Molecular taxonomic clarification of Ptilotus exaltatus and Ptilotus nobilis (Amaranthaceae)

2007 ◽  
Vol 20 (1) ◽  
pp. 72 ◽  
Author(s):  
Kok K. Lee ◽  
Dion K. Harrison ◽  
Margaret E. Johnston ◽  
Richard R. Williams
Keyword(s):  
Sequence Variation ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Morphological Characters ◽  
Nuclear Rdna ◽  
Monophyletic Clade ◽  
Morphological Taxonomy ◽  
Molecular Phylogenetic ◽  
Morphological Differences ◽  
Respective Species

A complete botanical key for the genus Ptilotus R.Brown (family Amarathaceae) has not yet been published. Identifying the 100 or more Ptilotus species using morphological characters has been difficult because plants often exhibit slight morphological differences and intermediate characteristics common to several species, subspecies, varieties and forms. Ptilotus exaltatus Nees and P. nobilis (Lindl) F.Muell share many morphological characteristics, but are classified as different species predominantly based on inflorescence colour. The current study involved a molecular phylogenetic analysis of 14 Ptilotus species using sequence data from the internal transcribed spacer (ITS) regions ITS 1 and ITS 2 within the 18S–26S nuclear rDNA. Of the 39 accessions analysed, all except those identified as P. exaltatus and P. nobilis clustered according to their respective species based on their morphological taxonomy. In contrast, all 18 P. exaltatus and P. nobilis accessions formed a distinct monophyletic clade with 99% bootstrap values and a low level of sequence variation (GD = 0.002). Taking into account the lack of reliable morphological characters for separating P. exaltatus and P. nobilis, together with the ITS sequence data showing little genetic divergence or genetic structure, we propose that P. exaltatus and P. nobilis are conspecific.

Homoplasy: from detecting pattern to determining process in evolution, but with a secondary role for morphology?

Zootaxa ◽  
2011 ◽  
Vol 2984 (1) ◽  
pp. 67 ◽  
Author(s):  
LEANDRO C. S. ASSIS ◽  
MARCELO R. DE CARVALHO ◽  
QUENTIN D. WHEELER
Keyword(s):  
Sequence Data ◽  
Morphological Characters ◽  
Flow Chart ◽  
Molecular Topology ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Secondary Role ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

David Wake and colleagues provided a thought-provoking review of the concept of homoplasy through the integration, within a phylogenetic framework, of genetic and developmental data (Wake et al. 2011). According to them (p. 1032) “Molecular sequence data have greatly increased our ability to identify homoplastic traits.” This is made clear, for example, in their flow chart for homoplasy detection (Figure 2, p. 1034), wherein homoplasy is discovered through the mapping of “traits of interest” onto a phylogram, a practice common in the molecular phylogenetic paradigm. The “mapping” is usually of morphological characters that are employed to support the chosen (molecular) topology, but which, as a consequence, do not themselves contribute to the formation of those topologies (Assis & Carvalho 2010).

A revision of the Leptogium saturninum group in North America

2016 ◽  
Vol 48 (5) ◽  
pp. 387-421 ◽  
Author(s):  
Daphne F. STONE ◽  
James W. HINDS ◽  
Frances L. ANDERSON ◽  
James C. LENDEMER
Keyword(s):  
North American ◽  
Morphological Study ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Lower Surface ◽  
Molecular Data ◽  
The North ◽  
Molecular Phylogenetic ◽  
Nrits Sequence

AbstractA revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.

Phylogenetic reassignment of basal cyclostome braconid parasitoid wasps (Hymenoptera) with description of a new, enigmatic Afrotropical tribe with a highly anomalous 28S D2 secondary structure

2020 ◽  
Vol 190 (3) ◽  
pp. 1002-1019 ◽  
Author(s):  
Donald L J Quicke ◽  
Sergey A Belokobylskij ◽  
Yves Braet ◽  
Cornelis van Achterberg ◽  
Paul D N Hebert ◽  
...  
Keyword(s):  
Sequence Data ◽  
Elongation Factor ◽  
Sequence Divergence ◽  
Sister Group ◽  
Morphological Characters ◽  
Dna Sequence Data ◽  
Elongation Factor 1 Alpha ◽  
Molecular Phylogenetic ◽  
Molecular Dataset ◽  
First Time

