Molecular Phylogeny of Axonopus (Poaceae, Panicoideae, Paspaleae): Monophyly, Synapomorphies, and Taxonomic Implications for Infrageneric Classification and Species Complexes

2020 ◽  
Vol 105 (4) ◽  
pp. 459-480
Author(s):  
Carolina Delfini ◽  
Juan M. Acosta ◽  
Vinicius Castro Souza ◽  
Fernando O. Zuloaga
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Character State ◽  
Infrageneric Classification ◽  
Ancestral Character State ◽  
Limited Sampling ◽  
Species Complexes ◽  
External Transcribed Spacer ◽  
Taxonomic Implications

Axonopus P. Beauv. comprises nearly 90, mostly New World, species characterized by having spikelets with the inverse position (i.e., the backs of the upper glume and the upper lemma turned away from the rachis). The genus has been divided into four sections, five series, and three subseries, based exclusively on morphological features. Previous phylogenetic analyses based on a limited sampling of species showed Axonopus to be a monophyletic genus. In this study we increased the number of species sampled (46 species in the combined tree) and sequenced four DNA regions (external transcribed spacer [ETS], internal transcribed spacer [ITS], trnL-F, and ndhF). We tested the monophyly of Axonopus and its traditional infrageneric categories using parsimony, likelihood, and Bayesian inference. Additionally, we performed ancestral character state reconstructions of 45 morphological characters to infer autapomorphies of the species and synapomorphies for the genus and clades. Our findings confirmed Axonopus as a monophyletic genus only when Centrochloa Swallen and Ophiochloa Filg., Davidse & Zuloaga are included within it. Our analyses also showed that, with the exception of section Lappagopsis, infrageneric categories from previous classifications of the genus are artificial. Twenty-one morphological character states were identified as potential autapomorphies; two were reconstructed as potential synapomorphies for Axonopus, whereas 12 were reconstructed as potential synapomorphies for specific clades within the genus. Further molecular analyses, including sequencing of unlinked nuclear genes, are needed in order to reach a robust phylogenetic classification of the genus.

scholarly journals Morphological characters in light of new molecular phylogenies: the caudal-fin skeleton of Ovalentaria

2022 ◽  
Vol 9 (1) ◽  
Author(s):  
Philipp Thieme ◽  
Nalani K. Schnell ◽  
Kerryn Parkinson ◽  
Timo Moritz
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Character State ◽  
Evolutionary Trend ◽  
Caudal Fin ◽  
X Ray ◽  
Ground Plan ◽  
Ancestral Character State ◽  
Morphological Approach ◽  
First Time

The Ovalentaria is a taxon of teleosts that has been proposed based on molecular analyses only. Previously widely separated families are assembled in this taxon. For the first time, the Ovalentaria are analysed using a comparative morphological approach. The caudal-fin skeleton of 355 species covering all 48 ovalentarian families are examined in cleared and stained specimens, µCT datasets and X-ray images as well as from the literature. A total of 38 morphological characters are evaluated and used for ancestral character state reconstructions and phylogenetic analyses. Results provide hypotheses for a scenario of the evolution of the caudal-fin skeleton and its ground plan in Ovalentaria. An evolutionary trend towards the reduction of skeletal elements in the caudal fin is observed. Connections between the evolution of the caudal-fin skeleton and modes of locomotion found in ovalentarian taxa are discussed. Phylogenetic analyses based on the caudal-fin morphology provide topologies for intra-ovalentarian relationships that largely agree with molecular hypotheses.

Molecular phylogenetic analyses and morphological variation point to taxonomic problems among four genera of parasitoid doryctine wasps (Hymenoptera : Braconidae)

2015 ◽  
Vol 29 (6) ◽  
pp. 591 ◽  
Author(s):  
Marco Gebiola ◽  
Antonio P. Garonna ◽  
Umberto Bernardo ◽  
Sergey A. Belokobylskij
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Evidence ◽  
A Posteriori ◽  
Morphological Examination ◽  
Ongoing Effort ◽  
The Status ◽  
Molecular Phylogenetic

