scholarly journals Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra

MycoKeys ◽  
2018 ◽  
Vol 43 ◽  
pp. 91-113 ◽  
Author(s):  
Felix Grewe ◽  
Elisa Lagostina ◽  
Huini Wu ◽  
Christian Printzen ◽  
H. Thorsten Lumbsch
Keyword(s):  
Sequence Data ◽  
Reproductive Mode ◽  
Fungal Species ◽  
Antarctic Species ◽  
Dna Sequence Data ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Scale Population ◽  
Relationship Of ◽  
Different Levels

Neuropogonoid species in the lichen-forming fungal genus Usnea exhibit great morphological variation that can be misleading for delimitation of species. We specifically focused on the species delimitation of two closely-related, predominantly Antarctic species differing in the reproductive mode and representing a so-called species pair: the asexual U.antarctica and the sexual U.aurantiacoatra. Previous studies have revealed contradicting results. While multi-locus studies based on DNA sequence data provided evidence that these two taxa might be conspecific, microsatellite data suggested they represent distinct lineages. By using RADseq, we generated thousands of homologous markers to build a robust phylogeny of the two species. Furthermore, we successfully implemented these data in fine-scale population genomic analyses such as DAPC and fineRADstructure. Both Usnea species are readily delimited in phylogenetic inferences and, therefore, the hypothesis that both species are conspecific was rejected. Population genomic analyses also strongly confirmed separated genomes and, additionally, showed different levels of co-ancestry and substructure within each species. Lower co-ancestry in the asexual U.antarctica than in the sexual U.aurantiacoatra may be derived from a wider distributional range of the former species. Our results demonstrate the utility of this RADseq method in tracing population dynamics of lichens in future analyses.

Generic Delimitations and Relationships of the Cape Genera Capnophyllum, Dasispermum, and Sonderina, the North African Genera Krubera and Stoibrax, and a New Monotypic Genus of the Subfamily Apioideae (Apiaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 580-594 ◽  
Author(s):  
Anthony R. Magee ◽  
Ben-Erik van Wyk ◽  
Patricia M. Tilney ◽  
Stephen R. Downie
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Monotypic Genus ◽  
North African ◽  
African Species ◽  
Dna Sequence Data ◽  
The North ◽  
Relationship Of

Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum, Dasispermum, Sonderina, and the only southern African species of Stoibrax (S. capense) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera. The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina. This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum, occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense. New combinations are formalized for Dasispermum capense, D. hispidum, D. humile, and D. tenue. An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum–Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii. This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum, analyses of DNA sequence data place Scaraboides closer to the Dasispermum–Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.

Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data

2014 ◽  
Vol 62 (3) ◽  
pp. 235 ◽  
Author(s):  
S. Safaei Chaei Kar ◽  
F. Ghanavati ◽  
M. R. Naghavi ◽  
H. Amirabadi-zade ◽  
R. Rabiee
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Group I ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Cultivated Species ◽  
Relationship Of

Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

scholarly journals Molecular phylogeny uncovers an overlooked species in the macrolichen family Parmeliaceae (Ascomycota) from India

2018 ◽  
Author(s):  
Pradeep K. Divakar ◽  
Ana Crespo
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Fungal Species ◽  
Species Boundaries ◽  
Data Set ◽  
Dna Sequence Data ◽  
Distinct Lineage ◽  
Phylogenetic Framework ◽  
Phenotypic Features ◽  
A New Species

Several obligately sexualy reproducing lichen-forming fungal species are disjunctly distributed in pantropical regions. Here, we aim to re-examine species boundaries within the sexually reproducing, disjunctly distributed species, Hypotrachyna intercalanda. We gathered a three-locus DNA sequence data set of Hypotrachyna subgen. Parmelinopsis, especially including the samples from India, and these data were analysed in a phylogenetic framework. Our results show that specimens of H. intercalanda, as currently circumscribed, do not form a monophyletic group but fall into two well-supported independent clades. Morphological and chemical features were re-evaluated. Corroborating with the phenotypic features, the sample recovered in clade 2 occurring in southern India are described as a new species, viz. Hypotrachyna upretii Divakar and A. Crespo sp. nov. Our study adds a further example of a previously overlooked, geographically distinct, lineage that was uncovered using molecular data. Additionally, our study underlines the need of critical reexamination of phenotypic features of samples falling into different clades.

scholarly journals iMKT: the integrative McDonald and Kreitman test

2019 ◽  
Vol 47 (W1) ◽  
pp. W283-W288 ◽  
Author(s):  
Jesús Murga-Moreno ◽  
Marta Coronado-Zamora ◽  
Sergi Hervas ◽  
Sònia Casillas ◽  
Antonio Barbadilla
Keyword(s):  
Reference Site ◽  
Population Genomics ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Protein Coding ◽  
Web Based ◽  
Dna Sequence Data ◽  
Protein Coding Genes ◽  
Population Genomic ◽  
Testing Complex

Abstract The McDonald and Kreitman test (MKT) is one of the most powerful and widely used methods to detect and quantify recurrent natural selection using DNA sequence data. Here we present iMKT (acronym for integrative McDonald and Kreitman test), a novel web-based service performing four distinct MKT types. It allows the detection and estimation of four different selection regimes −adaptive, neutral, strongly deleterious and weakly deleterious− acting on any genomic sequence. iMKT can analyze both user's own population genomic data and pre-loaded Drosophila melanogaster and human sequences of protein-coding genes obtained from the largest population genomic datasets to date. Advanced options in the website allow testing complex hypotheses such as the application example showed here: do genes located in high recombination regions undergo higher rates of adaptation? We aim that iMKT will become a reference site tool for the study of evolutionary adaptation in massive population genomics datasets, especially in Drosophila and humans. iMKT is a free resource online at https://imkt.uab.cat.

