Number Of Parsimony Informative Characters Research Articles

Phylogenetic placement of Trifolium kentuckiense (Fabaceae), a new member of the native eastern North American clover clade

In 2013, a new species of clover endemic to Kentucky was described. This species, Trifolium kentuckiense (Fabaceae), has yet to be placed in a phylogeny but is hypothesized to be most closely related to T. reflexum based on morphology. We present phylogenetic evidence from the nuclear (ITS) and plastid genomes (trnL and ndhA introns) that T. kentuckiense is a member of a clade of seven Trifolium species native to eastern North America. Within this clade, T. kentuckiense is strongly placed in a clade with three other annual/biennial Trifolium species (T. bejariense, T. carolinianum, and T. reflexum); it is sister to T. reflexum, although support for this relationship is weak. Our results support previous findings that suggest the ndhA intron is much more variable than the trnL intron in the Eurosid I clade. The ndhA intron contained over twice the number of parsimony informative characters when compared to the trnL intron, though ITS was more variable than either region. We also provide a dichotomous key to native and nonnative members of Trifolium for Kentucky and its surrounding states. We suggest determinations of historic specimens of Trifolium, particularly those identified as T. reflexum, be reassessed to obtain localities that may still support populations of this recently described species. We also provide guidance on when and in what habitats to search for new populations of this extremely rare taxon.

Phylogenetic positions of seven poorly known species of Ferula (Apiaceae) with remarks on the phylogenetic utility of the plastid trnH-psbA, trnS-trnG, and atpB-rbcL intergenic spacers

Ferula L. is one of the most species-rich and taxonomically difficult genera of Apiaceae. In this study, we obtained nrDNA ITS sequences of seven poorly known species of Ferula (Ferula anatolica, Ferula sp. (tentatively identified as F. candelabrum by collectors), F. drudeana, F. huber-morathii, F. marmarica, F. talassica, and F. tunetana) and explored their phylogenetic positions using 148 ITS sequences of the subtribe Ferulinae from GenBank. Five of these newly sequenced species fall into three groups, corresponding to clades recognized in earlier molecular studies. Ferula sp. are added to clade, which is mostly composed of Central Asian species. This placement showed that identification as F. candelabrum was erroneous. The second clade, which is mostly composed of Mediterranean taxa, includes two species from North Africa: F. marmarica and F. tunetana. Despite the well-supported monophyly of this clade, the relationships inside this group need to be revised, as broadly distributed F. communis is paraphyletic with respect to other species. Ferula drudeana and F. huber-morathii, two narrow endemics from Turkey, are placed in the Central Asian clade. Two species, F. anatolica and F. talassica, do not fall into any of the recognized clades. In addition, we examined the sequence variation of three potentially highly variable pDNA regions, the trnH-psbA, trnS-trnG, and atpB-rbcL intergenic spacers, for a subset of 18 specimens. The resulting pDNA and ITS based phylogenetic trees were incongruent, as supported by significant ILD tests. The cause of this incongruence can be manifold, including hybridization, a lack of a phylogenetic signal, and homoplastic substitutions. Our analyses suggest that only trnS-trnG can be added to the list of pDNA markers used for phylogenetic studies of Ferula, as it has the highest number of parsimony informative characters and is easy to amplify from degraded material.

Application of the phylogenetic informativeness method to chloroplast markers: A test case of closely related species in tribe Hydrangeeae (Hydrangeaceae)

In evolutionary biology appropriate marker selection for the reconstruction of solid phylogenetic hypotheses is fundamental. One of the most challenging tasks addresses the appropriate choice of genomic regions in studies of closely related species. Robust phylogenetic frameworks are central to studies dealing with questions ranging from evolutionary and conservation biology, biogeography to plant breeding. Phylogenetic informativeness profiles provide a quantitative measure of the phylogenetic signal in markers and therefore a method for locus prioritization. The present work profiles phylogenetic informativeness of mostly non-coding chloroplast regions in an angiosperm lineage of closely related species: the popular ornamental tribe Hydrangeeae (Hydrangeaceae, Cornales, Asterids). A recent phylogenetic study denoted a case of resolution contrast between the two strongly supported clades within tribe Hydrangeeae. We evaluate the phylogenetic signal of 13 highly variable plastid markers for estimating relationships within and among the currently recognized monophyletic groups of this tribe. A selection of combined loci based on their phylogenetic informativeness retrieved more robust phylogenetic hypotheses than simply combining individual markers performing best with respect to resolution, nodal support and accuracy or those presenting the highest number of parsimony informative characters. We propose the rpl32–ndhF intergenic spacer (IGS), trnV–ndhC IGS, trnL–rpl32 IGS, psbT–petB region and ndhA intron as the best candidates for future phylogenetic studies in Hydrangeeae and potentially in other Asterids. We also contrasted the phylogenetic informativeness of coded indels against substitutions concluding that, despite their low phylogenetic informativeness, coded indels provide additional phylogenetic signal that is nearly free of noise. Phylogenetic relationships obtained from our total combined analyses showed improved resolution and nodal support with respect to recently published results.

