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.

Palicella lueckingii (Lecanorales, Ascomycota), a new lichen species inhabiting Araucaria from the extratropical South America

Phytotaxa ◽  
2018 ◽  
Vol 344 (1) ◽  
pp. 24 ◽  
Author(s):  
PAMELA RODRIGUEZ-FLAKUS
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
South America ◽  
Gene Locus ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Bayesian Analyses ◽  
Morphological Studies ◽  
Molecular Phylogenetic ◽  
Araucaria Araucana

Palicella lueckingii is a newly described corticolous lecideoid lichen from the Malalcahuelo National Reserve growing on the bark of Araucaria araucana in Chile. Detailed morphological studies and inference from molecular phylogenetic analyses, based on maximum likelihood and Bayesian analyses of single gene locus (ITS), clearly indicate that the new species is a member of the recently introduced genus Palicella. Palicella lueckingii is most closely related to P. glaucopa, but clearly differs in having smaller ascospores, comparatively thicker thallus, epruinose apothecia, lack of oil droplets inside of exciple and presence of thiophanic acid as a major metabolite.

Taxonomy and phylogeny of Chara (Charophyceae, Characeae) from Brazil with emphasis on the midwest and southeast regions

Phytotaxa ◽  
2017 ◽  
Vol 302 (2) ◽  
pp. 101 ◽  
Author(s):  
FABIO RENATO BORGES ◽  
ORLANDO NECCHI JR
Keyword(s):  
Molecular Markers ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
American Studies ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
South American ◽  
Bayesian Analyses ◽  
Sem Analyses

South American studies on the genus Chara are relatively scarce, most consisting of floristic surveys and using only traditional morphological characters. This study is a first approach to the systematics of the genus Chara applying modern techniques (DNA sequences and oospore SEM analyses) in addition to the alpha-taxonomy investigations that have been conducted in Brazil. Twelve populations of Chara were analyzed from the midwest and southeast regions of Brazil. Sequences of three molecular markers were applied to infer phylogenies. The ultrastructure of the oospore wall and currently used morphological characters were analyzed for Chara populations. Maximum likelihood and Bayesian analyses of sequences of rbcL, ITS2, and matK were congruent in that they grouped the species in six clades, each representing one species: Chara braunii C.C. Gmelin, C. foliolosa C.L.Willdenow, C. guairensis R.Bicudo, C. haitensis M.P.J.F. Turpin, C. hydropitys H. Reichenbach and C. rusbyana M. Howe. Morphological characters, including ultrastructure of oospore wall, provided good evidences to characterize each species. Molecular data supported the recent view that some traditional infra-generic taxa (e.g. subgenus Charopsis and subsection Willdenowia) are not supported in phylogenetic analyses, whereas some species (e.g. C. foliolosa, C. haitensis, C. hydropitys and C. rusbyana previously considered as varieties and forms of C. zeylanica) were consistently distinguished in the analyses for the three molecular markers.

scholarly journals A new genus and four new species in the /Psathyrella s.l. clade from China

MycoKeys ◽  
2021 ◽  
Vol 80 ◽  
pp. 115-131
Author(s):  
Tolgor Bau ◽  
Jun-Qing Yan
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Bayesian Analyses ◽  
Distinct Lineage

Based on traditional morphological and phylogenetic analyses (ITS, LSU, tef-1α and β-tub) of psathyrelloid specimens collected from China, four new species are here described: Heteropsathyrella macrocystidia, Psathyrella amygdalinospora, P. piluliformoides, and P. truncatisporoides. H. macrocystidia forms a distinct lineage and groups together with Cystoagaricus, Kauffmania, and Typhrasa in the /Psathyrella s.l. clade, based on the Maximum Likelihood and Bayesian analyses. Thus, the monospecific genus Heteropsathyrella gen. nov. is introduced for the single species. Detailed descriptions, colour photos, and illustrations are presented in this paper.

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.