Doryctinae (Hymenoptera : Braconidae) is a large and diverse subfamily of parasitic wasps that has received much attention recently, with new species and genera described and phylogenies based on morphological and/or molecular data that have improved higher-level classification and species delimitation. However, the status of several genera is still unresolved, if not controversial. Here we focus on two related groups of such genera, Dendrosoter Wesmael–Caenopachys Foerster and Ecphylus Foerster–Sycosoter Picard & Lichtenstein. We integrated morphological and molecular (COI and 28S–D2 genes) evidence to highlight, by phylogenetic analyses (maximum likelihood and Bayesian) and a posteriori morphological examination, previously overlooked variation, which is here illustrated and discussed. Monophyly of Dendrosoter and Caenopachys and the presence of synapomorphic morphological characters support synonymy of Caenopachys under Dendrosoter. Low genetic differentiation and high variability for putatively diagnostic morphological characters found in both C. hartigii (Ratzeburg) and C. caenopachoides (Ruschka) supports synonymy of D. caenopachoides under D. hartigii, syn. nov. Morphological and molecular evidence together also indicate independent generic status for Sycosoter, stat. rev., which is here resurrected. This work represents a further advancement in the framework of the ongoing effort to improve systematics and classification of the subfamily Doryctinae.

scholarly journals An updated infrageneric classification of the oaks: review of previous taxonomic schemes and synthesis of evolutionary patterns

2017 ◽  
Author(s):  
Thomas Denk ◽  
Guido W. Grimm ◽  
Paul S. Manos ◽  
Min Deng ◽  
Andrew Hipp
Keyword(s):  
Molecular Phylogenetics ◽  
Morphological Characters ◽  
Evolutionary Patterns ◽  
Traditional Concept ◽  
Infrageneric Classification ◽  
Systematic Scheme ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Phylogenetic Lineages

In this paper, we review major classification schemes proposed for oaks by John Claudius Loudon, Anders Sandøe Ørsted, William Trelease, Otto Karl Anton Schwarz, Aimée Antoinette Camus, Yuri Leonárdovich Menitsky, and Kevin C. Nixon. Classifications of oaks (Fig. 1) have thus far been based entirely on morphological characters. They differed profoundly from each other because each taxonomist gave a different weight to distinguishing characters; often characters that are homoplastic in oaks. With the advent of molecular phylogenetics our view has considerably changed. One of the most profound changes has been the realisation that the traditional split between the East Asian subtropical to tropical subgenus Cyclobalanopsis and the subgenus Quercus that includes all other oaks is artificial. The traditional concept has been replaced by that of two major clades, each comprising three infrageneric groups: a Palearctic-Indomalayan clade including Group Ilex (Ilex oaks), Group Cerris (Cerris oaks) and Group Cyclobalanopsis (cycle-cup oaks), and a predominantly Nearctic clade including Group Protobalanus (intermediate or golden cup oaks), Group Lobatae (red oaks) and Group Quercus (white oaks, with most species in America and some 30 species in Eurasia). The main morphological feature characterising these phylogenetic lineages is pollen morphology, a character overlooked in traditional classifications. This realisation, along with the now available (molecular-)phylogenetic framework, opens new avenues for biogeographic, ecological and evolutionary studies and a re-appraisal of the fossil record. We provide an overview about recent advances in these fields and outline how the results of these studies contribute to the establishment of a unifying systematic scheme of oaks. Ultimately, we propose an updated classification of Quercus recognising two subgenera with eight sections. This classification considers morphological traits, molecular-phylogenetic relationships, and the evolutionary history of one of the most important temperate woody plant genera.

scholarly journals Sareomycetes cl. nov.: A new proposal for placement of the resinicolous genus Sarea (Ascomycota, Pezizomycotina)

2020 ◽  
Vol 6 (1) ◽  
pp. 25-37 ◽  
Author(s):  
C. Beimforde ◽  
A.R. Schmidt ◽  
J. Rikkinen ◽  
J.K. Mitchell
Keyword(s):  
Bayesian Inference ◽  
Genetic Variability ◽  
Sequence Data ◽  
Current Knowledge ◽  
Phylogenetic Analyses ◽  
Protein Coding ◽  
Infrageneric Classification ◽  
New Class ◽  
Molecular Studies

