Recent Origin and Phylogenetic Utility of Divergent ITS Putative Pseudogenes: A Case Study from Naucleeae (Rubiaceae) (original) (raw)
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Phylogenetic Analysis of Chloroplast DNA Variation inCoffeaL
Molecular Phylogenetics and Evolution, 1998
Coffee trees (family Rubiaceae) are classified in two genera, Coffea and PsiZanthus, each genus being divided into two subgenera (Bridson and Verdcourt, 1988). All Coffea species are native to the intertropical The trnLrtntF intergenic spacer of cpDNA has been sequenced from 38 tree samples representing 23 Coflea taxa. and the related. genus PsiZanthus. These sespecific hybrid&ation onvergence (Doebley, 1992; Riese-109
The use of herbarium specimens in DNA phylogenetics: Evaluation and improvement
Plant Systematics and Evolution, 1995
Abstraet: Variation in chloroplast rbcL sequences was studied in representative species of four different lineages: the tribe Rubieae (Rubiaceae), and the genera Drosera (Droseraceae), Nothofagus (Nothofagaceae) and llex (Aquifoliaceae). Each lineage has its particular non-overlapping set of rbcL polymorphic sites, indicating that common unconstrained rbcL sites are not shared. Large differences in the rate and pattern of nucleotide substitution are observed among the four lineages. The genus Ilex has the lowest rate of substitution, the lowest transition/transversion ratio, the lowest synonymous/ replacement ratio and the lowest number of substitutions at the third codon position. An apparent relationship of these measures to the age of the lineages is observed. The A + T content and codon use among the four lineages are very similar and, apparently, cannot account for the observed differences in pattems of nucleotide substitution. However, the A + T content of the two bases immediately flanking the polymorphic sites is higher in Ilex than in the other lineages. This could be correlated with the transversion/transition bias observed in Ilex. The particularly low synonymous/replacement ratio found in Ilex could also be explained by the small population sizes of species in this genus.
Journal of Phycology, 2001
To better assess the current state of phaeophycean phylogeny, we compiled all currently available rbc L, 18S, and 26S rDNA sequences from the EMBL/GenBank database and added 21 new rbc L sequences of our own. We then developed three new alignments designed to maximize taxon sampling while minimizing information loss due to partial sequences. Phylogenetic analyses were performed on separate and combined data sets (with and without taxa from the sister classes Tribophyceae and Phaeothamniophyceae as outgroups) using a variety of assumption sets, tree-drawing algorithms (parsimony, neighbor joining, and likelihood), and resampling methods (bootstrap, decay, jackknife). Partition homogeneity testing (PHT) by codon position within rbc L showed that all positions could be used despite mild third position saturation. PHT by gene and domain within rDNA showed that the 26S D1 and D2 regions do not enhance phylogenetic signal even when combined with the 18S. The rbc L and rDNA (excluding the 26S D1 and D2) could be combined under PHT. The topology of the combined tree was the same as that of the rbc L tree alone, but bootstrap support was consistently higher in the combined analysis, applied to more branches, and enabled the establishment of sister group relationships among six orders. Although the taxon sampling for the combination tree was lower ( n ϭ 22) than for individual gene analyses ( n ϭ 58 for rbc L and n ϭ 59 for rDNA), results show that the Laminariales (previously reported) and Sphacelariales (new) are both paraphyletic. Choristocarpus tenellus (Kützing) Zanardini is the most basal phaeophyte and the Dictyotales the most basal order. In contrast, the Laminariales sensu stricto ( s.s. ) and Ectocarpales sensu lato ( s.l. ) are the most derived. For phylogenetic studies in the Phaeophyceae, rbc L has more resolving power than rDNA, though the reason for this is unclear based on the fact that both genes are highly conserved.