Abstract A new tribe of braconid wasps provisionally included in the Rhyssalinae, Laibaleini trib. nov., type genus Laibalea gen. nov. (type species Laibalea enigmatica sp. nov.), from Kenya and the Central African Republic, is described. A molecular dataset, with emphasis on basally derived taxa based on four gene fragments (28S D2–D3 expansion region, COI barcode, elongation factor 1-alpha and 16S ribosomal DNA), was analysed both alone and in combination with a morphological dataset. Molecular phylogenetic placement of the new species into an existing subfamily is complicated by the extreme sequence divergence of the three sequences obtained for Laibalea. In both the combined sequence analysis and the combined DNA plus morphological tree, Laibalea is recovered as a sister group to the Rhyssalinae plus all non-cyclostome lineage braconids excluding Mesostoinae, Maxfischeriinae and Aphidiinae. A consensus of morphological characters and molecular analyses suggests inclusion of Laibalea either in the otherwise principally Holarctic subfamily Rhyssalinae or perhap more basally, in the principally Gondwanan Mesostoinae s.l., although we cannot exclude the possibility that it might represent a separate basal lineage. We place Laibalea in its own tribe, provisionally included in Rhyssalinae. The DNA sequence data are presented for several genera for the first time. Avga, the type genus of Avgini, is shown not to belong to Mesostoinae s.l. or Hormiinae, but its exact relationships remain uncertain. The generic compositions of Rhyssalinae and Mesostoinae s.l. are revised. Anachyra, Apoavga, Neptihormius, Neoavga and Opiopterus are shown to belong to Mesostoinae s.s. A key to the tribes of Rhyssalinae is provided.

Eucheumatopsis sanibelensis sp. nov. from the Gulf coast of Florida, USA

Phytotaxa ◽  
2020 ◽  
Vol 440 (3) ◽  
pp. 215-224 ◽  
Author(s):  
ELIAS S. PETERSON ◽  
CRAIG W. SCHNEIDER ◽  
GARY W. SAUNDERS
Keyword(s):  
Gulf Coast ◽  
Sequence Data ◽  
Algal Species ◽  
Morphological Characteristics ◽  
Caribbean Sea ◽  
Lsu Rdna ◽  
Eastern Gulf Of Mexico ◽  
Single Location ◽  
Red Algal ◽  
Morphological Differences

Based upon COI-5P, LSU rDNA and rbcL sequence data, as well as its morphological characteristics, a new red algal species, Eucheumatopsis sanibelensis E.S.Peterson, C.W.Schneider et G.W.Saunders sp. nov., was discovered on the Gulf coast of Florida, USA and shown to be distinct from the generitype E. isiformis with a type locality in the eastern Caribbean Sea. The new more attenuate taxon from Sanibel Island represents only the second species in this newly described genus, a genus recently segregated from Eucheuma based upon significant molecular and morphological differences. The two species have overlapping geographic distributions in the eastern Gulf of Mexico, but thus far E. sanibelensis is only known from a single location.

scholarly journals Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Zhang ◽  
Yupei Zhou ◽  
Wei Sun ◽  
Lili Zhao ◽  
D. Pavlic-Zupanc ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Type Specimens ◽  
Natural Classification ◽  
Dna Sequence Data

The genus Botryosphaeria includes more than 200 epithets, but only the type species, Botryosphaeria dothidea and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 “Botryosphaeria” species are reassessed to clarify their identity and phylogenetic position. nuDNA sequences of four regions, ITS, LSU, tef1-α and tub2, are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, Botryosphaeria cruenta and Botryosphaeria hamamelidis are transferred to Neofusicoccum. The generic status of Botryosphaeria aterrima and Botryosphaeria mirabile is confirmed in Botryosphaeria. Botryosphaeria berengeriana var. weigeliae and B. berengeriana var. acerina are treated synonyms of B. dothidea. Botryosphaeria mucosa is transferred to Neodeightonia as Neodeightonia mucosa, and Botryosphaeria ferruginea to Nothophoma as Nothophoma ferruginea. Botryosphaeria foliicola is reduced to synonymy with Phyllachorella micheliae. Botryosphaeria abuensis, Botryosphaeria aesculi, Botryosphaeria dasylirii, and Botryosphaeria wisteriae are tentatively kept in Botryosphaeria sensu stricto until further phylogenetic analysis is carried out on verified specimens. The ordinal status of Botryosphaeria apocyni, Botryosphaeria gaubae, and Botryosphaeria smilacinina cannot be determined, and tentatively accommodate these species in Dothideomycetes incertae sedis. The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.

