scholarly journals On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

2021 ◽  
Vol 12 ◽  
Author(s):  
Na Su ◽  
Bin-bin Liu ◽  
Jun-ru Wang ◽  
Ru-chang Tong ◽  
Chen Ren ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Phylogenetic Network ◽  
Single Copy ◽  
Morphological Evidence ◽  
Molecular Evidence ◽  
Variable Regions ◽  
Dna Sequence Data

The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.

scholarly journals Two new genera of Acanthaceae from tropical Africa

Kew Bulletin ◽  
2019 ◽  
Vol 74 (3) ◽  
Author(s):  
Iain Darbyshire ◽  
Carrie A. Kiel ◽  
Thomas F. Daniel ◽  
Lucinda A. McDade ◽  
W. R. Quentin Luke
Keyword(s):  
New Genus ◽  
Sequence Data ◽  
Strong Support ◽  
Cylindrical Tube ◽  
Morphological Evidence ◽  
Molecular Evidence ◽  
New Genera ◽  
African Species ◽  
Lower Lip ◽  
Dna Sequence Data

Summary DNA sequence data, macro-morphological evidence and pollen analysis are used to clarify the phylogenetic placement of two African species of Acanthaceae: Schaueria populifolia C.B.Clarke and Rhinacanthus ndorensis Schweinf. The combined data demonstrate that these species are only distantly related to the genera in which they are currently placed and provide strong support for recognition of new genera to accommodate them. Two new genera are therefore proposed and a taxonomic account is provided for each of these. The first, Champluviera I.Darbysh., T.F.Daniel & C.A.Kiel, is based primarily on S. populifolia but Chlamydocardia nuda C.B.Clarke (= Justicia tigrina Heine) is also included within this new genus based on shared morphological traits, at least one of which is synapomorphic and restricted to these species. Based on molecular evidence, Champluviera is placed in a well-supported clade of several genera that are together sister to the core Isoglossinae lineage of tribe Justicieae. The genus may be recognised morphologically by the combination of a dense spiciform terminal thyrse with the bracts, bracteoles and calyx lobes all slender and closely resembling one another; a bilabiate corolla lacking a rugula and with intricate speckling or striping on the lips; and, in particular, the putatively synapomorphic trait of anther thecae with broad, flattened, basal appendages that have an irregularly toothed fringe. The second new genus, Kenyacanthus I.Darbysh. & C.A.Kiel, is based on R. ndorensis and is so far thought to be monospecific. It is placed between core Diclipterinae and Monechma Group II within the expanded subtribe Diclipterinae in tribe Justicieae. Kenyacanthus can be recognised morphologically by having the combination of a trailing or procumbent habit; fasciculate inflorescences; bracts, bracteoles and calyces with hyaline margins; a bilabiate corolla with a slender cylindrical tube longer than the limb and with a shallow rugula; stenotribic flowers, with the stamens held against the lower lip; and anthers with only slightly offset thecae that lack appendages.

Morphological and molecular evidence places Maronina into synonymy with Protoparmelia (Ascomycota: Lecanorales)

2011 ◽  
Vol 43 (6) ◽  
pp. 561-567 ◽  
Author(s):  
K. PAPONG ◽  
G. KANTVILAS ◽  
H. T. LUMBSCH
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Distinct Species ◽  
Genetic Distances ◽  
Molecular Evidence ◽  
New Combinations ◽  
Secondary Chemistry ◽  
Phenotypic Characters ◽  
Dna Sequence Data ◽  
Phylogenetic Placement

AbstractThe phylogenetic placement of the genus Maronina was studied, based chiefly on phenotypic characters such as thallus colour and anatomy, secondary chemistry, the anatomy of the excipulum and the ascus-type. DNA sequence data of mitochondrial and nuclear ribosomal loci from some of the species support the hypothesis that Maronina is nested within Protoparmelia. Hence, Maronina is reduced to synonymy with Protoparmelia. Comparison of genetic distances suggests that the two varieties within M. orientalis should be regarded as distinct species. Consequently, the new combinations Protoparmelia australiensis (Hafellner & R. W. Rogers) Kantvilas et al., P. corallifera (Kantvilas & Papong) Kantvilas et al., P. hesperia (Kantvilas & Elix) Kantvilas et al., P. multifera (Nyl.) Kantvilas et al., and P. orientalis (Kantvilas & Papong) Kantvilas et al. are proposed.