Molecular Phylogenetics and Evolution, 2005
This study focused on clarifying phylogenetic relationships and evolution within Caricaceae. Our phylogenetic analysis based on nucleotide sequences from the ITS of the ribosomal DNA and three chloroplast fragments (matK, trnL-trnF, and psbA-trnH) included 29 taxa belonging to Wve genera: the neotropical genera Carica, Vasconcellea, Jarilla, and Jacaratia and the equatorial African genus Cylicomorpha. Having a relatively low mutation rate, matK, and trnL-trnF were used for estimating relationships at the generic level, while intrageneric evolution within Vasconcellea was studied with the more variable ITS and psbA-trnH sequences. Gaps, coded as binary characters, were added to the sequence alignments before performing Maximum Parsimony and Maximum Likelihood analyses. Monophyly of Caricaceae as well as phylogenetic distance between Carica and Vasconcellea species, previously belonging to the same genus, and monophyly of the resurrected genus Vasconcellea were emphasized. Within Vasconcellea, the largest genus of this family, two well-conWrmed evolutionary lineages could be discerned: (1) V. £ heilbornii, V. weberbaueri, V. stipulata, and V. parviXora and (2) a clade holding all other taxa of the genus. Incongruence between nuclear ITS and chloroplast psbA-trnH datasets, shown to be signiWcantly caused by some taxa of the genus Vasconcellea, indicated that reticulate events in this genus might be more frequent than previously suspected. Moreover, intra-individual ITS sequence heterogeneity provided further evidence for the hybrid or introgressed origin of diVerent taxa and one presumed hybrid belonging to this genus.
Inferring phylogenetic relationships among closely related plant species is often difficult due to the lack of molecular markers exhibiting enough nucleotide variability at this taxonomic level. Moreover, gene tree does not necessary represent the true species tree because of random sorting of polymorphic alleles in different lineages. A solution to these problems is to use many amplified fragment length polymorphisms (AFLP) distributed throughout the whole genome, to infer cladistic and phenetic among-species relationships. Phylogenetic relationships among interfertile species of Trollius L. (Ranunculaceae) were investigated using nuclear DNA (ITS1 + 5.8S rRNA + ITS2) and chloroplast DNA (trnL intron and trnL–trnF intergene spacer) sequences, and AFLP markers. ITS sequences were not informative at the intrageneric level, but confirmed the sister relationship between Trollius and Adonis genera, and provided new information on the phylogenetic relationships among five Ranunculaceae genera. Chloroplast DNA was more informative among Trollius species, but not consistent with the sections previously described. AFLP proved to be a powerful tool to resolve the complex genetic relationships between the morphological entities constituting the genus Trollius. Although as much as 76.1% of the total AFLP variability was found within a priori defined morphological groups, the remaining 23.9% variability differentiating groups was sufficient to generate congruent and robust cladistic and phenetic trees. Several morphological traits, independent from those used to define groups, were mapped onto the molecular phylogeny, and their evolution discussed in relation to the absence/presence of pollinator-seed parasite Chiastocheta flies.
Phylogenetics of sees plants: An analysis of nucleotide sequences from the plastid gene rbcL
1993
We present the results of two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups. The data are exclusively from the chloroplast gene rbcL, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO or RuBPCase). We used two different state-transformation assumptions resulting in two sets of cladograms: (i) equal-weighting for the 499-taxon analysis; and (ii) a procedure that differentially weights transversions over transitions within characters and codon positions among characters for the 475-taxon analysis. The degree of congruence between these results and other molecular, as well as morphological, cladistic studies indicates that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Because the topologies presented are necessarily approximate and cannot be evaluated adequately for internal support, these results should be assessed from the perspective of their predictive value and used to direct future studies, both molecular and morphological. In both analyses, the three genera of Gnetales are placed together as the sister group of the flowering plants, and the anomalous aquatic Ceratophyllum (Ceratophyllaceae) is sister to all other flowering plants. Several major lineages identified correspond well with at least some recent taxonomic schemes for angiosperms, particularly those of Dahlgren and Thorne. The basalmost clades within the angiosperms are orders of the apparently polyphyletic subclass Magnoliidae sensu Cronquist. The most conspicuous feature of the topology is that the major division is not monocot versus dicot, but rather one correlated with general pollen type: uniaperturate versus triaperturate. The Dilleniidae and Hamamelidae are the only subclasses that are grossly polyphyletic; an examination of the latter is presented as an example of the use of these broad analyses to focus more restricted studies. A broadly circumscribed Rosidae is paraphyletic to Asteridae and Dilleniidae. Subclass Caryophyllidae is monophyletic and derived from within Rosidae in the 475-taxon analysis but is sister to a group composed of broadly delineated Asteridae and Rosidae in the 499-taxon study.
LAS Johnson Review No. 2. Use of nuclear genes for phylogeny reconstruction in plants
2004
Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies.