A new species of Trichoglossum (Geoglossales, Ascomycota) from Thailand

Phytotaxa ◽  
2017 ◽  
Vol 316 (2) ◽  
pp. 161 ◽  
Author(s):  
ANUSHA H. EKANAYAKA ◽  
KEVIN D. HYDE ◽  
E.B. GARETH JONES ◽  
QI ZHAO ◽  
ABDALLAH M. ELGORBAN ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Tree ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Its Sequence ◽  
Morphological Examination ◽  
Molecular Phylogenetic ◽  
A New Species

The genus Trichoglossum (Geoglossaceae) is characterized by black, clavate, stipitate apothecia with hymenial setae. We collected T. cf. octopartitum from China and a new species of Trichoglossum from Thailand, the latter named as T. septatum. According to morphological examination and molecular phylogenetic analyses of ITS sequence data, T. septatum diverges from other Trichoglossum species. Full descriptions, colour figures, and a phylogenetic tree to show the positions of T. cf. octopartitum and T. septatum are provided, and the two species are compared with allied taxa. The important morphological characteristics of Trichoglossum species are also summarized.

Molecular phylogeny of Acrobeloides and Cephalobus (Nematoda: Cephalobidae) reveals paraphyletic taxa and recurrent evolution of simple labial morphology

Nematology ◽  
2006 ◽  
Vol 8 (6) ◽  
pp. 819-836 ◽  
Author(s):  
Steven Nadler ◽  
Ashleigh Smythe
Keyword(s):  
Molecular Phylogeny ◽  
Large Subunit ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Lateral Field ◽  
The Core ◽  
Morphological Taxonomy ◽  
Dominant Feature ◽  
The Family ◽  
Molecular Phylogenetic

AbstractMembers of the family Cephalobidae (Nematoda) are among the most common and morphologically striking soil nematodes. Many members of Cephalobidae have extensive lip elaborations called probolae, but two taxonomically problematic genera, Acrobeloides and Cephalobus, have simple, low probolae. We sequenced a portion of the nuclear large subunit ribosomal DNA for 33 cultures of Acrobeloides and Cephalobus. A phylogenetic analysis of these data, plus sequences representing other members of Cephalobina, revealed a core clade of 22 closely related taxa, but did not represent Acrobeloides and Cephalobus as monophyletic. The dominant feature used in morphological taxonomy of Cephalobidae, the lip region, was homoplastic according to the molecular phylogenetic hypothesis. Contrary to previous suggestions, taxa with simple probolae have arisen multiple times from taxa with complex probolae. Cultures were also examined for mode of reproduction (presumed parthenogenetic vs sexual) and three morphological characters commonly used in generic diagnoses: the shape of the corpus in profile; the number of lateral incisures; and the terminal extent of the lateral field. Most cultures, including all 22 members of the core clade, lacked males and were presumed to be parthenogenetic, but several independent origins of sexually reproducing taxa were found. Of the morphological characters, only the corpus shape was consistent with the molecular phylogeny, however, the utility of this character is also questioned. Many genera with complex probolae were also paraphyletic, including Nothacrobeles, Zeldia and Cervidellus, indicating the need for more comprehensive phylogenies and a broad taxonomic revision of the family.

scholarly journals Morphology and molecules support the new monotypic genus Fenghwaia (Rhamnaceae) from south China

PhytoKeys ◽  
2021 ◽  
Vol 171 ◽  
pp. 25-35
Author(s):  
Gang-Tao Wang ◽  
Jiang-Ping Shu ◽  
Guo-Bin Jiang ◽  
Yu-Qiang Chen ◽  
Rui-Jiang Wang
Keyword(s):  
New Genus ◽  
Sequence Data ◽  
Morphological Characters ◽  
Monotypic Genus ◽  
Conservation Assessment ◽  
Dna Sequence Data ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Combined Features ◽  
Near Threatened

