scholarly journals An updated tribal classification of Lamiaceae based on plastome phylogenomics

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Fei Zhao ◽  
Ya-Ping Chen ◽  
Yasaman Salmaki ◽  
Bryan T. Drew ◽  
Trevor C. Wilson ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Character Evolution ◽  
Bayesian Analyses ◽  
Protein Coding ◽  
Future Studies ◽  
The Past ◽  
Phylogenetic Framework ◽  
Tribal Classification ◽  
Stable Classification

Abstract Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract

Hybrid Models for Conjoint Analysis: An Expository Review

1984 ◽  
Vol 21 (2) ◽  
pp. 155-169 ◽  
Author(s):  
Paul E. Green
Keyword(s):  
Conjoint Analysis ◽  
Hybrid Models ◽  
Comparative Performance ◽  
Future Studies ◽  
The Past ◽  
Industry Applications ◽  
Validation Tests ◽  
Data Collection Effort

Over the past few years hybrid models for conjoint analysis have been developed to reduce data collection effort and time. Hybrid models combine features of self-explicated utility measurement with more traditional conjoint analysis. A classification of hybrid models is presented, followed by a review of their comparative performance in cross-validation tests. Though hybrid models represent an attempt to cope with an important practical problem in industry applications of conjoint techniques, these models entail a number of untested assumptions requiring further theoretical analysis and empirical research. Suggestions are offered on future studies that are essential before the role of hybrid models in conjoint methods can be evaluated properly.

scholarly journals Evaluating species in Botryosphaeriales

2021 ◽  
Author(s):  
W. Zhang ◽  
J.Z. Groenewald ◽  
L. Lombard ◽  
R.K. Schumacher ◽  
A.J.L. Phillips ◽  
...  
Keyword(s):  
South Africa ◽  
Woody Plants ◽  
Phylogenetic Analyses ◽  
Culture Collection ◽  
Morphological Data ◽  
Culture Collections ◽  
Future Studies ◽  
The Past ◽  
Wide Range ◽  
Solid Foundation

The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae (Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S. hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods.

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.

Towards a monophyletic classification of Lejeuneaceae V: the systematic position of Pictolejeunea

Phytotaxa ◽  
2016 ◽  
Vol 280 (3) ◽  
pp. 259 ◽  
Author(s):  
JULIA BECHTELER ◽  
GAIK EE LEE ◽  
ALFONS SCHÄFER-VERWIMP ◽  
MATT A. M. RENNER ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Sister Relationship ◽  
Bayesian Analyses ◽  
Outgroup Species ◽  
Made In

With more than 1,000 species in some 70 genera, Lejeuneaceae represent the largest family of liverworts. Although much progress has been made in recent years, the supraspecific classification of Lejeuneaceae has not yet been satisfactorily solved. Maximum likelihood and Bayesian analyses of a three marker dataset (nrITS, cp DNA rbcL and trnL-trnF) derived from 85 accessions of Lejeuneeae and 13 outgroup species revealed Pictolejeunea picta in a sister relationship to the remainder of Lejeuneeae, the most speciose tribe of Lejeuneaceae. Based on the outcome of the phylogenetic analyses, we establish subtribe Pictolejeuneinae subtr. nov.

scholarly journals The Culicidae (Diptera): a review of taxonomy, classification and phylogeny*

Zootaxa ◽  
2007 ◽  
Vol 1668 (1) ◽  
pp. 591-638 ◽  
Author(s):  
RALPH E. HARBACH
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Traditional Classification ◽  
Phenetic Classification ◽  
Cladistic Analyses ◽  
Morphological And Molecular Data ◽  
Stable Classification