Botanical Journal of the Linnean Society
The aim of this study was to identify major clades in the economically important and taxonomically difficult genus Ferula (Apiaceae tribe Scandiceae subtribe Ferulinae) to provide a classification framework. Phylogenetic relationships among 126 of Ferula spp. and eight species of its sister genus Leutea were evaluated based on nuclear ribosomal (nr) DNA ITS and three plastid regions: the rps16 intron, the rpoC1 intron and the rpoB-trnC intergenic spacer. One hundred and fifty-three accessions were considered including type specimens of seven species. Congruence between nrDNA and plastid DNA data was assessed using a hierarchical likelihood ratio test. Phylogenetic trees were inferred using maximum likelihood and Bayesian methods. Terminals introducing topological conflict were ascertained using two approaches: identifying (1) these with significantly different positions between nrDNA and plastid DNA trees; and (2) a set of rogue taxa in combined trees that, when removed, increased tree resolution and bootstrap support. The results demonstrate significant incongruence between nrDNA and plastid DNA data that persisted after the removal of 41 terminals identified as having significantly different position in nrDNA and plastid DNA trees or after the removal of 13 terminals identified as rogue taxa. Comparison of nrDNA and plastid DNA trees suggest intensive reticulate evolution, particularly in the Irano-Turanian floristic region. Traditional classification systems of the genus are not supported by molecular data, whereas some lineages apparent in molecular trees, particularly Chinese and Mediterranean endemics, are congruent with morphological characters and/or biogeography. We select lectotypes for several infrageneric names and propose a new classification system of the genus with four subgenera and ten sections.
Molecular Phylogenetics and Evolution, 2005
Noncoding DNA sequences from numerous regions of the chloroplast genome have provided a signiWcant source of characters for phylogenetic studies in seed plants. In lycophytes and monilophytes (leptosporangiate ferns, eusporangiate ferns, Psilotaceae, and Equisetaceae), on the other hand, relatively few noncoding chloroplast DNA regions have been explored. We screened 30 lycophyte and monilophyte species to determine the potential utility of PCR ampliWcation primers for 18 noncoding chloroplast DNA regions that have previously been used in seed plant studies. Of these primer sets eight appear to be nearly universally capable of amplifying lycophyte and monilophyte DNAs, and an additional six are useful in at least some groups. To further explore the application of noncoding chloroplast DNA, we analyzed the relative phylogenetic utility of Wve cpDNA regions for resolving relationships in Botrychium s.l. (Ophioglossaceae). Previous studies have evaluated both the gene rbcL and the trnL UAA -trnF GAA intergenic spacer in this group. To these published data we added sequences of the trnS GCU -trnG UUC intergenic spacer + the trnG UUC intron region, the trnS GGA -rpS4 intergenic spacer + rpS4 gene, and the rpL16 intron. Both the trnS GCU -trnG UUC and rpL16 regions are highly variable in angiosperms and the trnS GGA -rpS4 region has been widely used in monilophyte phylogenetic studies. Phylogenetic resolution was equivalent across regions, but the strength of support for the phylogenies varied among regions. Of the Wve sampled regions the trnS GCU -trnG UUC spacer + trnG UUC intron region provided the strongest support for the inferred phylogeny.
Plant Systematics and Evolution, 1991
A restriction site map of the chloroplast genome of Caltha palustris L. (Ranunculaceae) has been constructed for 13 restriction endonucleases using filter hybridization with cloned tobacco chloroplast DNA fragments. A size of 153.8 kb has been estimated for the Ca#ha chloroplast genome. Forty-six chloroplast genes and four open reading frames have been mapped using small tobacco chloroplast gene probes. Chloroplast DNA sequence divergence has been estimated for all pairs of five species of Ranunculaceae, Caltha palustris, Ranunculus bulbosus, R. fascicularis, R. recurvatus, and Trollius ledebourii, and ranges between 0.2% and 9.6% for the total genome. Divergence values are much higher in the small and large single copy regions than in the inverted repeat. Phylogenetic relationships between the five species have been hypothesized using chloroplast DNA restriction site mapping. One hundred and six informative restriction site mutations have been detected using eleven restriction endonucleases. Cladistic analyses o f the restriction site mutations have been performed using Wagner and Dollo parsimony algorithms, and confidence intervals have been calculated for the resulting monophyletic groups using bootstrapping. It is demonstrated that restriction site comparisons are applicable to the Ranunculaceae on intergeneric level, with the exception of groups having extensive genomic rearrangements. Moreover, sequence divergence is low enough at the interspecific level to allow phylogenetic analyses within genera such as Ranunculus.