Fenghwaia, a new monotypic genus, along with the new species Fenghwaia gardeniicarpa, is described from Guangdong Province, China. The combined features of inferior ovary, cylindrical drupaceous fruits and orbicular and dorsiventrally-compressed seeds with an elongate and pronounced basal appendage make the new genus significantly different from other genera of the family. In addition, its pollen morphology also showed great similarity to other species of this stenopalynous family. The molecular phylogenetic analysis, based on nuclear ribosomal internal transcribed spacer (ITS) and plastid trnL-F intron spacer (trnL-F) DNA sequence data from the new genus and the other 375 species representing 58 genera of Rhamnaceae, indicates that Fenghwaia is nested within the ‘rhamnoid’ group and sister to the tribe Rhamneae and then both sister to the tribe Maesopsideae. A taxonomic classification key to the ‘rhamnoid’ group is provided, based on morphological characters. A global conservation assessment is also performed and classifies Fenghwaia gardeniicarpa as Near Threatened (NT).

scholarly journals Arceuthobium tsugense (Viscaceae): four subspecies with contrasting morphologies and host distributions

2017 ◽  
Vol 11 (2) ◽  
pp. 363-390
Author(s):  
Robert L. Mathiasen ◽  
Shawn C. Kenaley
Keyword(s):  
Morphological Characteristics ◽  
Morphological Characters ◽  
Flowering Plants ◽  
The Other ◽  
Multivariate Statistical Analyses ◽  
Dwarf Mistletoe ◽  
Multivariate Statistical ◽  
Morphometric Analyses ◽  
Morphological Differences ◽  
Discriminant Function Analyses

There have been four subspecies of hemlock dwarf mistletoe (Arceuthobium tsugense: Viscaceae) described by various investigators of this complex group of parasitic flowering plants: subsp. tsugense, subsp. amabilae, subsp. contortae, and subsp. mertensianae. As suggested by their subspecific epithets, these taxa differ in their host affinities; parasitizing different and the same hosts to varying degrees. Although these taxa also have morphological differences, their classifica-tion has been under debate for many years. Therefore, we compared the morphological characteristics of each subspecies using both univariate and multivariate statistical analyses in order to better assess their differences. Because some investigators have grouped hemlock dwarf mistletoe with western dwarf mistletoe (A. campylopodum), we also compared the subspecies of hemlock dwarf mistletoe with western dwarf mistletoe. Our morphometric analyses demonstrated that all of the subspecies are morphologically distinct from western dwarf mistletoe and that subsp. contortae is the most morphologically differentiated of the subspecies. Overlap in the morphological characters across two of the other three subspecies was evident; yet, subsp. amabilae and subsp. mertensianae were also consistently delimited using female and male plant morphologies. Statistical comparisons of female or male plants via standard and stepwise discriminant function analyses demonstrated that without consideration of host plant, female and male A. tsugense subsp. tsugense are morphologically similar to corresponding plants of subsp. amabilae and mertensianae but not subsp. contortae or A. campylopodum.

scholarly journals Molecular phylogenetic analysis of the north-temperate Labrador Teas (Ericaceae: Rhododendron Subsect. Ledum) suggests a complex genetic history

2017 ◽  
Vol 11 (1) ◽  
pp. 53-65
Author(s):  
Andrew Hart ◽  
Kathleen Kron ◽  
Emily Gillespie
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Nuclear Data ◽  
Morphological Characters ◽  
Hybrid Origin ◽  
The North ◽  
Biogeographic History ◽  
Molecular Phylogenetic ◽  
Vegetative Characters ◽  
Floral Characters

The Labrador teas are a group of nearly circumboreal shrubs or sub-shrubs inhabiting damp habitats. The 4–7 currently recognized species are classified within Rhododendron subg. Rhododendron section Rhododendron subsect. Ledum. In floral characters, these species are extremely similar. In vegetative characters, species limits in the Labrador teas have been difficult to determine because many of the traditionally used morphological characters vary continually across the geographic range. This study investigated evolutionary history and preliminary consideration of some species boundaries in the Labrador teas using DNA sequence data from five molecular markers to generate a preliminary phylogeny of R. subsect. Ledum. Data were analyzed using Maximum Parsimony, Maximum Likelihood and Bayesian methods. The nuclear data indicate a monophyletic subsect. Ledum, but chloroplast data indicate that the North American taxa have an evolutionary history separate from the European and Asian taxa, suggesting that one or both lineages of subsect. Ledum may be of hybrid origin. Additionally, our analyses suggest that taxa combined in recent treatments (i.e. Rhododendron tomentosum) represent separate lineages and should be recognized as distinct instead of included within more broadly defined species, however our current level of sampling cannot completely resolve this issue. This study lays the groundwork for future phylogenetic studies within subsect. Ledum, illustrating the need to sample more intensively across taxa in order to capture what appears to be a complex genetic and biogeographic history.

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