Molecular Evolution and Phylogenetic Utility of the Chloroplastrpl16Intron inChusqueaand the Bambusoideae (Poaceae)

Kelchner, Scot A.; Clark, Lynn G.

doi:10.1006/mpev.1997.0432

Cited by 225 publications

(205 citation statements)

References 52 publications

Supporting

Mentioning

193

Contrasting

Order By: Relevance

“…The outgroup (Cannabaceae) differ from the ingroup by six indels (2, 14, 18, 19, 20 & 21), although indel 19 (a 6 bp insertion) has been subsequently lost in both species of Procris. This case of homoplasy (reversal or parallel origins) is interesting, since the indel is not a duplication of adjacent sequence, a type that has been observed to be common in spacer regions , Kelchner & Clark 1997. It is possible that secondary structure of the trnL-F spacer region may be responsible for the loss of the inserted region in its entirety, although there was no evidence of complementary segments of sequence on either side of the insertion which might promote the formation of a loop (Kelchner & Wendel 1996).…”

Section: Discussionmentioning

confidence: 98%

Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data

Hadiah¹,

Quinn²,

Conn³

2003

Telopea

View full text Add to dashboard Cite

using chloroplast DNA data. Telopea 10(1) [235][236][237][238][239][240][241][242][243][244][245][246]. Phylogenetic analyses of the Urticales, based on chloroplast DNA data, support the monophyly of the Urticaceae, Boehmeria, Pilea and Procris, but not of Elatostema. Our result suggests that the circumscription of Procris is to be extended or included within Elatostema. At the tribal level, both Boehmerieae and Lecantheae appear paraphyletic, although this may be an artefact of the low taxon sampling. Preliminary analyses of relationships within Elatostema do not support the recognition of the subgenus Pellionia.

show abstract

Section: Discussionmentioning

confidence: 98%

Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data

Hadiah¹,

Quinn²,

Conn³

2003

Telopea

View full text Add to dashboard Cite

show abstract

“…The rps16 region was amplified using the primers rps16F and rps16R2 (Oxelman & al., 1997). The rpl16 intron was amplified using primers rpl16 71F (Jordan & al., 1996) and rpl16 1516R (Kelchner & Clark, 1997). The intergenic spacer between the atpB and rbcL genes was amplified using primers 2 and 5 (Manen & al., 1994).…”

Section: Version Of Recordmentioning

confidence: 99%

Phylogenetic placement and generic re‐circumscriptions of the multilocular generaArenifera,OctopomaandSchlechteranthus(Aizoaceae: Ruschieae): Evidence from anatomical, morphological and plastid DNA data

Powell

Boatwright

Klak

et al. 2016

TAXON

View full text Add to dashboard Cite

Ruschieae is the largest tribe in the highly speciose subfamily Ruschioideae (Aizoaceae). A generic-level phylogeny for the tribe was recently produced, providing new insights into relationships between the taxa. Octopoma and Arenifera are woody shrubs with multilocular capsules and are distributed across the Succulent Karoo. Octopoma was shown to be polyphyletic in the tribal phylogeny, but comprehensive sampling is required to confirm its polyphyly. Arenifera has not previously been sampled and therefore its phylogenetic placement in the tribe is uncertain. In this study, phylogenetic sampling for nine plastid regions matK, rpl16, rps16, was expanded to include all species of Octopoma and Arenifera, to assess phylogenetic placement and relationships of these genera. Three phylogenetic analyses were carried out, maximum parsimony, maximum likelihood and Bayesian inference. Leaf anatomical sections were studied to further inform generic circumscriptions. The phylogenies showed Octopoma to be polyphyletic, with the type, O. octojuge, and the related O. nanum, resolved as sister to Zeuktophyllum and Smicrostigma, while the other species were placed in the Conophytum-clade. Arenifera was also shown to be polyphyletic, with the type, A. pillansii, placed in the xeromorphic-clade, and the remainder of the species recovered among the Octopoma species in the Conophytum-clade (forming the Octopoma subglobosum-Arenifera spinescens subclade). Generic affinities of the O. subglobosum-A. spinescens subclade were assessed in relation to the sister taxon Schlechteranthus. The leaf anatomy was found to be informative within the study group. Bladder cells were observed in Arenifera pillansii, a hypodermis in Little Karoo Octopoma (O. octojuge, O. nanum, O. quadrisepalum) and epidermal cells forming blunt papillae in Schlechteranthus and the O. subglobosum-A. spinescens subclade. Upon assessment of the anatomical, morphological and phylogenetic data, Schlechteranthus is here expanded to include the species in the O. subglobosum-A. spinescens subclade. Eight new combinations are made in Schlechteranthus. As a result, Arenifera is again monotypic and the circumscription of Octopoma is refined to include three species restricted to the Little Karoo. Two subgenera within Schlechteranthus s.l. (subg. Schlechteranthus, subg. Microphyllus) are erected to accommodate differences in leaf size, capsule size, closing body size and locule number.

show abstract

“…Huntley and Clark 2007;Messer and Arndt 2007), and yet they are detected only poorly by most alignment programs. Furthermore, small inversions often go undetected because the programs do not look for them explicitly, and therefore interpret them as multiple adjacent substitutions (Kelchner and Wendel 1996;Kelchner and Clark 1997;Graham et al 2000;Quandt and Stech 2005).…”

Section: Terminologymentioning

confidence: 99%

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

Morrison

Morgan

Kelchner

2015

Aust. Systematic Bot.

View full text Add to dashboard Cite

Abstract. Sequence alignment is just as much a part of phylogenetics as is tree building, although it is often viewed solely as a necessary tool to construct trees. However, alignment for the purpose of phylogenetic inference is primarily about homology, as it is the procedure that expresses homology relationships among the characters, rather than the historical relationships of the taxa. Molecular homology is rather vaguely defined and understood, despite its importance in the molecular age. Indeed, homology has rarely been evaluated with respect to nucleotide sequence alignments, in spite of the fact that nucleotides are the only data that directly represent genotype. All other molecular data represent phenotype, just as do morphology and anatomy. Thus, efforts to improve sequence alignment for phylogenetic purposes should involve a more refined use of the homology concept at a molecular level. To this end, we present examples of molecular-data levels at which homology might be considered, and arrange them in a hierarchy. The concept that we propose has many levels, which link directly to the developmental and morphological components of homology. Of note, there is no simple relationship between gene homology and nucleotide homology. We also propose terminology with which to better describe and discuss molecular homology at these levels. Our over-arching conceptual framework is then used to shed light on the multitude of automated procedures that have been created for multiple-sequence alignment. Sequence alignment needs to be based on aligning homologous nucleotides, without necessary reference to homology at any other level of the hierarchy. In particular, inference of nucleotide homology involves deriving a plausible scenario for molecular change among the set of sequences. Our clarifications should allow the development of a procedure that specifically addresses homology, which is required when performing alignment for phylogenetic purposes, but which does not yet exist.

show abstract

Molecular Evolution and Phylogenetic Utility of the Chloroplastrpl16Intron inChusqueaand the Bambusoideae (Poaceae)

Cited by 225 publications

References 52 publications

Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data

Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data

Phylogenetic placement and generic re‐circumscriptions of the multilocular generaArenifera,OctopomaandSchlechteranthus(Aizoaceae: Ruschieae): Evidence from anatomical, morphological and plastid DNA data

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

Contact Info

Product

Resources

About