Elusive Relationships Within Order Fabales: Phylogenetic Analyses Using matK and rbcL Sequence Data

The order Fabales, including Leguminosae, Polygalaceae, Quillajaceae and Surianaceae, represents a novel hypothesis emerging from angiosperm molecular phylogenies. Despite good support for the order, molecular studies to date have suggested contradictory, poorly supported interfamilial relationships. Our reappraisal of relationships within Fabales addresses past taxon sampling deficiencies, and employs parsimony and Bayesian approaches using sequences from the plastid regions rbcL (166 spp.) and matK (78 spp.). Five alternative hypotheses for interfamilial relationships within Fabales were recovered. The Shimodaira-Hasegawa test found the likelihood of a resolved topology significantly higher than the one calculated for a polytomy, but did not favour any of the alternative hypotheses of relationship within Fabales. In the light of the morphological evidence available and the comparative behavior of rbcL and matK, the topology recovering Polygalaceae as sister to the rest of the order Fabales with Leguminosae more closely related to Quillajaceae + Surianaceae, is considered the most likely hypothesis of interfamilial relationships of the order. Dating of selected crown clades in the Fabales phylogeny using penalized likelihood suggests rapid radiation of the Leguminosae, Polygalaceae, and (Quillajaceae + Surianaceae) crown clades.

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Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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Mimaporia, a new genus of Epicopeiidae (Lepidoptera), with description of a new species from Vietnam

Zootaxa ◽

10.11646/zootaxa.4254.5.3 ◽

2017 ◽

Vol 4254 (5) ◽

pp. 537 ◽

Cited By ~ 5

Author(s):

CHIA-HSUAN WEI ◽

SHEN-HORN YEN

Keyword(s):

New Species ◽

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Sister Group ◽

Morphological Evidence ◽

New Taxon ◽

The Family ◽

A New Species

The Epicopeiidae is a small geometroid family distributed in the East Palaearctic and Oriental regions. It exhibits high morphological diversity in body size and wing shape, while their wing patterns involve in various complex mimicry rings. In the present study, we attempted to describe a new genus, and a new species from Vietnam, with comments on two assumed congeneric novel species from China and India. To address its phylogenetic affinity, we reconstructed the phylogeny of the family by using sequence data of COI, EF-1α, and 28S gene regions obtained from seven genera of Epicopeiidae with Pseudobiston pinratanai as the outgroup. We also compared the morphology of the new taxon to other epicopeiid genera to affirm its taxonomic status. The results suggest that the undescribed taxon deserve a new genus, namely Mimaporia gen. n. The species from Vietnam, Mimaporia hmong sp. n., is described as new to science. Under different tree building strategies, the new genus is the sister group of either Chatamla Moore, 1881 or Parabraxas Leech, 1897. The morphological evidence, which was not included in phylogenetic analyses, however, suggests its potential affinity with Burmeia Minet, 2003. This study also provides the first, although preliminary, molecular phylogeny of the family on which the revised systematics and interpretation of character evolution can be based.

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Molecular and morphological evidence indicates that Pseudorhabdosynochus lantauensis (Monogenea: Diplectanidae) represents two species

Parasitology ◽

10.1017/s0031182004007152 ◽

2005 ◽

Vol 130 (6) ◽

pp. 669-677 ◽

Cited By ~ 25

Author(s):

X. Y. WU ◽

N. B. CHILTON ◽

X. Q. ZHU ◽

M. Q. XIE ◽

A. X. LI

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Strong Support ◽

Morphological Characteristics ◽

Sufficient Evidence ◽

Bootstrap Support ◽

Morphological Evidence ◽

Lsu Rdna ◽

Epinephelus Coioides

Sequences of the first internal transcribed spacer (ITS-1) and the D1-D3 domains of the large subunit (LSU) of the ribosomal DNA (rDNA) were determined for multiple specimens of 4 operational taxonomic units (OTUs) of the monogenean, Pseudorhabdosynochus lantauensis. OTUs were defined based on their collecting localities, host and/or morphological characteristics. All P. lantauensis specimens of one group (OTUs 1 and 3) differed in their sequences of the ITS-1 and partial LSU rDNA when compared with specimens of a second group (OTUs 2 and 4) by 12% and 2%, respectively. Results of the phylogenetic analyses of the LSU rDNA sequence data showed total (100%) bootstrap support for the separation of P. lantauensis into 2 distinct clades. At least 11 of the 18 nucleotide differences in the LSU sequence between the two P. lantauensis clades were derived (i.e. autapomorphic) characters when the morphologically distinct species, P. epinepheli and P. coioidesis, were used as outgroups. Furthermore, there were several autapomorphic character states for each P. lantauensis clade. This provides sufficient evidence to reject the null hypothesis that P. lantauensis represents a single species. Morphological and morphometric differences between these two clades provided additional strong support for the separation of P. lantauensis into two species. These two parasite species were found to co-exist on one of the two species of serranid fish (i.e. Epinephelus coioides) examined in the South China Sea (Guangdong Province, China).