Resinicolous fungi constitute a heterogeneous assemblage of fungi that live on fresh and solidified plant resins. The genus Sarea includes, according to current knowledge, two species, S. resinae and S. difformis. In contrast to other resinicolous discomycetes, which are placed in genera also including non-resinicolous species, Sarea species only ever fruit on resin. The taxonomic classification of Sarea has proven to be difficult and currently the genus, provisionally and based only on morphological features, has been assigned to the Trapeliales (Lecanoromycetes). In contrast, molecular studies have noted a possible affinity to the Leotiomycetes. Here we review the taxonomic placement of Sarea using sequence data from seven phylogenetically informative DNA regions including ribosomal (ITS, nucSSU, mtSSU, nucLSU) and protein-coding (rpb1, rpb2, mcm7) regions. We combined available and new sequence data with sequences from major Pezizomycotina classes, especially Lecanoromycetes and Leotiomycetes, and assembled three different taxon samplings in order to place the genus Sarea within the Pezizomycotina. Based on our data, none of the applied phylogenetic approaches (Bayesian Inference, Maximum Likelihood and Maximum Parsimony) supported the placement of Sarea in the Trapeliales or any other order in the Lecanoromycetes. A placement of Sarea within the Leotiomycetes is similarly unsupported. Based on our data, Sarea forms an isolated and highly supported phylogenetic lineage within the " Leotiomyceta". From the results of our multilocus phylogenetic analyses we propose here a new class, order, and family, Sareomycetes, Sareales and Sareaceae in the Ascomycota to accommodate the genus Sarea. The genetic variability within the newly proposed class suggests that it is a larger group that requires further infrageneric classification.

scholarly journals A Phylogenetic Investigation of the New Zealand  Pteridaceae Ferns

2021 ◽  
Author(s):  
◽  
Whitney L M Bouma
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Native Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxonomic Confusion ◽  
Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

Monograph of Elaphoglossum sect. Polytrichia subsect. Apoda (Dryopteridaceae)

2021 ◽  
Author(s):  
Fernando B. Matos ◽  
Josmaily L&#243riga ◽  
Robbin C. Moran
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Character State ◽  
Similar Species ◽  
Southern Mexico ◽  
Distribution Maps ◽  
Molecular Phylogenetic ◽  
Identification Of Species ◽  
First Time ◽  
A New Species

We present a monographic treatment for the 13 species of Elaphoglossum sect. Polytrichia subsect. Apoda (Dryopteridaceae). Molecular phylogenetic analyses have recovered this subsection as monophyletic within the so-called “subulate-scaled clade” of Elaphoglossum. Morphologically, the species of E. subsect. Apoda are usually characterized by the presence of brightly colored stem scales (yellowish, orangish, orreddish, as opposed to castaneous to black), evenly distributed subulate scales on laminar surfaces, tiny glandular hairs on different parts of the leaves, and adult sterile leaves without hydathodes. The species can be divided into two groups: one with subsessile and the other with long-petiolate leaves. Elaphoglossum subsection Apoda is distributed from southern Mexico and the Antilles to Bolivia and midwestern Brazil. Elaphoglossum atehortuae, a new species from the Amazon region of Ecuador, is described, illustrated, and compared to its most similar species. It is unusual within this group for lacking subulate scales on both surfaces of the laminae, a character state that it shares with E. backhouseanum. Two species, E. polyblepharum and E. trichophorum, are included in the group for the first time, whereas E. procurrens and E. siliquoides are excluded based on morphological characters and previously published molecular phylogenies. We also provide comments for E. ×morphohybridum, which is a hybrid between E. alvaradoanum and E. crinitum. Lectotypes are designated for Acrostichum apodum, A. platyneuron, A. cubense, A. procurrens, A. trichophorum, and Elaphoglossum auripilum, and epitypes are designated for A. apodum. To facilitate the identification of species, we provide keys, descriptions, illustrations, comments, synonyms, distribution maps, spore images, and a list of specimens examined.

Molecular phylogeny of the grasshopper family Pyrgomorphidae (Caelifera, Orthoptera) reveals rampant paraphyly and convergence of traditionally used taxonomic characters

Zootaxa ◽  
2021 ◽  
Vol 4969 (1) ◽  
pp. 101-118
Author(s):  
SUNDUS ZAHID ◽  
RICARDO MARIÑO-PÉREZ ◽  
HOJUN SONG
Keyword(s):  
Molecular Phylogeny ◽  
Classification Scheme ◽  
Phylogenetic Reconstruction ◽  
Large Degree ◽  
Morphological Characters ◽  
Character State ◽  
Important Species ◽  
Natural Classification ◽  
Genome Data ◽  
Ancestral Character State

The grasshopper family Pyrgomorphidae is one of the most colorful orthopteran lineages, and includes biologically fascinating and culturally important species. Recent attempts to reconstruct the phylogeny of this family have resulted in a large degree of conflicts between a morphology-based study and a molecular-based study, mainly due to convergent morphological traits that affected phylogenetic reconstruction. In this study, a molecular phylogeny of Pyrgomorphidae based on 32 ingroup species and mitochondrial genome data is proposed, which is used to test the monophyly of the taxonomic groupings used in the current classification scheme. Using the ancestral character state reconstruction analyses and character mapping, we demonstrate that some of the morphological characters, including the male genitalia, which were considered to be taxonomically important, have evolved convergently across the phylogeny. We discuss the discrepancies between our phylogeny and the previous studies and propose an approach to establish a natural classification scheme for Pyrgomorphidae. 