scholarly journals The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 261 ◽  
Author(s):  
Yongfu Li ◽  
Steven Paul Sylvester ◽  
Meng Li ◽  
Cheng Zhang ◽  
Xuan Li ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Sequence Data ◽  
Genome Structure ◽  
Phylogenetic Reconstruction ◽  
Strong Support ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Critically Endangered Species ◽  
Genomic Study

Magnolia zenii is a critically endangered species known from only 18 trees that survive on Baohua Mountain in Jiangsu province, China. Little information is available regarding its molecular biology, with no genomic study performed on M. zenii until now. We determined the complete plastid genome of M. zenii and identified microsatellites. Whole sequence alignment and phylogenetic analysis using BI and ML methods were also conducted. The plastome of M. zenii was 160,048 bp long with 39.2% GC content and included a pair of inverted repeats (IRs) of 26,596 bp that separated a large single-copy (LSC) region of 88,098 bp and a small single-copy (SSC) region of 18,757 bp. One hundred thirty genes were identified, of which 79 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Thirty seven simple sequence repeats (SSRs) were also identified. Comparative analyses of genome structure and sequence data of closely-related species revealed five mutation hotspots, useful for future phylogenetic research. Magnolia zenii was placed as sister to M. biondii with strong support in all analyses. Overall, this study providing M. zenii genomic resources will be beneficial for the evolutionary study and phylogenetic reconstruction of Magnoliaceae.

Revision of Batrachospermum sections Acarposporophytum and Aristata (Batrachospermales, Rhodophyta) with the establishment of the new genera Acarposporophycos and Visia

Phytotaxa ◽  
2019 ◽  
Vol 395 (2) ◽  
pp. 51 ◽  
Author(s):  
ORLANDO NECCHI JR ◽  
AURO GARCIA FILHO ◽  
MONICA O. PAIANO
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Sequence Divergence ◽  
Morphological Evidence ◽  
Similar Species ◽  
Type Specimens ◽  
Generic Level ◽  
Dna Sequence Data ◽  
Cell Layers

Sections of the paraphyletic genus Batrachospermum have been recently investigated using molecular (DNA sequence data) and morphological evidence. Some sections have been recognized as distinct genera in order to resolve paraphyly. Batrachospermum species of sections Acarposporophytum and Aristata are showed to form well-supported clades and, in this study, we propose to raise them to the generic level, Acarposporophycos gen. nov. and Visia gen. nov., respectively. In addition, we re-evaluated the characters used to circumscribe species by reexamining type specimens as well as new collections. Acarposporophycos, with the sole species A. brasiliensis, is characterized by the lack of carposporophytic stage, with the fertilized carpogonia germinating to form directly the filaments of the ‘Chantransia’ stage on the gametophyte. Of the five previously accepted species in the genus Visia, we recognize four species: V. cayennensis—type species (synonym Batrachospermum beraense), V. cylindrocellularis, V. longiarticulata and V. turgida. The species are circumscribed on the basis of morphological characteristics (shape and cell layers of primary fascicles, occurrence of secondary fascicles, post-fertilization development of carpogonia) and DNA sequence data (rbcL and COI-5P). Specimens described as Visia cayennensis from Australia and Brazil had a high sequence divergence in comparison to those from or near the type locality (French Guiana), and are here referred to as Visia spp. Further studies are recommended to better discriminate these morphologically similar species on a broad geographical scale and define their status at the species level. Descriptions, identification key and photomicrographs are presented for each recognized species.

