scholarly journals ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8392 ◽  
Author(s):  
Janice Valencia-D ◽  
José Murillo-A ◽  
Clara Inés Orozco ◽  
Carlos Parra-O ◽  
Kurt M. Neubig
Keyword(s):  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Bootstrap Support ◽  
Nucleotide Substitutions ◽  
Plastid Genomes ◽  
The Family ◽  
High Bootstrap ◽  
Single Genus

Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.

Revision of Family Megacalanidae (Copepoda: Calanoida)

Zootaxa ◽  
2017 ◽  
Vol 4229 (1) ◽  
pp. 1 ◽  
Author(s):  
JANET M. BRADFORD-GRIEVE ◽  
LEOCADIO BLANCO-BERCIAL ◽  
GEOFFREY A. BOXSHALL
Keyword(s):  
Cladistic Analysis ◽  
Detailed Examination ◽  
Molecular Data ◽  
Bootstrap Support ◽  
Species Status ◽  
Large Size ◽  
The Family ◽  
High Bootstrap ◽  
Taxonomic Confusion ◽  
Nomen Novum

The Megacalanidae were revised based on new and archived material. Taxonomic confusion that has existed in the family is discussed and a method is suggested for stabilising names. A detailed examination of the morphology of this family, using the light microscope, has added further useful characters that distinguish genera and species. The added, hitherto undescribed species include character states incompatible with aspects of previous generic definitions (e.g. presence or absence of setae on the maxillule coxal endite). Nevertheless, the cladistic and molecular analyses confirmed that there are at least four monophyletic clades mostly with high bootstrap support. These clades represent already defined genera, one of which [Elenacalanus nom. nov. (nomen novum)] replaces the preoccupied name Heterocalanus Wolfenden, 1906. Four previously described species have been re-assigned to Elenacalanus in new combinations: E. princeps (Brady, 1883), E. eltaninae (Björnberg, 1968), E. sverdrupi (Johnson, 1958) and E. inflatus (Björnberg, 1968). Eleven new species are described: three Megacalanus, one Bradycalanus, six Bathycalanus, and one Elenacalanus nom. nov. Bradycalanus pseudotypicus enormis Björnberg, 1968 has been raised to species status based on genetic data although it can be only be distinguished morphologically from Br. typicus by its large size. All four genera are differentially diagnosed and keys are provided to the genera and species. We confirm that all male right antennules are geniculate in the Megacalanidae. Thirteen males are known. Of these males, eight are newly described (M. frosti n. sp., M. ericae n. sp., M. ohmani n. sp., Bathycalanus bradyi (Wolfenden, 1905a), Ba. dentatus n. sp., Ba. milleri n. sp., Ba. unicornis Björnberg, 1968, and Elenacalanus tageae n. sp.). We cannot be absolutely certain that the correct males have been assigned to the appropriate female so our decisions await testing with new data. The cladistic analysis provides the first morphology-based phylogeny. This scheme served as a working hypothesis which was tested and corroborated using the newly gathered molecular data. Vertical and horizontal distributions are summarised. 

scholarly journals A supermatrix-based molecular phylogeny of the family Drosophilidae

2010 ◽  
Vol 92 (1) ◽  
pp. 25-38 ◽  
Author(s):  
KIM VAN DER LINDE ◽  
DAVID HOULE ◽  
GREG S. SPICER ◽  
SCOTT J. STEPPAN
Keyword(s):  
Drosophila Melanogaster ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Molecular Data ◽  
The Other ◽  
Bootstrap Support ◽  
Bayesian Approaches ◽  
Considerable Uncertainty ◽  
Sister Clade ◽  
The Family

