What does it take to resolve relationships and to identify species with molecular markers? An example from the epiphytic Rhipsalideae (Cactaceae)

Premise of the study: The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomie units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insuf...

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Published inAmerican journal of botany Vol. 98; no. 9; pp. 1549 - 1572
Main Authors Korotkova, Nadja, Borsch, Thomas, Quandt, Dietmar, Taylor, Nigel P., Müller, Kai F., Barthlott, Wilhelm
Format Journal Article
LanguageEnglish
Published United States Botanical Society of America 01.09.2011
Botanical Society of America, Inc
Subjects
Biological taxonomies
Cactaceae
Cactaceae - genetics
Cactus
Datasets
DNA barcoding
DNA Primers
DNA, Plant - genetics
Flowers
Flowers & plants
Genera
Genes, Plant
Genetic Markers
Hatiora
Introns
inversion
Lepismium
Nonnative species
Phylogenetics
Plants
Plastids
Rhipsalidopsis
Rhipsalis
Schlumbergera
species‐level phylogeny
Systematics and Phytogeography
Taxa
Taxonomy
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Summary:Premise of the study: The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomie units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphytic tribe Rhipsalideae and evaluates the utility of a spectrum of plastid genomic regions. Methods: We present a phylogenetic study including 52 of the 53 Rhipsalideae species and all the infraspecific taxa. Seven regions (trnK intron, matK, rbcL, rps3-rpl16, rpl16 intron, psbA-trnH, trnQ-rps16), ca. 5600 nucleotides (nt) were sequenced per sample. The regions used were evaluated for their phylogenetic performance and performance in DNA-based species recognition based on operational taxonomie units (OTUs) defined beforehand. Key results: The Rhipsalideae are monophyletic and contain five clades that correspond to the genera Rhipsalis, Lepismium, Schlumbergera, Hatiora, and Rhipsalidopsis. The species-level tree was well resolved and supported; the rpl16 and trnK introns yielded the best phylogenetic signal. Although the psbA-trnH and trnQ-rps16 spacers were the most successful individual regions for OTU identification, their success rate did not significantly exceed 70%. The highest OTU identification rate of 97% was found using the combination of psbA-trnH, rps3-rpl16, trnK intron, and trnQ-rps16 as a minimum possible marker length (ca. 1660 nt). Conclusions: The phylogenetic performance of a marker is not determined by the level of sequence variability, and species discrimination power does not necessarily correlate with phylogenetic utility.
Bibliography:and R. Bauer (Offenburg) for material of
Calymmanthium substerile
L. Zabel and B. Große‐Veldmann helped in the laboratory and M. Krug with the analysis of the phylogenetic structure. We appreciate financial support from the Akademie der Wissenschaften und der Literatur, Mainz in the context of the project “Biodiverstät im Wandel”. This study fulfills parts of the requirements for the first author to obtain a doctoral degree from the University of Bonn.
This study would not have been possible without the Cactaceae living collections at the Botanical Gardens Bonn and BGBM. We are grateful to W. Lobin (curator) and O. Kriesten and B. Emde (Bonn) and to A.‐D. Stevens, U. Radke, C. Schrader, and H. Wilke from BGBM. We thank U. Eggli, Sukkulenten Sammlung Zürich, Switzerland, for providing material of
Schlumbergera microsphaerica
ObjectType-Article-1
SourceType-Scholarly Journals-1
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content type line 23
ISSN:0002-9122
1537-2197
DOI:10.3732/ajb.1000502