubriflora C. Wright mostclosely.

The revision of species-rich genera: a phylogenetic framework for the strategic revision of Pilea (Urticaceae) based on cpDNA, nrDNA, and morphology.

The revision of species-rich genera underpins research and supports the sustainable use and monitoring of biological diversity. One fifth to one quarter of the diversity of all seed plant species occurs in such genera, but difficulties with the revision of species-rich genera has resulted in many of them being ignored since the late 1800s. Pilea, with 600-715 species is in need of revision. The only realistic approach is in manageable subunits, which requires confirmation of monophyly and identification of monophyletic subdivisions. Parsimony analyses of trnL-F, ITS, and morphology data were used to test the monophyly of, and explore intrageneric relationships within, Pilea. Analysis of trnL-F data confirms and recovers two morphologically diagnosable monophyletic clades that include all of the taxa within Pilea. Overlaying geographic distribution on a most parsimonious tree indicates a strong association between geography and phylogenetic relatedness. It is suggested that a strategic revision within the framework of morphologically and geographically diagnosable units might enable the revision of the group using an iterative approach. Analysis of the outgroup taxa supports the inclusion of Poikilospermum within the Urticaceae and suggests that the Urticaceae tribes could be placed into two clades that are supported by floral morphology.