scholarly journals A phylogenetic study of Laeliinae (Orchidaceae) based on combined nuclear and plastid DNA sequences

2009 ◽  
Vol 104 (3) ◽  
pp. 417-430 ◽  
Author(s):  
Cássio van den Berg ◽  
Wesley E. Higgins ◽  
Robert L. Dressler ◽  
W. Mark Whitten ◽  
Miguel A. Soto-Arenas ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Plastid Dna ◽  
Phylogenetic Study

Hybridization in the Temperate Bamboos (Poaceae: Bambusoideae: Arundinarieae): A Phylogenetic Study Using AFLPs and cpDNA Sequence Data

2021 ◽  
Vol 46 (1) ◽  
pp. 48-69
Author(s):  
Jimmy K. Triplett ◽  
Lynn G. Clark
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Intergeneric Hybrid ◽  
Plastid Dna ◽  
Sensu Stricto ◽  
Phylogenetic Study ◽  
Aflp Data ◽  
The North ◽  
Cpdna Sequence

Abstract—The temperate bamboos are a taxonomically difficult group with nearly 600 species in approximately 30 genera and at least 12 constituent lineages. In this study, phylogenetic relationships were explored using amplified fragment length polymorphism (AFLP) data in comparison with a phylogeny based on plastid DNA sequences, with an emphasis onArundinariaof North America and its allies in East Asia (theArundinariaclade). Molecular analyses involved 248 individuals in 10 genera and 60 species. Hybridization was detected both within and among genera. Comparative analyses indicated hybrid origins for species in several widespread and well-known genera, includingHibanobambusa,Sasaella, andSemiarundinaria. Evidence also indicated thatPseudosasa japonica(the type species ofPseudosasa) is an intergeneric hybrid involvingPleioblastusandSasamorpha. In addition, cryptic hybrids were detected within and amongPleioblastus,Sasa, andSasamorpha. After accounting for hybrids, phylogenetic analyses of AFLP data provided resolution for core lineages in theArundinariaclade, includingPleioblastussensu stricto,Sasas. s., andSasamorpha.AFLP data also provided evidence for the monophyly of the North American cane bamboos (Arundinaria, three species) but failed to identify their closest relative among the East Asian taxa. The broader evolutionary implications of hybridization in the temperate bamboos are discussed along with recommendations for future studies.

Magnolia sinostellata and relatives (Magnoliaceae)

Phytotaxa ◽  
2013 ◽  
Vol 154 (1) ◽  
pp. 47 ◽  
Author(s):  
YA-LING WANG ◽  
ERLAND EJDER ◽  
JIAN-FEN YANG ◽  
RAO LIU ◽  
LI-MING YE ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Plastid Dna ◽  
Distinct Species ◽  
Morphological Characters ◽  
Phylogenetic Study ◽  
Wild Populations ◽  
Species Status ◽  
Separate Species ◽  
Magnolia Sinostellata ◽  
Normal Meiosis

Magnolia sinostellata has been considered a synonym of Magnolia stellata by several taxonomists due to many shared morphological characters. With similar leaves and twigs, Magnolia amoena is distributed in areas near M. sinostellata. These three species were studied by comparing morphological, cytological and palynological characters, creating a maximum parsimony phylogenetic tree based on plastid DNA sequences and studying these taxa in the field. The results are as follows: M. sinostellata is a diploid, 2n=2x=38, and there are heterozygotes with paracentric inversion chromosomes in wild populations. Magnolia stellata is also a diploid, and there are heterozygotes with pericentric inversion chromosomes in wild populations. The abnormal chromosome behaviour in meiosis has serious effects on survival of the two species. Magnolia amoena is diploid with more or less normal meiosis except for a few lagging chromosomes in anaphase I and II. Magnolia stellata has a more complicated exine sculpture than the other two; exine structure is different in all three species. Separate species status for M. sinostellata is also supported by results of the plastid DNA phylogenetic study. Distributions, population descriptions and observations are provided, and based on all the evidence presented we conclude that M. sinostellata is a distinct species in M. subgenus Yulania. 

scholarly journals Molecular phylogeny ofSolms-laubachia(Brassicaceae) s.l., based on multiple nuclear and plastid DNA sequences, and its biogeographic implications