SummaryThe genus Drosophila is diverse and heterogeneous and contains a large number of easy-to-rear species, so it is an attractive subject for comparative studies. The ability to perform such studies is currently compromised by the lack of a comprehensive phylogeny for Drosophila and related genera. The genus Drosophila as currently defined is known to be paraphyletic with respect to several other genera, but considerable uncertainty remains about other aspects of the phylogeny. Here, we estimate a phylogeny for 176 drosophilid (12 genera) and four non-drosophilid species, using gene sequences for up to 13 different genes per species (average: 4333 bp, five genes per species). This is the most extensive set of molecular data on drosophilids yet analysed. Phylogenetic analyses were conducted with maximum-likelihood (ML) and Bayesian approaches. Our analysis confirms that the genus Drosophila is paraphyletic with 100% support in the Bayesian analysis and 90% bootstrap support in the ML analysis. The subgenus Sophophora, which includes Drosophila melanogaster, is the sister clade of all the other subgenera as well as of most species of six other genera. This sister clade contains two large, well-supported subclades. The first subclade contains the Hawaiian Drosophila, the genus Scaptomyza, and the virilis-repleta radiation. The second contains the immigrans-tripunctata radiation as well as the genera Hirtodrosophila (except Hirtodrosophila duncani), Mycodrosophila, Zaprionus and Liodrosophila. We argue that these results support a taxonomic revision of the genus Drosophila.

scholarly journals Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 543 ◽  
Author(s):  
Jun Li ◽  
Deng-Feng Xie ◽  
Xian-Lin Guo ◽  
Zhen-Ying Zheng ◽  
Xing-Jin He ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Relationship ◽  
Nucleotide Diversity ◽  
Population Genomics ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Bootstrap Support ◽  
Plastid Genomes ◽  
Medicinal Value ◽  
High Bootstrap

Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes of Bupleurum chinense and Bupleurum commelynoideum were sequenced, and their gene content, order, and structure were counted and analyzed. The only three published Bupleurum species (B. boissieuanum, B. falcatum, and B. latissimum) and other fifteen allied species were selected to conduct a series of comparative and phylogenetic analyses. The genomes of B. chinense and B. commelynoideum were 155,869 and 155,629 bp in length, respectively, both of which had a typical quadripartite structure. The genome length, structure, guanine and cytosine (GC) content, and gene distribution were highly similar to the other three Bupleurum species. The five Bupleurum species had nearly the same codon usages, and eight regions (petN-psbM, rbcL-accD, ccsA-ndhD, trnK(UUU)-rps16, rpl32-trnL(UAG)-ccsA, petA-psbJ, ndhF-rpl32, and trnP(UGG)-psaJ-rpl33) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in Bupleurum. Phylogenetic analysis revealed that all Bupleurum species clustered into a monophyletic clade with high bootstrap support and diverged after the Chamaesium clade. Overall, our study provides new insights into DNA barcoding and phylogenetic relationship between Bupleurum and its related genera, and will facilitate the population genomics, conservation genetics, and phylogenetics of Bupleurum in Apiaceae.

A molecular phylogenetic analysis of Diuris (Orchidaceae) based on AFLP and ITS reveals three major clades and a basal species

2009 ◽  
Vol 22 (1) ◽  
pp. 1 ◽  
Author(s):  
James O. Indsto ◽  
Peter H. Weston ◽  
Mark A. Clements
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Bootstrap Support ◽  
Its2 Region ◽  
Molecular Phylogenetic ◽  
Strong Bootstrap Support ◽  
Evidence Analysis

Diuris is a terrestrial orchid genus of at least 61 and possibly more than 100 species, restricted to Australia except for one species endemic in Timor. Distinctive species groups have respective eastern and western centres of distribution. Although species affinities have been vaguely understood for many years, no formal infrageneric treatment has been undertaken as Diuris possesses few reliable morphological characters for a classification system. We have undertaken cladistic parsimony and Bayesian phylogenetic analyses of Diuris by using the ITS1–5.8S–ITS2 region of nuclear rDNA and morphological characters, with a subset of samples also studied by amplified fragment length polymorphism (AFLP) as an independent test of phylogenetic relationships. Four major clades with strong bootstrap support were resolved and are named here according to a recently published classification; D. sulphurea forms a lineage (subg. Paradiuris) of its own that is well supported as the sister to the rest of Diuris. Two other major eastern clades contained species related to D. maculata (subg. Xanthodiuris) and D. punctata (subg. Diuris), respectively. Although these latter two subgenera are genetically well resolved, there is minimal genetic variation at species level, consistent with recent, rapid speciation. A fourth clade (subg. Hesperodiuris) has a centre of distribution in Western Australia, and has more genetic and morphological variation than the eastern subgenera. Total evidence analysis provides support for the western clade being sister group to the two eastern subgenera Diuris and Xanthodiuris; however, this relationship was not resolved by molecular data. Hybridisation is known to be common among species within subgenera Diuris and Xanthodiuris. Instances of incongruence between different datasets were found suggestive of hybridisation events between species of different sections of Diuris.