New genetic lineages within Moroccan day geckos Quedenfeldtia (Sphaerodactylidae) revealed by mitochondrial and nuclear DNA sequence data

2017 ◽  
Vol 38 (1) ◽  
pp. 97-101 ◽  
Author(s):  
David James Harris ◽  
Daniela Rosado ◽  
Raquel Xavier ◽  
Daniele Salvi
Keyword(s):  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Taxonomic Revision ◽  
Substantial Portion ◽  
Genetic Lineages ◽  
Mountainous Regions ◽  
Dna Sequence Data ◽  
Atlas Mountains ◽  
Morphological Assessment

The genus Quedenfeldtia is composed of two species, Q. moerens and Q. trachyblepharus, both endemic to the Atlas Mountains region of Morocco. Previous studies recovered two main genetic lineages within each Quedenfeldtia species, although sampling did not cover a substantial portion of their known distribution. In this study we collected individuals from previously unsampled localities of Quedenfeldtia and carried out genetic analyses in order to assess the range of previously identified lineages and the occurrence of additional lineages. Phylogenetic reconstruction based on both mitochondrial (12S and ND4 + tRNA) and nuclear (MC1R) markers revealed that while the new individuals of Q. moerens belong to previously described lineages, two new lineages of Q. trachyblepharus were uncovered from the northern and southern parts of the range. Genetic divergence of these new lineages (8-9% ND4 + tRNA p-distance) was higher than values observed between other lizard sister species. In the future a thorough morphological assessment is needed to complement this study and allow a taxonomic revision of these taxa. The results of this study highlight the importance of biodiversity assessments in mountainous regions characterized by high endemicity but which are difficult to access.

Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades

Zootaxa ◽  
2020 ◽  
Vol 4734 (1) ◽  
pp. 1-61 ◽  
Author(s):  
DAVID A. BEAMER ◽  
TRIP LAMB
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Large Species ◽  
Eastern United States ◽  
Species Delineation ◽  
Molecular Systematic ◽  
Dna Sequence Data ◽  
Species Complexes ◽  
Sampling Regime ◽  
Comprehensive Recovery

Dusky salamanders (Desmognathus) constitute a large, species-rich group within the family Plethodontidae, and though their systematic relationships have been addressed extensively, most studies have centered on particular species complexes and therefore offer only piecemeal phylogenetic perspective on the genus. Recent work has revealed Desmognathus to be far more clade rich—35 reciprocally monophyletic clades versus 22 recognized species—than previously imagined, results that, in turn, provide impetus for additional survey effort within clades and across geographic areas thus far sparsely sampled. We conceived and implemented a sampling regime combining level IV ecoregions and independent river drainages to yield a geographic grid for comprehensive recovery of all genealogically exclusive clades. We sampled over 550 populations throughout the distribution of Desmognathus in the eastern United States of America and generated mitochondrial DNA sequence data (mtDNA; 1,991 bp) for 536 specimens. A Bayesian phylogenetic reconstruction of the resulting haplotypes revealed forty-five reciprocally monophyletic clades, eleven of which have never been included in a comprehensive phylogenetic reconstruction, and an additional three not represented in any molecular systematic survey. Although general limitations associated with mtDNA data preclude new species delineation, we profile each of the 45 clades and assign names to 10 new clades (following a protocol for previous clade nomenclature). We also redefine several species complexes and erect new informal species complexes. Our dataset, which contains topotypic samples for nearly every currently recognized species and most synonymies, will offer a robust framework for future efforts to delimit species within Desmognathus. 

scholarly journals Two new Chrysomyxa rust species on the endemic plant, Picea asperata in western China, and expanded description of C. succinea

Phytotaxa ◽  
2017 ◽  
Vol 292 (3) ◽  
pp. 218 ◽  
Author(s):  
JING CAO ◽  
CHENGMING TIAN ◽  
YINGMEI LIANG ◽  
CHONGJUAN YOU
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Morphological Characters ◽  
Western China ◽  
Endemic Plant ◽  
Internal Transcribed Spacer Region ◽  
Dna Sequence Data ◽  
Species Cluster ◽  
Picea Asperata ◽  
First Time

Two new rust species, Chrysomyxa diebuensis and C. zhuoniensis, on Picea asperata are recognized by morphological characters and DNA sequence data. A detailed description, illustrations, and discussion concerning morphologically similar and phylogenetically closely related species are provided for each species. From light and scanning electron microscopy observations C. diebuensis is characterized by the nailhead to peltate aeciospores, with separated stilt-like base. C. zhuoniensis differs from other known Chrysomyxa species in the annulate aeciospores with distinct longitudinal smooth cap at ends of spores, as well as with a broken, fissured edge. Analysis based on internal transcribed spacer region (ITS) partial gene sequences reveals that the two species cluster as a highly supported group in the phylogenetic trees. Correlations between the morphological and phylogenetic features are discussed. Illustrations and a detailed description are also provided for the aecia of C. succinea in China for the first time.

Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data

Phytotaxa ◽  
2015 ◽  
Vol 219 (3) ◽  
pp. 261 ◽  
Author(s):  
Julian Aguirre-Santoro ◽  
Julio Betancur ◽  
Gregory K. Brown ◽  
Timothy M. Evans ◽  
Fabiano Salgueiro ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Geographic Ranges ◽  
Dna Sequence Data ◽  
Disjunct Genus

A phylogenetic study testing the monophyly of the geographically disjunct genus Ronnbergia (Bromeliaceae, Bromelioideae) is presented. The phylogenetic analyses were based on taxon sampling that included all but one species of Ronnbergia, and representative lineages across the subfamily Bromelioideae. Three chloroplast DNA sequence markers (matK, psbA-trnH, and trnL-trnF) and morphological data were used for the phylogenetic reconstruction. Both the molecular and morphological datasets supported the polyphyly of Ronnbergia, either independently or in combination. These findings suggest that the geographic disjunction of this genus is most likely a product of taxonomic misinterpretation. The results also indicate that the species currently circumscribed in Ronnbergia are closely related to species in the genus Aechmea with similar geographic ranges. The datasets do not have enough resolution power to reconstruct a deep phylogenetic history that involves all the species of Ronnbergia. Nevertheless, this study provides clues for future approaches that should focus on a larger species sampling and the use of multi-locus DNA sequence data.

Generic delimitation and phylogenetic uncertainty: an example from a group that has undergone an explosive radiation

2005 ◽  
Vol 18 (1) ◽  
pp. 41 ◽  
Author(s):  
L. A. Orthia ◽  
L. G. Cook ◽  
M. D. Crisp
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Sequence Data ◽  
Evolutionary Relationships ◽  
Recent Proposal ◽  
Generic Delimitation ◽  
Dna Sequence Data ◽  
Single Genus ◽  
Phylogeny Estimation

Phylogenetic trees can provide a stable basis for a higher-level classification of organisms that reflects evolutionary relationships. However, some lineages have a complex evolutionary history that involves explosive radiation or hybridisation. Such histories have become increasingly apparent with the use of DNA sequence data for phylogeny estimation and explain, in part, past difficulties in producing stable morphology-based classifications for some groups. We illustrate this situation by using the example of tribe Mirbelieae (Fabaceae), whose generic classification has been fraught for decades. In particular, we discuss a recent proposal to combine 19 of the 25 Mirbelieae genera into a single genus, Pultenaea sens. lat., and how we might find stable and consistent ways to squeeze something as complex as life into little boxes for our own convenience.

Pilea nonggangensis (Urticaceae), a new species from Guangxi, China

Phytotaxa ◽  
2017 ◽  
Vol 313 (1) ◽  
pp. 130 ◽  
Author(s):  
LONG-FEI FU ◽  
SHI-LIAN HUANG ◽  
ALEX K. MONRO ◽  
YING LIU ◽  
FANG WEN ◽  
...  
Keyword(s):  
New Species ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Species Conservation ◽  
Its Region ◽  
Systematic Position ◽  
Molecular Evidence ◽  
Conservation Assessment ◽  
Dna Sequence Data ◽  
A New Species

Pilea nonggangensis Y. G. Wei, L. F. Fu & A. K. Monro, a new species from Guangxi, China is described and illustrated. The new species is morphologically most similar to P. basicordata from which it differs by being dioecious, having peltate leaf blades, membranous stipules, paired inflorescences and larger bracts. Nuclear ribosomal internal transcribed spacer (ITS) region and plastid trnL-F intron spacer (trnL-F) DNA sequence data from the new species and 20 local congeneric species are used to resolve the systematic position of the new species within Pilea. Despite vastly different morphology the molecular evidence suggests that P. nonggangensis is most closely related to P. pseudonotata. A Global Species Conservation Assessment classifies P. nonggangensis as Vulnerable (VU).

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