Delving deeper into the phylogenetics of the herbaceous bamboos (Poaceae, Bambusoideae, Olyreae): evaluation of generic boundaries within the Parodiolyra/Raddiella clade uncovers a new genus

2019 ◽  
Vol 192 (1) ◽  
pp. 61-81 ◽  
Author(s):  
Iasmin L C Oliveira ◽  
Andreza O Matos ◽  
Christian Silva ◽  
Maria Luiza S Carvalho ◽  
Christopher D Tyrrell ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Morphological Evidence ◽  
Taxon Sampling ◽  
Plastid Genomes ◽  
Herbaceous Bamboos

Abstract The present study aims to expand the knowledge of phylogenetic relationships in Olyrinae, a subtribe of herbaceous bamboos (Poaceae: Bambusoideae: Olyreae). Our focus is on Parodiolyra and Raddiella, two historically related genera that, with their sister Diandrolyra, form one of the four main lineages in the subtribe. Previous phylogenetic analyses suggested that Parodiolyra is not monophyletic, but its taxonomic boundaries and its relationship with Raddiella remain uncertain due to low sampling. We increased the taxon sampling and sequenced five regions of the nuclear and plastid genomes for this lineage and other representatives of Olyreae. We used maximum parsimony, maximum likelihood, Bayesian inference and coalescence analysis. Our results corroborate the paraphyly of Parodiolyra, with P. micrantha sister to a clade including the remaining Parodiolyra and Raddiella. All remaining Parodiolyra form a well-supported clade, but Raddiella had conflicting resolutions, being either monophyletic or not. Thus, based on phylogenetic and morphological evidence, we here recircumscribe Parodiolyra, transferring P. micrantha and P. colombiensis to the new genus Taquara (described here). Regarding Raddiella, sampling is still not comprehensive and does not allow a decision on to its taxonomic status to be made at this time. Inclusion of other phreatophytic species may be crucial to resolve the problem of conflicting topologies.

The phylogenetic relationships between Amphinomidae, Archinomidae and Euphrosinidae (Amphinomida: Aciculata: Polychaeta), inferred from molecular data

2008 ◽  
Vol 88 (3) ◽  
pp. 509-513 ◽  
Author(s):  
Helena Wiklund ◽  
Arne Nygren ◽  
Fredrik Pleijel ◽  
Per Sundberg
Keyword(s):  
Maximum Likelihood ◽  
Hydrothermal Vent ◽  
Phylogenetic Relationships ◽  
18S Rdna ◽  
Single Species ◽  
Molecular Data ◽  
Junior Synonym ◽  
28S Rdna ◽  
Bayesian Analyses ◽  
The Family

Amphinomida is an ‘isolated’ clade within the polychaete group Aciculata and traditionally includes the families Amphinomidae, Archinomidae and Euphrosinidae. Archinomidae were erected for a single species, the hydrothermal vent polychaete Archinome rosacea. Originally, A. rosacea was assigned to Euphrosinidae although it shares more morphological similarities with Amphinomidae. In this study we assess the position of Archinome, Euphrosinidae and Amphinomidae by using molecular data from nuclear 18S rDNA and 28S rDNA. Parsimony, maximum likelihood and Bayesian analyses are performed on the nucleotide datasets covering in total 19 terminals from Amphinomidae, Euphrosinidae, Archinomidae and outgroups. Our results conclusively show that Euphrosinidae and Amphinomidae are sister taxa and that Archinome is sister to Chloeia within Amphinomidae. Based on these results the family name Archinomidae is treated as a junior synonym of Amphinomidae.

Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea : Decapoda : Thalassinidea) using nuclear 18S rDNA and mitochondrial 16S rDNA

2002 ◽  
Vol 16 (6) ◽  
pp. 839 ◽  
Author(s):  
C. C. Tudge ◽  
C. W. Cunningham
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
16S Rdna ◽  
18S Rdna ◽  
Strong Support ◽  
Ribosomal Genes ◽  
Bayesian Analyses ◽  
The Family ◽  
Mitochondrial 16S Rdna

Partial sequences of the 18S nuclear and 16S mitochondrial ribosomal genes were obtained for 14�species of thalassinidean shrimp (families Callianassidae, Laomediidae, Strahlaxiidae, Thalassinidae and Upogebiidae) and a further six species in related decapod infraorders (families Aeglidae, Astacidae, Lithodidae, Palinuridae, Raninidae and Scyllaridae). Maximum-likelihood and Bayesian analyses show equivocal support for the monophyly of the Thalassinidea, but show strong support for division of the infraorder into two major clades. This dichotomy separates representatives in the Upogebiidae, Laomediidae and Thalassinidae from those in the Strahlaxiidae and Callianassidae. The Laomediidae is shown to be paraphyletic, with the thalassinid species, Thalassina squamifera, being placed on a branch between Axianassa and a clade comprising Jaxea and Laomedia, the three current laomediid genera. For a monophyletic Laomediidae, the family Axianassidae should be resurrected for the genus Axianassa.

scholarly journals Venation patterns of neotropical blueberries (Vaccinieae: Ericaceae) and their phylogenetic utility

Phytotaxa ◽  
2013 ◽  
Vol 96 (1) ◽  
pp. 1 ◽  
Author(s):  
PAOLA PEDRAZA-PEÑALOSA ◽  
NELSON R. SALINAS ◽  
WARD C. WHEELER
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Operational Definition ◽  
Phylogenetic Framework

The description of venation patterns in neotropical Vaccinieae has been problematic because of the lack of an operational definition. Moreover, the underlying homologies remain unknown across and within lineages, thus precluding the use of venation characters in phylogenetic analyses. Venation patterns are often obscured in herbarium and living specimens due to the characteristic coriaceous and thick nature of Ericaceae leaves. Therefore, to obtain an unobstructed view of the veins, leaf clearings of 16 putative generic lineages of Vaccinieae were prepared and described. The main venation patterns were then defined and traditional definitions of venation were discussed in the light of the observed patterns. Selected characters were scored and the evolution of venation characters was discussed using a phylogenetic framework derived from molecular data analyzed under Maximum Likelihood. Venation descriptions and photographs are provided for 33 species.

scholarly journals Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12104
Author(s):  
Bastian Bentlage ◽  
Allen G. Collins
Keyword(s):  
Maximum Likelihood ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Life Cycles ◽  
Tree Topologies ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Inference Methods

Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.

Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.

Phytotaxa ◽  
2018 ◽  
Vol 369 (2) ◽  
pp. 63 ◽  
Author(s):  
DONG-QIN DAI ◽  
LI-ZHOU TANG ◽  
CHAO LIU ◽  
HAI-BO WANG ◽  
KEVIN D. HYDE
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Tree ◽  
Type Species ◽  
Sequence Data ◽  
Sensu Stricto ◽  
New Order ◽  
Bayesian Analyses ◽  
Phylogenic Analysis ◽  
The Family

The family Parmulariaceae comprises three polyphyletic genera, but with very little data in GenBank and is presently placed in the order Asterinales. In this study, we re-analyze the available sequence data for taxa of the family and re-examine the type species of Hemigrapha, Inocyclus and Parmularia. The phylogenetic tree generated from maximum likelihood and Bayesian analyses of combined LSU-SSU sequence data demonstrate the relationships among Hemigrapha, Inocyclus and Parmularia species, and the relations of Buelliella, Karschia, Labrocarpon, Lembosia, Melaspileella, Melaspileopsis and Stictographa. We introduce Parmulariales ord. nov. to accommodate Parmulariaceae and the order Asterinales accommodates Asterinaceae, Asterotexaceae, Hemigraphaceae fam. nov., Melaspileellaceae fam. nov. and Stictographaceae fam. nov. Notes for each new order and families are provided. We confirm that Asterinaceae sensu lato is distant from Asterinaceae sensu stricto in the phylogenic analysis. The classification presented here is provisional, as more species are needed to re-collected and sequenced. We expect further support for our ordinal and familial lineages, as well as further novel lineages.

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