Molecular Phylogeny of Ladybird Beetles (Coccinellidae: Coleoptera) Inferred from Mitochondrial 16S rDNA Sequences

Although ladybird beetles (Coccinellidae: Coleoptera) are charismatic and have great ecological and economic significance, understanding of the evolutionary history of Coccinellidae remains poor. Many hypothesis of evolutionary relationships based on morphological features have been proposed, but none have been verified using a formal phylogenetic analysis. The objectives of this study was to apply molecular evidence of 16S rDNA to construct a molecular phylogeny for ladybird beetles, examining the monophyly of the tribes and several lower-level taxa within the group, and to establish basic phylogenetic patterns. 16S rDNA fragments were sequenced from 47 species of in-group and two species of out-group taxa. DNA data showed evidences of rapid evolution and saturation, having AT and transition at a higher level. 16S rDNA gene region indicated the availability of phylogenetic signals with the presence of skewness with significant hierarchical structure as well as having higher number of parsimony informative characters. Trees were reconstructed using multiple methods and characters mapped on the topology via Neigbour Joining and Minimum Evolution methods. 16S rDNA phylogenetic analyses were supported well on below tribe level relationships of the subfamilies. The genus level is prominent accumulating together the species belonging to same genus in all tribes. Results suggest that the molecular data provide robust support across the topology below tribe level and below genus level and that this topology provides important new insights as well as confirming the existing positions of the species in the evolution of the ladybird beetles. DOI: 10.4038/tar.v21i2.2602 Tropical Agricultural Research Vol. 21(2): 209-217 (2009)

A molecular phylogenetic study of Hemsleya (Cucurbitaceae) based on ITS, rpl16, trnH-psbA, and trnL DNA sequences

This paper presents the first molecular phylogeny of the genus Hemsleya using nuclear ITS and plastid trnH-psbA, rpl16, and trnL DNA sequences to examine the relationships among Hemsleya species. Phylogenetic relationships were elucidated using a combined analysis of all four datasets, however, the number of parsimony-informative characters was still insufficient to resolve all relationships. Parsimony and Bayesian trees were highly congruent. Twenty-three species of Hemsleya split into two major clades corresponding to two subgenera, i.e., subg. Graciliflorae and subg. Hemsleya. These results are partly in agreement with Li’s sectional classification. However, the molecular data are inconsistent with Li’s classification at the subsectional level. The molecular phylogeny revealed a striking overall correlation between the phylogenetic relationships of the species and their geographical distribution. The Kangdian ancient landmass could be the center of origin of the genus.

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield phylogenetic structure at various levels of a tree (i.e., along the spine and at the tips of the branches). Here, we demonstrate the phylogenetic utility of a heretofore unused portion of a plastid protein-coding gene, hypothetical chloroplast open reading frame 1 (ycf1), in orchids. All portions of ycf1 examined are highly variable, yet alignable across Orchidaceae, and are phylogenetically informative at the level of species. In Orchidaceae, ycf1 is more variable than matK both in total number of parsimony informative characters and in percent variability. The nrITS region is more variable than ycf1, but is more difficult to align. Although we only demonstrate the phylogenetic utility of ycf1 in orchids, it is likely to be similarly useful among other plant taxa.

The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae

The phylogenetic utility of chloroplast ( atpB-rbcL, petD, rps16, trnL-F) and nuclear (ETS, ITS) DNA regions was investigated for the tribe Spermacoceae of the coffee family (Rubiaceae). ITS was, despite often raised cautions of its utility at higher taxonomic levels, shown to provide the highest number of parsimony informative characters, in partitioned Bayesian analyses it yielded the fewest trees in the 95% credible set, it resolved the highest proportion of well resolved clades, and was the most accurate region as measured by the partition metric and the proportion of correctly resolved clades (well supported clades retrieved from a combined analysis regarded as “true”). For Hedyotis, the nuclear 5S-NTS was shown to be potentially as useful as ITS, despite its shorter sequence length. The chloroplast region being the most phylogenetically informative was the petD group II intron. We also present a phylogeny of Spermacoceae based on a Bayesian analysis of the four chloroplast regions, ITS, and ETS combined. Spermacoceae are shown to be monophyletic. Clades supported by high posterior probabilities are discussed, especially in respect to the current generic classification. Notably, Oldenlandia is polyphyletic, the two subgenera of Kohautia are not sister taxa, and Hedyotis should be treated in a narrow sense to include only Asian species.

Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci

Plant molecular systematic studies of closely related taxa have relied heavily on sequence data from nuclear ITS and cpDNA. Positive attributes of using ITS sequence data include the rapid rate of evolution compared to most plastid loci and availability of universal primers for amplification and sequencing. On the other hand, ITS sequence data may not adequately track organismal phylogeny if concerted evolution and high rDNA array copy number do not permit identification of orthologous copies. Shaw et al. (American Journal of Botany 92: 142-166) recently identified nine plastid regions that appear to provide more potentially informative characters than many other plastid loci. In the present study, sequences of these loci and ITS were obtained for six taxonomic groups in which phylogenetic relationships have been difficult to establish using other data. The relative utility of these regions was compared by assessing the number of parsimony informative characters, character congruence, resolution of inferred trees, clade support, and accuracy. No single locus emerged as the best in all lineages for any of these measures of utility. Results further indicated that in preliminary studies, sampling strategy should include at least four exemplar taxa. The importance of sampling data from independent distributions is also discussed.

Phylogenetic utility of protein (RPB2, β-tubulin) and ribosomal (LSU, SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota, Fungi)

The Sordariomycetes is an important group of fungi whose taxonomic relationships and classification is obscure. There is presently no multi-gene molecular phylogeny that addresses evolutionary relationships among different classes and orders. In this study, phylogenetic analyses with a broad taxon sampling of the Sordariomycetes were conducted to evaluate the utility of four gene regions (LSU rDNA, SSU rDNA, beta-tubulin and RPB2) for inferring evolutionary relationships at different taxonomic ranks. Single and multi-gene genealogies inferred from Bayesian and Maximum Parsimony analyses were compared in individual and combined datasets. At the subclass level, SSU rDNA phylogenies demonstrate their utility as a marker to infer phylogenetic relationships at higher levels. All analyses with SSU rDNA alone, combined LSU rDNA and SSU rDNA, and the combined 28 S rDNA, SSU rDNA and RPB2 datasets resulted in three subclasses: Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae, which correspond well to established morphological classification schemes. At the ordinal level, the best resolved phylogeny was obtained from the combined LSU rDNA and SSU rDNA datasets. Individually, the RPB2 gene dataset resulted in significantly higher number of parsimony informative characters. Our results supported the recent separation of Boliniaceae, Chaetosphaeriaceae and Coniochaetaceae from Sordariales and placement of Coronophorales in Hypocreomycetidae. Microascales was found to be paraphyletic and Ceratocystis is phylogenetically associated to Faurelina, while Microascus and Petriella formed another clade and basal to other members of Halosphaeriales. In addition, the order Lulworthiales does not appear to fit in any of the three subclasses. Congruence between morphological and molecular classification schemes is discussed.

A preliminary analysis of phylogenetic relationships ofArundinaria and related genera based on nucleotide sequences of nrDNA (ITS region) and cpDNA (trnL-F intergenic spacer)

Phylogenetic relationships ofArundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS) and the cpDNAtrnL-F intergenic spacer (IGS). Comparison withtrnL-F IGS sequence, the ITS region provided the higher number of parsimony informative characters, and the interspecific variation of the ITS sequence was higher than that of thetrnL-FIGS sequence. The tree obtained by combining both sets of data showed that the species sampled inArundinaria and the related genera were monophyletic and divided into two clades. The relationships and positioning of all the taxa surveryed (includingA. oleosa, A. hsienchuensis, A. chino, A. amara, A. yixingensis, A. amabilis, A. fortunei, A. pygmaea, A. gramineus, A. fargesii, A. faberi, A. hupehense, Pseudosasa japonica cv. Tsutsumiana, P. japonica andBrachystachyum densiflorum) were also discussed. The results from the sequences were broadly consistent with morphological characters, appearing all these taxa sampled belong to the genus ofArundinaria. The topologies of the trees generated from individual data and the combined data were similar.

Multi-gene phylogenies indicate ascomal wall morphology is a better predictor of phylogenetic relationships than ascospore morphology in the Sordariales (Ascomycota, Fungi)

Ascospore characters have commonly been used for distinguishing ascomycete taxa, while ascomal wall characters have received little attention. Although taxa in the Sordariales possess a wide range of variation in their ascomal walls and ascospores, genera have traditionally been delimited based on differences in their ascospore morphology. Phylogenetic relationships of multiple representatives from each of several genera representing the range in ascomal wall and ascospore morphologies in the Sordariales were estimated using partial nuclear DNA sequences from the 28S ribosomal large subunit (LSU), β-tubulin, and ribosomal polymerase II subunit 2 (RPB2) genes. These genes also were compared for their utility in predicting phylogenetic relationships in this group of fungi. Maximum parsimony and Bayesian analyses conducted on separate and combined data sets indicate that ascospore morphology is extremely homoplastic and not useful for delimiting genera. Genera represented by more than one species were paraphyletic or polyphyletic in nearly all analyses; 17 species of Cercophora segregated into at least nine different clades, while six species of Podospora occurred in five clades in the LSU tree. However, taxa with similar ascomal wall morphologies clustered in five well-supported clades suggesting that ascomal wall morphology is a better indicator of generic relationships in certain clades in the Sordariales. The RPB2 gene possessed over twice the number of parsimony-informative characters than either the LSU or β-tubulin gene and consequently, provided the most support for the greatest number of clades.

