scholarly journals Phylogenetic Placement of the Plesioclytini (Coleoptera: Cerambycidae: Cerambycinae)

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 597
Author(s):  
Laura N. Sutherland ◽  
Kyle E. Schnepp ◽  
Gareth S. Powell ◽  
Seth M. Bybee
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Reconstruction ◽  
Data Availability ◽  
Phylogenetic Placement ◽  
Longhorn Beetle ◽  
Single Genus ◽  
Additional Support ◽  
Morphological Investigations

The tribe Plesioclytini was recently erected for a single genus of cerambycine longhorn beetle. The group was diagnosed from a proposed sister lineage, the diverse Clytini; however, a formal phylogenetic analysis was not performed due to limitations in data availability. Here, we present a phylogenetic reconstruction from five loci, that Plesioclytini is not sister to Clytini, but is instead only distantly related. Subsequent morphological investigations provide additional support for this placement.

A REVISED GENERIC SYNOPSIS OF HYACINTHACEAE IN SUB-SAHARAN AFRICA, BASED ON MOLECULAR EVIDENCE, INCLUDING NEW COMBINATIONS AND THE NEW TRIBE PSEUDOPROSPEREAE

2003 ◽  
Vol 60 (3) ◽  
pp. 533-568 ◽  
Author(s):  
J. C. MANNING ◽  
P. GOLDBLATT ◽  
M. F. FAY
Keyword(s):  
Phylogenetic Analysis ◽  
Sub Saharan Africa ◽  
Molecular Evidence ◽  
New Combinations ◽  
Generic Level ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Single Genus ◽  
New Tribe ◽  
Sub Saharan

A revised generic synopsis of sub-Saharan Hyacinthaceae is presented, based on a molecular phylogenetic analysis of the family. Generic rank is accorded only to reciprocally monophyletic clades that can be distinguished by recognizable morphological discontinuities, thereby permitting an appropriate generic assignment of species not included in the analysis. Three subfamilies are recognized within the region. Subfamily Ornithogaloideae, characterized by flattened or angular seeds with tightly adhering testa, is considered to include the single genus Ornithogalum, which is expanded to include the genera Albuca, Dipcadi, Galtonia, Neopatersonia and Pseudogaltonia. Recognizing any of these segregates at generic level renders the genus Ornithogalum polyphyletic, while subdivision of Ornithogalum into smaller, morphologically distinguishable segregates in order to preserve the monophyly of each is not possible. Subfamily Urgineoideae, characterized by flattened or winged seeds with brittle, loosely adhering testa, comprises the two mainland African genera Bowiea and Drimia. The latter is well circumscribed by its deciduous, short-lived perianth and includes the previously recognized genera Litanthus, Rhadamanthus, Schizobasis and Tenicroa. The monotypic Madagascan Igidia is provisionally included in the subfamily as a third genus on the basis of its seeds, pending molecular confirmation of its relationships. Subfamily Hyacinthoideae resolves into three clades, distinguished as tribes Hyacintheae (strictly northern hemisphere and not treated further), Massonieae and Pseudoprospereae tribus nov. Full descriptions and a key to their identification are provided for all genera. New combinations reflecting the generic circumscriptions adopted here are made for most African and all Indian and Madagascan species.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

New olenelline trilobites from the Northwest Territories, Canada, and the phylogenetic placement of Judomia absita Fritz, 1973

Zootaxa ◽  
2011 ◽  
Vol 2918 (1) ◽  
pp. 15 ◽  
Author(s):  
I. WESLEY GAPP ◽  
BRUCE S. LIEBERMAN ◽  
MICHAEL C. POPE ◽  
KELLY A. DILLIARD
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Northwest Territories ◽  
Phylogenetic Analyses ◽  
Geographic Range ◽  
Early Cambrian ◽  
Phylogenetic Placement ◽  
The Subject ◽  
Three New Species ◽  
One New Species