Characterization of the mitochondrial genome and phylogeny of the black arowana (Osteoglossum ferreirai)

Biologia ◽  
2014 ◽  
Vol 69 (9) ◽  
Author(s):  
Xidong Mu ◽  
Yi Liu ◽  
Xuejie Wang ◽  
Chao Liu ◽  
Hongmei Song ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Nucleotide Composition ◽  
Gene Arrangement ◽  
Bootstrap Support ◽  
Radiation Process ◽  
Molecular Approaches ◽  
The Family ◽  
High Bootstrap ◽  
Relationship Of

AbstractIn this study, we sequenced and assembled the mitochondrial (mt) genome of Osteoglossum ferreirai to re-assess the phylogenetic relationship of the family Osteoglossidae. We determined that the mitogenome of O. ferreirai contains the entire set of 37 mt genes, and the nucleotide composition and gene arrangement were similar to those of other bonytongues. Our phylogenetic analyses exhibited monophyly of the family Osteoglossidae with high bootstrap support, which is in agreement with the currently accepted phylogenetic viewpoint that is based on both morphological and molecular approaches. These findings provide additional informative data for the further study of phylogenetic relationships and help to elucidate a key component of the species radiation process within the family Osteoglossidae.

The evolution of fruit in Scandiceae subtribe Scandicinae (Apiaceae)

2001 ◽  
Vol 79 (11) ◽  
pp. 1358-1374 ◽  
Author(s):  
Krzysztof Spalik ◽  
Aneta Wojewódzka ◽  
Stephen R Downie
Keyword(s):  
Phylogenetic Trees ◽  
Sister Group ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Bootstrap Support ◽  
Sister Group Relationship ◽  
Vascular Bundles ◽  
Fruit Morphology ◽  
The Family ◽  
Fruit Characters

Evolutionary relationships among 66 representatives of the family Apiaceae, including 37 species of tribe Scandiceae subtribe Scandicinae, were inferred from separate and combined analyses of fruit morphology and anatomy and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences. Phylogenetic trees inferred from analysis of 35 fruit characters were not congruent to those derived from molecular data and, overall, had much lower bootstrap support values than the latter. Contrary to molecular data, fruit characters did not support the monophyly of subtribe Scandicinae. Fruit data do, however, corroborate the monophyly of nearly every genus within Scandicinae, the affinity of members of the "crown" clade—Anthriscus, Kozlovia (including Krasnovia and Neoconopodium), Geocaryum, Myrrhis, and Osmorhiza—that had been identified in previous molecular analyses, and the sister group relationship between the "crown" clade and the genus Scandix. Phylogenies derived from the analysis of combined ITS and fruit characters were congruent to those inferred from molecular data alone. Reconstructions of ancestral character states using the results of the combined analysis suggest that among extant Scandicinae, the fruits of Athamanta have retained the most plesiomorphic characters. Evolutionary tendencies that have occurred in the fruits of Scandicinae include the broadening of the vascular bundles and vittae, the thickening of the cuticle and epidermal cell wall, the origin of bristles from hairs, the appearance of a pedicel-like appendage, the development of a long beak, and lateral wings. These changes are interpreted as adaptations to fruit dispersal and seed defense.Key words: Apiaceae, Scandiceae subtribe Scandicinae, ITS, fruit morphology.