The taxonomy, classification and phylogeny of family Culicidae are reviewed. The application of explicit methods of phylogenetic analysis has revealed weaknesses in the traditional classification of mosquitoes, but little progress has been made to achieve a robust, stable classification that reflects evolutionary relationships. The current phenetic classification is discussed in view of phylogeny reconstructions based on cladistic analyses of morphological and molecular data. It is concluded that the generic and suprageneric relationships and the validity and monophyly of the generic and subgeneric groupings of Culicidae are in need of extensive reappraisal. If the classification is to reflect evolutionary history, changes to the nomenclature of mosquitoes are inevitable. There is strong morphological and molecular evidence that subfamily Anophelinae and tribes Aedini, Culicini and Sabethini of subfamily Culicinae are monophyletic, but the other taxonomic groupings are not demonstrably monophyletic or have not been subjected to phylogenetic analyses.

scholarly journals One Hundred Mitochondrial Genomes of Cicadas

2018 ◽  
Vol 110 (2) ◽  
pp. 247-256 ◽  
Author(s):  
Piotr Łukasik ◽  
Rebecca A Chong ◽  
Katherine Nazario ◽  
Yu Matsuura ◽  
De Anna C Bublitz ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Evolutionary Rates ◽  
Future Research ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Coding Regions ◽  
Mitochondrial Genome Evolution ◽  
Taxonomic Framework

Abstract Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.

scholarly journals Phylogenomics resolves deep subfamilial relationships in Malvaceae s.l.

2021 ◽  
Author(s):  
Tijana Cvetković ◽  
Fabiola Areces-Berazain ◽  
Damien D Hinsinger ◽  
Daniel C Thomas ◽  
Jan J Wieringa ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Economic Importance ◽  
Plant Family ◽  
Bayesian Analyses ◽  
Plastid Genomes ◽  
Great Economic Importance ◽  
The Family ◽  
Evolutionary Studies ◽  
Phylogenetic Framework

Abstract Malvaceae s.l., the most diverse family within Malvales, includes well-known species of great economic importance like cotton, cacao, and durian. Despite numerous phylogenetic analyses employing multiple markers, relationships between several of its nine subfamilies, particularly within the largest lineage/Malvadendrina, remain unclear. In this study, we attempted to resolve the relationships within the major clades of Malvaceae s.l. using plastid genomes of 48 accessions representing all subfamilies. Maximum likelihood and Bayesian analyses recovered a fully resolved and well-supported topology confirming the split of the family into/Byttneriina (/Grewioideae +/Byttnerioideae) and/Malvadendrina. Within/Malvadendrina,/Helicteroideae occupied the earliest branching position, followed by/Sterculioideae./Brownlowioideae,/Tiliodeae, and/Dombeyoideae formed a clade sister to/Malvatheca (/Malvoideae +/Bombacoideae), a grouping morphologically supported by the lack of androgynophore. Results from dating analyses suggest that all subfamilies originated during hot or warm phases in the Late Cretaceous to Paleocene. This study presents a well-supported phylogenetic framework for Malvaceae s.l. that will aid downstream revisions and evolutionary studies of this economically important plant family.

scholarly journals Sea lettuce systematics: lumping or splitting?

2018 ◽  
Author(s):  
Manuela Bernardes Batista ◽  
Regina L. Cunha ◽  
Rita Castilho ◽  
Paulo Antunes Horta
Keyword(s):  
Phylogenetic Relationships ◽  
Upper Cretaceous ◽  
Phylogenetic Analyses ◽  
Brazilian Coast ◽  
Nominal Species ◽  
Bayesian Analyses ◽  
The Pacific ◽  
Phylogenetic Framework ◽  
Flow Through ◽  
Daunting Challenge