Phylogenetics of scolopendromorph centipedes: can denser taxon sampling improve an artificial classification?

2013 ◽  
Vol 27 (5) ◽  
pp. 578 ◽  
Author(s):  
Varpu Vahtera ◽  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
Bayesian Inference ◽  
New World ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxon Sampling ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Artificial Classification

Previous phylogenetic analyses of the centipede order Scolopendromorpha indicated a fundamental division into blind and ocellate clades. These analyses corroborated the monophyly of most families and tribes but suggested that several species-rich, cosmopolitan genera in traditional and current classifications are polyphyletic. Denser taxon sampling is applied to a dataset of 122 morphological characters and sequences for four nuclear and mitochondrial loci. Phylogenetic analyses including 98 species and subspecies of Scolopendromorpha employ parsimony under dynamic and static homology schemes as well as maximum likelihood and Bayesian inference of multiple sequence alignments. The monotypic Australian genera Notiasemus and Kanparka nest within Cormocephalus and Scolopendra, respectively, and the New Caledonian Campylostigmus is likewise a clade within Cormocephalus. New World Scolopendra are more closely related to Hemiscolopendra and Arthrorhabdus than to Scolopendra s.s., which is instead closely allied to Asanada; the tribe Asanadini nests within Scolopendrini for molecular and combined datasets. The generic classification of Otostigmini has a poor fit to phylogenetic relationships, although nodal support within this tribe is weak. New synonymies are proposed for Ectonocryptopinae Shelley & Mercurio, 2005 (= Newportiinae Pocock, 1896), Asanadini Verhoeff, 1907 (= Scolopendrini Leach, 1814), and Kanparka Waldock & Edgecombe, 2012 (= Scolopendra Linnaeus, 1758). Scolopendrid systematics largely depicts incongruence between phylogeny and classification rather than between morphology and molecules.

Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

2020 ◽  
Vol 84 (4) ◽  
pp. 317-330
Author(s):  
Francisco J. García-Cárdenas ◽  
Mónica Núñez-Flores ◽  
Pablo J. López-González
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

Phylogeny, major clades and infrageneric classification of Corymbia (Myrtaceae), based on nuclear ribosomal DNA and morphology

2009 ◽  
Vol 22 (5) ◽  
pp. 384 ◽  
Author(s):  
Carlos Parra-O. ◽  
Michael J. Bayly ◽  
Andrew Drinnan ◽  
Frank Udovicic ◽  
Pauline Ladiges
Keyword(s):  
Ribosomal Dna ◽  
Convergent Evolution ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
Nuclear Rdna ◽  
Infrageneric Classification ◽  
Taxonomic Categories

Phylogenetic relationships of sections and species within Corymbia (Myrtaceae), the bloodwood eucalypts, were evaluated by using combined analyses of nuclear rDNA (ETS + ITS) and morphological characters. Combining morphological characters with molecular data provided resolution of relationships within Corymbia. The analyses supported the monophyly of the genus and recognition of the following two major clades, treated here as new subgenera: subgenus Corymbia, including informal sections recognised by Hill and Johnson (1995), namely Rufaria (red bloodwoods), Apteria and Fundoria; and subgenus Blakella, including sections Politaria (spotted gums), Cadagaria, Blakearia (paper-fruited bloodwoods or ghost gums) and Ochraria (yellow bloodwoods). Hill and Johnson’s section Rufaria is monophyletic if Apteria and Fundoria are included. It is evident that, among the red bloodwoods, series are not monophyletic and several morphological characters result from convergent evolution. There was strong morphological and molecular evidence that the three species of red bloodwoods that occur in south-western Western Australia (series Gummiferae: C. calophylla and C. haematoxylon, and series Ficifoliae: C. ficifolia) form a monophyletic group, separate from the eastern C. gummifera (series Gummiferae), which is probably sister to the clade of all other red bloodwoods. Phylogenetic results supported recognition of new taxonomic categories within Corymbia, and these are formalised here.

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