scholarly journals Phylogeny and morphology of Premilcurensis gen. nov. (Pleosporales) from stems of Senecio in Italy

Phytotaxa ◽  
2015 ◽  
Vol 236 (1) ◽  
pp. 40 ◽  
Author(s):  
Saowaluck Tibpromma ◽  
ITTHAYAKORN PROMPUTTHA ◽  
RUNGTIWA PHOOKAMSAK ◽  
SARANYAPHAT BOONMEE ◽  
ERIO CAMPORESI CAMPORESI ◽  
...  
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Bootstrap Support ◽  
Unique Combination ◽  
Comprehensive Description ◽  
High Bootstrap Support ◽  
The Family ◽  
Distinct Lineage ◽  
High Bootstrap

Premilcurensis senecionis gen. et and sp. nov. was collected on stems of Senecio sp. from Forlì-Cesena Province, Italy and is introduced in Phaeosphaeriaceae with the support of a unique combination of morphological characters and combined gene phylogenetic analyses. Premilcurensis is distinguished from other genera in Phaeosphaeriaceae in having fusiform to cylindrical, hyaline to yellow-green ascospores with 3–5 septa, and mucilaginous, wing-like appendages at the central septum. Phylogenies analyses show Premilcurensis as a distinct lineage from other genera in the family Phaeosphaeriaceae with high bootstrap support. A comprehensive description and micrographs of P. senecionis is provided and the new genus is compared with morphologically similar taxa.

Affinities of the Boletus chromapes group to Royoungia and the description of two new genera, Harrya and Australopilus

2012 ◽  
Vol 25 (6) ◽  
pp. 418 ◽  
Author(s):  
Roy E. Halling ◽  
Mitchell Nuhn ◽  
Todd Osmundson ◽  
Nigel Fechner ◽  
James M. Trappe ◽  
...  
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Sister Group ◽  
Molecular Data ◽  
Translation Elongation ◽  
Spore Deposit ◽  
Large Subunit Rdna ◽  
Translation Elongation Factor 1Α

Harrya is described as a new genus of Boletaceae to accommodate Boletus chromapes, a pink-capped bolete with a finely scabrous stipe adorned with pink scabers, a chrome yellow base and a reddish-brown spore deposit. Phylogenetic analyses of large-subunit rDNA and translation elongation factor 1α confirmed Harrya as a unique generic lineage with two species, one of which is newly described (H. atriceps). Some Chinese taxa were recently placed in a separate genus, Zangia, supported by both morphology and molecular data. Multiple accessions from Queensland, Australia, support the synonymy of at least three species in a separate Australian clade in the new genus, Australopilus. The truffle-like Royoungia is also supported as a separate lineage in this clade of boletes. Even though it lacks stipe characters, it possesses the deep, bright yellow to orange pigments in the peridium. Additional collections from Zambia and Thailand represent independent lineages of uncertain phylogenetic placement in the Chromapes complex, but sampling is insufficient for formal description of new species. Specimens from Java referable to Tylopilus pernanus appear to be a sister group of the Harrya lineage.

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

Zootaxa ◽  
2017 ◽  
Vol 4254 (5) ◽  
pp. 537 ◽  
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. 

scholarly journals Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision

2018 ◽  
Vol 63 (2) ◽  
pp. 45-64 ◽  
Author(s):  
Jolanta Miadlikowska ◽  
Nicolas Magain ◽  
Carlos J. Pardo-De la Hoz ◽  
Dongling Niu ◽  
Trevor Goward ◽  
...  
Keyword(s):  
High Specificity ◽  
Molecular Data ◽  
Fungal Species ◽  
Bootstrap Support ◽  
Phenotypic Traits ◽  
Phylogenetic Structure ◽  
Putative Species ◽  
Molecular Phylogenetic ◽  
High Bootstrap ◽  
Phylogenetic Revision

AbstractClosely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea.

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