2009 ◽  
Vol 47 (5) ◽  
pp. 402-415 ◽  
Author(s):  
Ji-Pei YUE ◽  
Hang SUN ◽  
David A. BAUM ◽  
Jian-Hua LI ◽  
Ihsan A. AL-SHEHBAZ ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Plastid Dna

Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

2020 ◽  
Vol 194 (1) ◽  
pp. 84-99
Author(s):  
Inelia Escobar ◽  
Eduardo Ruiz-Ponce ◽  
Paula J Rudall ◽  
Michael F Fay ◽  
Oscar Toro-Núñez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Morphological Evolution ◽  
Strong Support ◽  
Plastid Dna ◽  
Lineage Sorting ◽  
Generic Level ◽  
Molecular Analyses ◽  
Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

A Phylogenetic Analysis of Loasaceae Subfamily Loasoideae Based on Plastid DNA Sequences

2005 ◽  
Vol 166 (2) ◽  
pp. 289-300 ◽  
Author(s):  
Larry Hufford ◽  
Michelle M. McMahon ◽  
Robin O’Quinn ◽  
Muriel E. Poston
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Plastid Dna

Molecular phylogeny of the Fusarium solani species complex (FSSC) isolated from soils in Iran

Botany ◽  
2014 ◽  
Vol 92 (11) ◽  
pp. 815-820 ◽  
Author(s):  
Khosrow Chehri
Keyword(s):  
Dna Sequences ◽  
Fusarium Solani ◽  
Species Complex ◽  
Agricultural Soils ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Its Region ◽  
Phylogenetic Study ◽  
Fusarium Solani Species Complex

Members of Fusarium solani species complex (FSSC) are frequently isolated from soils, food, feeds, trees, and to some extent from humans and other animals. The taxonomic status of these fungi is being revised but no attempt has been made to identify those isolated in Iran, a mountainous country with a high biodiversity. The objective of the present research was to study the phylogenetic diversity of FSSC strains recovered from soils in Iran by analyzing morphological characteristics and DNA sequences. A total of 65 strains belonging to the FSSC were recovered from agricultural soils in western Iran. Based on differences in their morphological characters, 25 strains were selected for phylogenetic analysis employing translation elongation factor-1α (tef1) and internal transcribed spacer (ITS) region sequences. Comparisons of DNA sequence data revealed that all isolates belonged to Fusarium falciforme, Fusarium keratoplasticum, Fusarium petroliphilum, the unnamed species FSSC 5, and unknown species of Fusarium, which represents a new lineage within members of Clade 3. Based on morphological features and phylogenetic study, F. keratoplasticum and F. petroliphilum were reported for the first time in Iran.

scholarly journals Jumping through the hoops: the challenges of daffodil (Narcissus) classification

2019 ◽  
Vol 190 (4) ◽  
pp. 389-404 ◽  
Author(s):  
Kálmán Könyves ◽  
John David ◽  
Alastair Culham
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Plastid Dna ◽  
Microsatellite Data ◽  
Population Sampling ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Nuclear Microsatellite ◽  
Congruent Group ◽  
First Time

Abstract Hoop-petticoat daffodils are a morphologically congruent group comprised of two distinct lineages in molecular phylogenetic trees of Narcissus. It is possible that the morphological similarity is a product of both historic and current low-level gene flow between these lineages. For the first time, we report population sampling from across the entire range of distribution covering the Iberian Peninsula and Morocco. In total, 455 samples were collected from 59 populations. Plastid DNA sequences of matK and ndhF were generated alongside 11 microsatellite loci to permit comparison between plastid and nuclear lineage histories. The plastid DNA phylogenetic tree was highly congruent with previous molecular studies and supported the recognition of these two lineages of hoop-petticoat daffodils as separate sections. Assignment of samples to sections sometimes differed between plastid DNA and (nuclear) microsatellite data. In these cases, the taxa had previously been the focus of dissent in taxonomic placement based on morphology. These discrepancies could be explained by hybridization and introgression among the two lineages during the evolution of hoop-petticoat daffodils, and shows that placement of species in sections is dependent on the source of data used. This study underlines the complex evolutionary history of Narcissus and highlights the discrepancies between floral morphology and phylogeny, which provides a continuing challenge for the systematics of Narcissus.

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