The Early Cambrian olenelline trilobites are a diverse clade and have been the subject of several phylogenetic analyses. Here, three new species of Bradyfallotaspis Fritz, 1972 (B. coriae, B. nicolascagei, and B. sekwiensis) and one new species of Nevadia Walcott, 1910 (N. saupeae) are described from the Sekwi Formation of the Mackenzie Mountains, Northwest Territories, Canada. In addition, new specimens potentially referable to Nevadia ovalis McMenamin, 1987 were recovered that may expand that species’ geographic range, which was thought to be restricted to Sonora, Mexico. The results of a phylogenetic analysis incorporating several olenelline taxa, including Judomia absita Fritz, 1973 from the Sekwi Formation, are also presented herein. This species has been assigned to various olenelline genera, including Judomia Lermontova, 1951 and Paranevadella Palmer & Repina, 1993. Phylogenetic analysis suggests this species is closely related to Judomia tera Lazarenko, 1960 from Siberia. This phylogenetic relationship provides further support for the hypothesis that a close biogeographic relationship existed between Laurentia and Siberia during the Cambrian.

Pseudodactylaria brevis sp. nov. from Thailand confirms the status of Pseudodactylariaceae

Phytotaxa ◽  
2018 ◽  
Vol 369 (4) ◽  
pp. 241 ◽  
Author(s):  
CHUAN-GEN LIN ◽  
ERIC H. C. MCKENZIE ◽  
DARBHE J. BHAT ◽  
JIAN-KUI LIU ◽  
KEVIN D. HYDE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Its Sequence ◽  
Morphological Comparison ◽  
Phylogenetic Placement ◽  
Data Analyses ◽  
The Status ◽  
A New Species

A new species, Pseudodactylaria brevis, is described, illustrated and compared with other Pseudodactylaria and Dactylaria-like taxa. Evidence for the new species is provided by morphological comparison and sequence data analyses. Pseudodactylaria brevis can be distinguished from other Pseudodactylaria and Dactylaria-like species by its short hyaline conidiophores and fusiform, 1-septate hyaline conidia. Phylogenetic analysis of LSU and ITS sequence data was carried out to determine the phylogenetic placement of the species and confirm the taxonomic status of Pseudodactylariaceae.

Molecular insights into the phylogenetic placement of the poorly known genus Niceforonia Goin & Cochran, 1963 (Anura: Brachycephaloidea)

Zootaxa ◽  
2018 ◽  
Vol 4514 (4) ◽  
pp. 487
Author(s):  
ANDRÉS R. ACOSTA-GALVIS ◽  
JEFFREY W. STREICHER ◽  
LUIGI MANUELLI ◽  
TRAVIS CUDDY ◽  
RAFAEL O. DE SÁ
Keyword(s):  
Phylogenetic Analysis ◽  
New World ◽  
Taxonomic Revision ◽  
Phylogenetic Inference ◽  
Genetic Distances ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Placement ◽  
Molecular Phylogenetic ◽  
First Time

Among New World direct-developing frogs belonging to the clade Brachycephaloidea (= Terraranae), there are several genera with uncertain phylogenetic placements. One notable example is the genus Niceforonia Goin & Cochran 1963, which includes three species that are endemic to Colombia. Three specimens of the species Niceforonia nana were collected and for the first time the genus is included in a molecular phylogenetic analysis of mitochondrial (mtDNA; 12S and 16S) and nuclear (nucDNA; TYR and RAG1) markers. Molecular phylogenetic inference based on concatenated and separate mtDNA and nucDNA analyses recovered Niceforonia nana nested within Hypodactylus Hedges et al. 2008, rendering the latter genus paraphyletic. Consequently, herein we place the genus Hypodactylus in the synonymy of Niceforonia to resolve the paraphyly and place Niceforonia in the subfamily Hypodactylinae. Based on our revised concept of the genus Niceforonia we conducted preliminary morphological comparisons using specimens and literature descriptions. Finally, Nicefornia nana is quite divergent from other species of Niceforonia (uncorrected genetic distances of ca. 10% 16S and 7% TYR) suggesting that further taxonomic revision may be warranted. 

scholarly journals Phylogenetic placement of a recently discovered population of the threatened alpine she-oak skink Cyclodomorphus praealtus (Squamata: Scincidae) in Victoria