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

Fungal Systematics and Evolution ◽

10.3114/fuse.2020.06.02 ◽

2020 ◽

Vol 6 (1) ◽

pp. 25-37 ◽

Cited By ~ 1

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.

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Is Morphology Really at Odds with Molecules in Estimating Fern Phylogeny?

Systematic Botany ◽

10.1600/036364409789271209 ◽

2009 ◽

Vol 34 (3) ◽

pp. 455-475 ◽

Cited By ~ 58

Author(s):

Harald Schneider ◽

Alan R. Smith ◽

Kathleen M. Pryer

Keyword(s):

Phylogenetic Relationships ◽

Vascular Plants ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Spore Wall ◽

Morphological Evidence ◽

Bayesian Posterior Probability ◽

Seed Plants ◽

Dna Sequence Data ◽

Reproductive Characters

Using a morphological dataset of 136 vegetative and reproductive characters, we infer the tracheophyte phylogeny with an emphasis on early divergences of ferns (monilophytes). The dataset comprises morphological, anatomical, biochemical, and some DNA structural characters for a taxon sample of 35 species, including representatives of all major lineages of vascular plants, especially ferns. Phylogenetic relationships among vascular plants are reconstructed using maximum parsimony and Bayesian inference. Both approaches yield similar relationships and provide evidence for three major lineages of extant vascular plants: lycophytes, ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade, which comprises the fern and seed plant lineages. The fern lineage consists of five clades: horsetails, whisk ferns, ophioglossoids, marattioids, and leptosporangiate ferns. This lineage is supported by characters of the spore wall and has a parsimony bootstrap value of 76%, although the Bayesian posterior probability is only 0.53. Each of the five fern clades is well supported, but the relationships among them lack statistical support. Our independent phylogenetic analyses of morphological evidence recover the same deep phylogenetic relationships among tracheophytes as found in previous studies utilizing DNA sequence data, but differ in some ways within seed plants and within ferns. We discuss the extensive independent evolution of the five extant fern clades and the evidence for the placement of whisk ferns and horsetails in our morphological analyses.

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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

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz049 ◽

2019 ◽

Vol 192 (1) ◽

pp. 61-81 ◽

Cited By ~ 1

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.

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Confusion surrounding Didymosphaeria—phylogenetic and morphological evidence suggest Didymosphaeriaceae is not a distinct family

Phytotaxa ◽

10.11646/phytotaxa.176.1.12 ◽

2014 ◽

Vol 176 (1) ◽

pp. 102 ◽

Cited By ~ 21

Author(s):

HIRAN A. ARIYAWANSA ◽

ERIO CAMPORESI ◽

KASUN M. THAMBUGALA ◽

AUSANA MAPOOK ◽

JI-CHUAN KANG ◽

...

Keyword(s):

New Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Morphological Evidence ◽

Nucleotide Sequence Data ◽

The Family ◽

Family Based ◽

Phylogenetic Lineages ◽

A New Species

Didymosphaeriaceae is a ubiquitous fungal family that is reported to include saprobic, endophytic and pathogenic species associated with a wide variety of substrates. The family is characterized by 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci. In recent treatments Appendispora, Didymosphaeria, Roussoella, Phaeodothis and Verruculina were placed in the family. The aim of the present study is to delineate phylogenetic lineages within Didymosphaeriaceae and allied genera. A new species, Didymosphaeria rubi-ulmifolii, was isolated and identified based on morphological characters and phylogenetic analyses of partial 18S nrDNA and 28S nrDNA nucleotide sequence data. Didymosphaeria rubi-ulmifolii clustered with Montagnulaceae as a separate genus, while two putative strains (HKUCC 5834 and CMW 22186) of D. futilis from GenBank clustered with Cucurbitariaceae and Didymellaceae, respectively. The new species is characterized by immersed to slightly erumpent ascomata immersed under a clypeus, a peridium with compressed cells of textura intricata, long trabeculate pseudoparaphyses, anastomosing mostly above the asci and brown, 1-septate ascospores with granulate ornamentation. Phylogenetic analysis in combination with morphology and a review of literature show that Appendispora, Phaeodothis, Roussoella and Verruculina should be excluded from the family. Phaeodothis belongs in Montagnulaceae, Verruculina in Testudinaceae, while Appendispora and Roussoella belong in Roussoellaceae. The position of Didymosphaeriaceae as a distinct family, based on 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci is doubtful. Fresh collections of more Didymosphaeria strains are needed for epitypification and to obtain sequence data to establish if this family can be maintained.

