TY - JOUR
T1 - Phylogeny of the Asparagales based on three plastid and two mitochondrial genes
AU - Seberg, Ole
AU - Petersen, Gitte
AU - Davis, Jerrold I.
AU - Chris Pires, J.
AU - Stevenson, Dennis W.
AU - Chase, Mark W.
AU - Fay, Michael F.
AU - Devey, Dion S.
AU - Jørgensen, Tina
AU - Sytsma, Kenneth J.
AU - Pillon, Yohan
PY - 2012/5/1
Y1 - 2012/5/1
N2 - Premise of the study: The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial. Methods: Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequencywithin-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated. Key results: The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent. Conclusions: Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.
AB - Premise of the study: The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial. Methods: Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequencywithin-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated. Key results: The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent. Conclusions: Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.
KW - Faculty of Science
KW - Botany
U2 - 10.3732/ajb.1100468
DO - 10.3732/ajb.1100468
M3 - Journal article
C2 - 22539521
SN - 0002-9122
VL - 99
SP - 875
EP - 889
JO - American Journal of Botany
JF - American Journal of Botany
IS - 5
ER -