2021 ◽  
pp. 153-157
Author(s):  
Joanna Sumner ◽  
Margaret L. Haines ◽  
Peter Lawrence ◽  
Jenny Lawrence ◽  
Nick Clemann
Keyword(s):  
Phylogenetic Analysis ◽  
National Park ◽  
New South ◽  
New South Wales ◽  
Last Glacial ◽  
Evolutionarily Significant Units ◽  
Phylogenetic Placement ◽  
South Wales ◽  
Disjunct Populations ◽  
The Last Glacial

The alpine she-oak skink Cyclodomorphus praealtus is a threatened alpine endemic lizard from the mainland of Australia. The species is previously known from disjunct populations in Kosciuszko National Park in New South Wales and three isolated localities in the Victorian Alps. The New South Wales and Victorian populations represent separate evolutionarily significant units. In 2011, a fourth Victorian population was discovered. We conducted a phylogenetic analysis and determined that the newly discovered population is discrete and may have been separated from other populations since the end of the last glacial maxima. This population requires separate management.

Gintarasia and Xalocoa, two new genera to accommodate temperate to subtropical species in the predominantly tropical Graphidaceae (Ostropales, Ascomycota)

2013 ◽  
Vol 26 (6) ◽  
pp. 466 ◽  
Author(s):  
Ekaphan Kraichak ◽  
Sittiporn Parnmen ◽  
Robert Lücking ◽  
H. Thorsten Lumbsch
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Markers ◽  
Genetic Markers ◽  
Phylogenetic Position ◽  
New Combinations ◽  
New Genera ◽  
Phylogenetic Placement ◽  
Complex Chemistry ◽  
Subtropical Species

The phylogenetic placement of Chapsa lamellifera, C. megalophthalma and Diploschistes ocellatus was studied using a dataset of five genetic markers (mtSSU, nuLSU, RPB1, RPB2 and ITS). As extratropical species occurring in Australasia, C. lamellifera and C. megalophthalma differ from other species in that genus by having relatively large ascomata with muriform ascospores and complex chemistry of either the protocetraric or stictic acids chemosyndrome. D. ocellatus is unique within Diploschistes, in lacking lateral paraphyses and containing the norstictic acid chemosyndrome. Previous phylogenetic analysis gave inconclusive results regarding the phylogenetic position of these taxa, and hence in the present study, a larger sampling of molecular markers was employed. Our results demonstrated that the two Chapsa species and D. ocellatus are not part of their current genera. Consequently, the new genera Gintarasia Kraichak, Lücking & Lumbsch and Xalocoa Kraichak, Lücking & Lumbsch are described to accommodate these species. The new combinations Gintarasia lamellifera (Kantvilas & Vězda) Kraichak, Lücking & Lumbsch, G. lordhowensis (Mangold) Kraichak, Lücking & Lumbsch, G. megalophthalma (Müll. Arg.) Kraichak, Lücking & Lumbsch and Xalocoa ocellata (Vill.) Kraichak, Lücking & Lumbsch are also proposed.

scholarly journals Rates of evolution and fossils in phylogenetic analysis: a computer simulation approach

1992 ◽  
Vol 6 ◽  
pp. 140-140
Author(s):  
John P. Huelsenbeck ◽  
David M. Hillis
Keyword(s):  
Phylogenetic Analysis ◽  
Wide Spectrum ◽  
Phylogenetic Reconstruction ◽  
Length Distribution ◽  
Temporal Position ◽  
Rate Of Evolution ◽  
Rates Of Evolution ◽  
Phylogenetic Resolution ◽  
Main Determinants ◽  
The Relationship

Whereas many studies have examined the performance of various character-data sets in phylogenetic analysis, little work has been done on the effect that various classes of taxa have on phylogenetic reconstruction. In particular, the “fossil versus living taxa” debate has concentrated mainly on the effects of fossils in reconstructing vertebrate and plant relationships. While this work has contributed to the understanding of the role that fossils play in systematics, a computer model clarifies the relationship among the main determinants of the fossil-taxa problem. In addition, simulations of phylogenies over a wide spectrum of evolutionary rates clarify the relative efficiencies of various tree-estimation procedures.In this study, computer generated phylogenies were used to examine the relationship between the temporal position and completeness of additional taxa in a phylogenetic analysis and the rate of evolution or, equivalently, the temporal scope of the phylogenetic problem. In the simulations, four fossil taxa of varying temporal position and completeness were added to an analysis that included four living taxa. Additional taxa varied in completeness (25%, 50%, 75%, and 100% completeness) and in temporal position (0%, 33%, 66%, and 100% of the distance from the ancestor to the living time plane). Fifty trees were generated each for low, low intermediate, high intermediate, and high rates of evolution or temporal scope. Because additional taxa that are 100% complete and 100% of the distance to the living time plane are equivalent to the addition of living taxa, this study directly compares the effects of addition of living versus fossil taxa in phylogenetic analysis.The importance of fossil taxa varied depending on their completeness and temporal position and on the rate of evolution under which the phylogeny was generated. In general, high completeness and temporal position near the ancestor of a clade improved phylogenetic resolution as measured by the percentage of the tree-length distribution that contains the real tree. Furthermore, the conditions of completeness and temporal position under which fossil taxa improved phylogenetic resolution over living taxa became less restrictive as the rate of evolution or the temporal scope of the tree increased.

Phylogenetic analysis of the Neotropical Pristimantis leptolophus species group (Anura: Craugastoridae): molecular approach and description of a new polymorphic species 

Zootaxa ◽  
2017 ◽  
Vol 4242 (2) ◽  
pp. 313
Author(s):  
MAURICIO RIVERA-CORREA ◽  
CARLOS JIMÉNEZ-RIVILLAS ◽  
JUAN M. DAZA
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Reconstruction ◽  
Morphological Diversity ◽  
Molecular Data ◽  
Species Group ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Molecular Evidence ◽  
Polymorphic Species ◽  
Species Groups

Pristimantis, distributed throughout the New World tropics, is the most speciose vertebrate genus. Pristimantis presents an enormous morphological diversity and is currently divided into several demonstrably non-monophyletic phenetic species groups. With the purpose of increasing our understanding of Pristimantis systematics, we present the first phylogenetic analysis using molecular evidence to test the monophyly and infer evolutionary relationships within the Pristimantis leptolophus group, an endemic group of frogs from the highlands of the Colombian Andes. Our phylogenetic reconstruction recovers the group as monophyletic with high support, indicating general concordance between molecular data and morphological data. In addition, we describe a new polymorphic species lacking conspicuous tubercles, a regular attribute among species of the P. leptolophus species group and endemic from the Páramo de Sonsón complex (Antioquia, Colombia). The phylogenetic position of the new species is inferred and other systematic implications in the light of our results are discussed. 

Pseudodactylaria fusiformis sp. nov. from freshwater habitat in China

Phytotaxa ◽  
2020 ◽  
Vol 446 (2) ◽  
pp. 95-102
Author(s):  
YONG-ZHONG LU ◽  
JING-YI ZHANG ◽  
CHUAN-GEN LIN ◽  
ZONG-LONG LUO ◽  
JIAN-KUI (JACK) LIU
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Latitudinal Gradient ◽  
Sequence Data ◽  
Distinct Species ◽  
Freshwater Fungi ◽  
Morphological Comparison ◽  
Sister Relationship ◽  
Freshwater Habitat ◽  
Phylogenetic Placement

Pseudodactylaria fusiformis sp. nov. was collected during an investigation of freshwater fungi along a north-south latitudinal gradient in the Asian region. Evidence for the new species is provided by morphological comparison and sequence data analysis. Pseudodactylaria fusiformis differs from other species in having hyaline conidiophores and fusiform, 0–1-septate hyaline conidia without a sheath. Phylogenetic analysis based on combined ITS and LSU sequence data was carried out to determine the phylogenetic placement of the species. Six Pseudodactylaria taxa clustered together and formed a monotypic clade representing the genus, and five species are well recognized. Pseudodactylaria fusiformis and P. camporesiana share a sister relationship and they are phylogenetically distinct species. A detailed description and illustration are provided, as well as the comparisons with similar taxa.

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