Sequence variation at cpDNA regions of watermelon and related wild species: implications for the evolution of Citrullus haplotypes

Sequencing analysis of one coding and four noncoding cpDNA regions was conducted to infer biogeographic and evolutionary relationships in the genus Citrullus. Eighteen taxa from diverse geographical areas were included. A low number of parsimony informative characters (1.1%) was observed at the ∼4 kb section of cpDNA. Variability within Citrullus was detected primarily at noncoding regions of high A + T content. Substitution rates varied from 0-0.48% for ndhF with A + T content of 68.4% to 0.39- 1.69% for the intergenic region of atpA with A + T content of 82.8%, mainly resulting in indels and transversions. Indels at several regions acted as valuable parsimony informative markers. Citrullus lanatus var. lanatus, the cultivated watermelon, and C. ecirrhosus and C. rehmii from Namibia, lacked molecular variability. The genus Citrullus is supported monophyletically and shows two main clades, one of which contains C. colocynthis. In the other clade, C. rehmii is sister to a clade containing C. ecirrhosus and C. lanatus. Two clades were recovered within C. lanatus, consisting of domesticated watermelon and wild citron, var. citroides. Five haplotypes within C. colocynthis were used to deduce colonization routes of the species. Biogeographic patterns point to separate colonization events into Africa and the Far East.

Phylogeography of the Arctic‐Alpine Saxifraga oppositifolia (Saxifragaceae) and some related taxa based on cpDNA and ITS sequence variation

Saxifraga oppositifolia (Saxifragaceae) is an important model system for the evolution of Arctic-Alpine plant species. Sequences of the psbA-trnH intergenic spacer of chloroplast DNA and of the internal transcribed spacer region, ITS1-5.8S-ITS2, of the nuclear ribosomal DNA were used to investigate the intraspecific evolution and phylogeography of this species. Samples from nearly the species' entire circumpolar distribution were included in the analysis as well as samples from the closely related taxa S. smalliana from Alaska and S. blepharophylla and S. biflora from the Alps (S. aizoides served as outgroup). These latter taxa showed a low number of parsimony informative characters, in both cpDNA and ITS sequences, which separated them from S. oppositifolia. Two main cpDNA haplotypes were detected within S. oppositifolia, one with a Eurasian distribution and one with an East Asian-North American distribution. This confirmed the existence of two cpDNA lineages with different geographical distributions in this species, which had previously been reported based on a RFLP analysis. The ITS phylogeny was not useful with respect to the intraspecific evolution and phylogeography of S. oppositifolia, because it showed a largely unresolved topology with low statistical support. The cpDNA sequence analysis, however, also suggested a putative long-distance dispersal event. All investigated taxa had cpDNA haplotypes that were congruent with their geographical origin rather than their phylogeny. This could point to putative lineage sorting in S. oppositifolia and related taxa.

Phylogenetic analysis with newly characterized Babesia bovis hsp70 and hsp90 provides strong support for paraphyly within the piroplasms

Heat shock induced stress results in transcrip-tional activation of a conserved set of genes andsynthesis of heat shock-related proteins (hsps),which are present in all eukaryotes and prokary-otes [1]. Heat shock represents an unusual stresssituation for most organisms but, in shuttlingbetween vector and host, parasites are constantlysubjected to such stress [2]. Hsps assist the para-site in adapting to a new host environment duringdifferentiation and invasion [2] and are known tohave a chaperone function, forming complexeswith a diverse array of cellular proteins and pep-tides [3].Hsps offer legitimate targets for the evaluationof phylogenetic relationships since they are highlyconserved, with homology across their entirelength [4]. A target represented by a slowly evolv-ing gene (functionally more constrained) is con-sidered appropriate for studying ancientrelationships rather than more recent subspeciesand strain differences [5]. Each set of hsp se-quences provides unambiguous alignment, ensur-ing positional homology at each character in thedata matrix. Phylogenetic analysis utilizing aminoacid sequence of hsps also provides a large num-ber of parsimony informative characters. Twoadvantages this study has over most apicom-plexan phylogenetic analyses, which use thesmaller PCR products generated from the smallsubunit ribosomal RNA genes, are the larger data