AbstractPhylogenetic relationships within sea lettuce species belonging to the genus Ulva is a daunting challenge given the scarcity of diagnostic morphological features and the pervasive phenotypic plasticity. With more than 100 species described on a morphological basis, an accurate evaluation of its diversity is still missing. Here we analysed 277 chloroplast-encoded gene sequences (43 from this study), representing 35 nominal species of Ulva from the Pacific, Indian Ocean, and Atlantic (with a particular emphasis on the Brazilian coast) in an attempt to solve the complex phylogenetic relationships within this widespread genus. Maximum likelihood, Bayesian analyses and species delimitation tests support the existence of 22 evolutionary significant units (ESUs), lumping the currently recognized number of species. All individuals sampled throughout an extensive area of the Brazilian coast were included within two distinct ESUs. Most of the clades retrieved in the phylogenetic analyses do not correspond to a single nominal species. Geographic range evolution indicated that the ancestor of Ulva had a distribution restricted to the temperate North Pacific. The dating analysis estimated its origin during the Upper Cretaceous at 75.8 million years (myr) ago but most of the cladogenetic events within the genus occurred in the last ten myr. Pervasive human-mediated gene flow through ballast water and widespread morphologic plasticity are the most likely explanations for the difficulty in establishing a reliable phylogenetic framework for this conspicuous, widespred and many times abundant green algae morphotype.

Centipede systematics: progress and problems*

Zootaxa ◽  
2007 ◽  
Vol 1668 (1) ◽  
pp. 327-341 ◽  
Author(s):  
GREGORY D. EDGECOMBE
Keyword(s):  
Species Delimitation ◽  
Middle Devonian ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Ribosomal Genes ◽  
Model Species ◽  
Crown Group ◽  
Web Based ◽  
The Past

Breakthroughs in centipede systematics over the past 25 years have included: a stable morphology-based cladogram for ordinal interrelationships that is largely congruent with well-sampled nuclear ribosomal genes; the discovery of mid Palaeozoic crown-group fossils, including Silurian-Devonian stem-group Scutigeromorpha and an extinct order in the Middle Devonian; and, a web-based catalogue of all centipede species globally. Challenges include species delimitation in several groups, conflict between different kinds of molecular data (nuclear coding genes versus ribosomal genes), the inter-familial relationships and classification of the Geophilomorpha in particular, and effecting a synthesis between microanatomical studies of selected ‘model’ species and dense taxonomic sampling in numerical phylogenetic analyses.

scholarly journals Insight into the Systematics of Microfungi Colonizing Dead Woody Twigs of Dodonaea viscosa in Honghe (China)

2021 ◽  
Vol 7 (3) ◽  
pp. 180
Author(s):  
Dhanushka N. Wanasinghe ◽  
Peter E. Mortimer ◽  
Jianchu Xu
Keyword(s):  
Southern China ◽  
Phylogenetic Analyses ◽  
Fungal Species ◽  
Dodonaea Viscosa ◽  
Bayesian Analyses ◽  
Protein Coding ◽  
Multiple Substrates ◽  
Coding Regions ◽  
Family Analysis ◽  
Tropical Areas

Members of Dodonaea are broadly distributed across subtropical and tropical areas of southwest and southern China. This host provides multiple substrates that can be richly colonized by numerous undescribed fungal species. There is a severe lack of microfungal studies on Dodonaea in China, and consequently, the diversity, phylogeny and taxonomy of these microorganisms are all largely unknown. This paper presents two new genera and four new species in three orders of Dothideomycetes gathered from dead twigs of Dodonaea viscosa in Honghe, China. All new collections were made within a selected area in Honghe from a single Dodonaea sp. This suggests high fungal diversity in the region and the existence of numerous species awaiting discovery. Multiple gene sequences (non-translated loci and protein-coding regions) were analysed with maximum likelihood and Bayesian analyses. Results from the phylogenetic analyses supported placing Haniomyces dodonaeae gen. et sp. in the Teratosphaeriaceae family. Analysis of Rhytidhysteron sequences resulted in Rhytidhysteron hongheense sp. nov., while analysed Lophiostomataceae sequences revealed Lophiomurispora hongheensis gen. et sp. nov. Finally, phylogeny based on a combined dataset of pyrenochaeta-like sequences demonstrates strong statistical support for placing Quixadomyceshongheensis sp. nov. in Parapyrenochaetaceae. Morphological and updated phylogenetic circumscriptions of the new discoveries are also discussed.

Sign in / Sign up

Export Citation Format

Share Document