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Plastid phylogenomics and molecular evolution of Alismatales
Author(s) -
Ross T. Gregory,
Barrett Craig F.,
Soto Gomez Marybel,
Lam Vivienne K.Y.,
Henriquez Claudia L.,
Les Donald H.,
Davis Jerrold I.,
Cuenca Argelia,
Petersen Gitte,
Seberg Ole,
Thadeo Marcela,
Givnish Thomas J.,
Conran John,
Stevenson Dennis W.,
Graham Sean W.
Publication year - 2016
Publication title -
cladistics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.323
H-Index - 92
eISSN - 1096-0031
pISSN - 0748-3007
DOI - 10.1111/cla.12133
Subject(s) - biology , phylogenomics , monophyly , sister group , phylogenetic tree , evolutionary biology , maximum parsimony , clade , plastid , molecular phylogenetics , gene , genetics , chloroplast
Past phylogenetic studies of the monocot order Alismatales left several higher‐order relationships unresolved. We addressed these uncertainties using a nearly complete genus‐level sampling of whole plastid genomes (gene sets representing 83 protein‐coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter‐ and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister‐group of the rest of the order, one likelihood analysis indicated a contrasting Araceae‐sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral‐state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae.