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2.
Plant Biol (Stuttg) ; 17 Suppl 1: 50-8, 2015 Jan.
Article in English | MEDLINE | ID: mdl-24942778

ABSTRACT

Nuclear DNA sequence data are essential for obtaining a complete understanding of plant species relationships, yet these data have been conspicuously absent from phylogenetic analyses of Lemnaceae (duckweeds). Using a modified Sanger sequencing protocol, we obtained DNA sequences of duckweed nuclear ribosomal regions, including 18S and 26S rDNA genes, the external transcribed spacer (ETS) and the frequently used internal transcribed spacer (ITS). After obtaining sequence data for all Lemnaceae species, we ascertained that prior difficulty in sequencing the ITS regions likely resulted from extremely rigid secondary structures, precipitated by a high proportion of G/C nucleotides. In phylogenetic analyses, nuclear ribosomal data largely supported relationships that had been inferred using chloroplast DNA sequence data.


Subject(s)
Araceae/genetics , Cell Nucleus/genetics , DNA, Ribosomal/genetics , Phylogeny , DNA, Chloroplast/genetics , DNA, Ribosomal Spacer/genetics , Genome, Plant , Molecular Sequence Data , Nucleic Acid Conformation , Sequence Alignment , Sequence Analysis, DNA
3.
Mol Biol Evol ; 16(11): 1511-20, 1999 Nov.
Article in English | MEDLINE | ID: mdl-10555282

ABSTRACT

Simplified DNA sequence acquisition has provided many new data sets that are useful for phylogenetic reconstruction, including single- and multiple-copy nuclear and organellar genes. Although transcribed regions receive much attention, nontranscribed regions have recently been added to the repertoire of sequences suitable for phylogenetic studies, especially for closely related taxa. We evaluated the efficacy of a small portion of the histone repeat for phylogenetic reconstruction among Drosophila species. Histone repeats in invertebrates offer distinct advantages similar to those of widely used ribosomal repeats. First, the units are tandemly repeated and undergo concerted evolution. Second, histone repeats include both highly conserved coding and variable intergenic regions. This composition facilitates application of "universal" primers spanning potentially informative sites. We examined a small region of the histone repeat, including the intergenic spacer segments of coding regions from the divergently transcribed H2A and H2B histone genes. The spacer (about 230 bp) exists as a mosaic with highly conserved functional motifs interspersed with rapidly diverging regions; the former aid in alignment of the spacer. There are no ambiguities in alignment of coding regions. Coding and noncoding regions were analyzed together and separately for phylogenetic information. Parsimony, distance, and maximum-likelihood methods successfully retrieve the corroborated phylogeny for the taxa examined. This study demonstrates the resolving power of a small histone region which may now be added to the growing collection of phylogenetically useful DNA sequences.


Subject(s)
Drosophila/genetics , Histones/genetics , Phylogeny , Animals , Base Sequence , DNA , Molecular Sequence Data , Sequence Homology, Nucleic Acid
4.
Am J Bot ; 86(9): 1316-24, 1999 Sep.
Article in English | MEDLINE | ID: mdl-10487819

ABSTRACT

The genus Nuphar consists of yellow-flowered waterlilies and is widely distributed in north-temperate bodies of water. Despite regular taxonomic evaluation of these plants, no explicit phylogenetic hypotheses have been proposed for the genus. We investigated phylogenetic relationships in Nuphar using morphology and sequences of the chloroplast gene matK and of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Two major lineages within Nuphar are consistently resolved with the morphological and molecular data sets. One lineage comprises New World taxa and the other represents a primarily Old World lineage. Relationships within the major lineages were poorly resolved by morphology and ITS, yet certain relationships were elucidated by all analyses. Most notable is the strong support for a monophyletic lineage of dwarf taxa and the alliance of the North American N. microphylla with the Eurasian taxa. Minor discordance between the independent cladograms is accounted for by hybridization. The common taxonomic practice of uniting all North American and Eurasian taxa under one species is not supported phylogenetically.

5.
Mol Phylogenet Evol ; 2(4): 304-14, 1993 Dec.
Article in English | MEDLINE | ID: mdl-8049779

ABSTRACT

Within the angiosperm subclass Alismatidae (= superorder Alismatiflorae), contemporary taxonomists have often assigned the families Hydrocharitaceae and Najadaceae to different orders. The Najadaceae are presumably allied to a variety of aquatic families in the order Najadales, whereas the Hydrocharitaceae have been segregated as the order Hydrocharitales or placed within the order Alismatales. Analysis of DNA sequence data from the chloroplast gene rbcL, however, indicate that Najadaceae have a much closer phylogenetic relationship to Hydrocharitaceae than to families of the "Najadales" (Cymodoceaceae, Potamogetonaceae, Ruppiaceae, Scheuchzeriaceae, Zannichelliaceae, Zosteraceae). This association supports previous studies based upon examination of floral structure and seed coat anatomy. The rbcL sequence data also indicate that the Zosteraceae and Potamogetonaceae are closely related families. The rbcL sequence of Zostera is actually more similar to that of Potamogeton richardsonii than is the sequence of the latter to a congener, Potamogeton amplifolius. The marine, dioecious, hydrophilous genus Zostera has acquired a number of distinctive adaptations, but probably diverged relatively rapidly from freshwater Potamogetonaceae. Molecular data place Ruppiaceae as a sister group to the marine Cymodoceaceae and do not support the commonly accepted merger of Ruppiaceae and Potamogetonaceae.


Subject(s)
Phylogeny , Plants/classification , Plants/genetics , Base Sequence , DNA Primers/genetics , Genes, Plant , Molecular Sequence Data , Sequence Homology, Nucleic Acid , Species Specificity
6.
Proc Natl Acad Sci U S A ; 88(22): 10119-23, 1991 Nov 15.
Article in English | MEDLINE | ID: mdl-1946432

ABSTRACT

Aquatic plants are notoriously difficult to study systematically due to convergent evolution and reductionary processes that result in confusing arrays of morphological features. Plant systematists have frequently focused their attention on the "water lilies," putative descendants of the most archaic angiosperms. Classification of these 10 plant genera varies from recognition of one to three orders containing three to six families. We have used DNA sequence analysis as a means of overcoming many problems inherent in morphologically based studies of the group. Phylogenetic analyses of sequence data obtained from a 1.2-kilobase portion of the chloroplast gene rbcL provide compelling evidence for the recognition of three distinct lineages of "water lily" plants. Molecular phylogenies including woody Magnoliidae sequences and sequences of these aquatic plants depict Ceratophyllum as an early diverging genus. Our results support hypotheses that most taxonomic concepts of the order Nymphaeales reflect polyphyletic groups and that the unusual genus Ceratophyllum represents descendants of some of the earliest angiosperms.


Subject(s)
Biological Evolution , DNA/genetics , Plants/genetics , Base Sequence , Genome , Molecular Sequence Data , Phylogeny , Polymerase Chain Reaction , Probability , Sequence Homology, Nucleic Acid , Water
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