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Donadinia echinacea and Plectania sichuanensis, two novel species of Sarcosomataceae from southwestern China

Phytotaxa ◽

10.11646/phytotaxa.508.1.1 ◽

2021 ◽

Vol 508 (1) ◽

Author(s):

MING ZENG ◽

ELENI GENTEKAKI ◽

KEVIN D. HYDE ◽

QI ZHAO

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Sequence Data ◽

Novel Species ◽

Phylogenetic Analyses ◽

Southwestern China ◽

Taxon Sampling ◽

Oil Droplets ◽

Two New Species ◽

Dematiaceous Hyphomycete

This paper describes five sarcosomataceous samples collected from southwestern China and provides an updated two locus phylogeny of Sarcosomataceae. Two new species, Donadinia echinacea and Plectania sichuanensis, are described based on morphological and phylogenetic analyses. Donadinia echinacea is a dematiaceous hyphomycete with pleurogenous, guttulate conidia. Plectania sichuanensis is a cup-fungus distinguished by its ochre hymenium and ellipsoid ascospores with small multiple oil droplets. Phylogenetic analysis based on ITS and LSU sequence data using broad taxon sampling supports establishment of the new species along with eight distinct clades within Sarcosomataceae.

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Molecular phylogenetic evidence for paraphyly of Ceratovacuna and Pseudoregma (Hemiptera, Hormaphidinae) reveals late Tertiary radiation

Bulletin of Entomological Research ◽

10.1017/s0007485313000321 ◽

2013 ◽

Vol 103 (6) ◽

pp. 644-655

Author(s):

Zhang Rui-ling ◽

Huang Xiao-lei ◽

Jiang Li-yun ◽

Qiao Ge-xia

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Sampling Bias ◽

Morphological Evidence ◽

Rapid Radiation ◽

Long Wavelength ◽

Late Tertiary ◽

Molecular Phylogenetic ◽

Soldier Aphids

AbstractCeratovacuna and Pseudoregma are important groups in Cerataphidini (Hemiptera, Hormaphidinae) that not only produce soldier aphids in galls on the primary hosts but also produce horned soldiers on the herbaceous secondary hosts. However, due to sampling bias in previous studies, the phylogenetic relationships of these two genera remain inconclusive. In this study, based on more extensive sampling and examination of both mitochondrial (cytochrome c oxidase subunit I (COI); cytochrome b (Cytb)) and nuclear (elongation factor-1α (EF-1α); long-wavelength opsin (LWO)) genes, we reconstructed the phylogenetic relationships of Ceratovacuna and Pseudoregma. Phylogenetic analyses, along with morphological evidence, suggested that these two genera belong to the paraphyletic groups with species clustered into three main groups. The monophyly of Ceratovacuna and Pseudoregma as a whole was generally supported by all analyses. Monophyly of Pseudoregma was also supported. The estimated divergence times demonstrated that diversification of Ceratovacuna and Pseudoregma occurred approximately at 10 mya. The relatively low resolution for the basal relationships of the three main clades may indicate that these two genera have experienced a rapid radiation along with speciation burst of their secondary hosts during the late Tertiary.

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Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

PeerJ ◽

10.7717/peerj.8999 ◽

2020 ◽

Vol 8 ◽

pp. e8999

Author(s):

Sigrid Liede-Schumann ◽

Guido W. Grimm ◽

Nicolai M. Nürk ◽

Alastair J. Potts ◽

Ulrich Meve ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Cape Floristic Region ◽

Rapid Radiation ◽

Widespread Species ◽

Dna Sequence Data ◽

Phylogenetic Affinities ◽

African Genus

Background Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum, together with the highly succulent and species-rich tribe Ruschieae, constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. Methods Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence dataset comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. Results Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.

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