title: Molecular phylogeny of the nettle family (Urticaceae) inferred from multiple loci of three genomes and extensive generic sampling.
abstract: 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.
authors.affiliation: Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Zeng-Yuan
authors.initials: ZY
authors.lastname: Wu
authors.forename: Alex K
authors.initials: AK
authors.lastname: Monro
authors.forename: Richard I
authors.initials: RI
authors.lastname: Milne
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.forename: Ting-Shuang
authors.initials: TS
authors.lastname: Yi
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D018745:Genome, Plant; D016013:Likelihood Functions; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA; D027003:Urticaceae / Q000145:classification* / Q000235:genetics
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer; D012337:RNA, Ribosomal, 18S
keywords: Cecropiaceae; Molecular phylogeny; Phylogenetic trees; Three genomes; Urticaceae; infra-familial relationships