Preliminary use of DNA sequences for Dohrniphora (Diptera: Phoridae) phylogeny and taxonomy JOHN M. HASH, BRIAN V. BROWN & PAUL T. SMITH (USA)

Zootaxa ◽  
2011 ◽  
Vol 2991 (1) ◽  
pp. 13
Author(s):  
JOHN M. HASH ◽  
BRIAN V. BROWN ◽  
PAUL T. SMITH
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Male And Female ◽  
Dna Sequence Data ◽  
16S Gene ◽  
Monophyletic Lineage ◽  
Relationship Of

Phylogenetic analysis of DNA sequence data from the nuclear CAD (rudimentary) and mitochondrial NDI, COI, and 16S gene regions (2817 bp total) recovered exemplars of the genus Dohrniphora as a monophyletic lineage. The data also supported the sister-group relationship of Dohrniphora + Diplonevra and were used to associate a morphologically dissimilar male and female of the species D. ecitophila. Further, we discuss the implications of this designation and provide support for the synonymy of D. ecitophila and D. geminata as proposed by Borgmeier (1968).

Dwarf minke whales from the South Pacific share a matrilineal lineage distinct from Balaenoptera acutorostrata acutorostrata and B. a. scammoni

2019 ◽  
Vol 41 (2) ◽  
pp. 231
Author(s):  
Omar Ramirez-Flores ◽  
Alastair Birtles ◽  
Diana Pazmino ◽  
Kyall R. Zenger ◽  
Lynne Van-Herwerden
Keyword(s):  
Sequence Data ◽  
South Pacific ◽  
Nuclear Data ◽  
Minke Whale ◽  
Balaenoptera Acutorostrata ◽  
Conservation Action ◽  
Dna Sequence Data ◽  
Minke Whales ◽  
Satellite Tagging ◽  
Relationship Of

Dwarf minke whales are regarded as an undescribed subspecies of common minke whales (Balaenoptera acutorostrata), but appropriate conservation action requires taxonomic confirmation. The relationship of the Australian Great Barrier Reef (GBR) dwarf minke whale aggregation to other minke whales is unknown. This study aims to clarify the phylogenetic relationship of GBR dwarf minke whales, using partial mitochondrial DNA sequence data from 23 GBR dwarf minke whales, compared with other available minke whale sequences. GBR dwarf minke whales share haplotypes with other West South Pacific (WSP) dwarf minke whales. Satellite tagging studies corroborate these findings, indicating that GBR dwarf minke whales migrate south along the east Australian coast towards the Southern Ocean. Despite nuclear data not being available, GBR and WSP dwarf minke whales share a distinctive mitochondrial lineage compared with other common minke whales and should be managed independently of North Pacific and Atlantic Ocean common minke whale populations.

Nerve cells of Xenoturbella bocki (phylum uncertain) and Harrimania kupfferi (Enteropneusta) are positively immunoreactive to antibodies raised against echinoderm neuropeptides

2005 ◽  
Vol 85 (6) ◽  
pp. 1519-1524 ◽  
Author(s):  
Thomas Stach ◽  
Samuel Dupont ◽  
Olle Israelson ◽  
Geraldine Fauville ◽  
Hiroaki Nakano ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Dna Sequence ◽  
Sequence Data ◽  
Nerve Cells ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Close Phylogenetic Relationship ◽  
Positive Immunoreactivity ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

The phylogenetic position of Xenoturbella spp. has been uncertain since their discovery in 1949. It has been recently suggested that they could be related to Ambulacraria within Deuterostomia. Ambulacraria is a taxon that has been suggested to consist of Hemichordata and Echinodermata. The hypothesis that X. bocki was related to Ambulacraria as well as the hypothesis of a monophyletic Ambulacraria is primarily based on the analysis of DNA sequence data. We tested both phylogenetic hypotheses using antibodies raised against SALMFamide 1 and 2 (S1, S2), neuropeptides isolated from echinoderms, on X. bocki and the enteropneust Harrimania kupfferi. Both species showed distinct positive immunoreactivity against S1 and S2. This finding supports the Ambulacraria-hypothesis and suggests a close phylogenetic relationship of X. bocki to Ambulacraria. In particular, the presence of immunoreactivity against S2 can be interpreted as a synapomorphy of Enteropneusta, Echinodermata, and Xenoturbella spp.

scholarly journals Phylogenetic Relationships of Antpitta Genera (Passeriformes: Formicariidae)

The Auk ◽  
2005 ◽  
Vol 122 (2) ◽  
pp. 673-683 ◽  
Author(s):  
Nathan H. Rice
Keyword(s):  
Mitochondrial Genome ◽  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Morphological Characters ◽  
Sister Relationship ◽  
Dna Sequence Data ◽  
Monophyletic Lineage ◽  
New Interpretation ◽  
Relationship Of

Abstract Phylogenetic relationships among the antpitta genera were studied using DNA sequence data from the mitochondrial genome. The clade representing the traditional “antpitta” genera (Grallaria, Grallaricula, Hylopezus, Myrmothera, and Pittasoma) was found to be paraphyletic, owing to the sister relationship of Pittasoma and Conopophaga. In a previously unreported relationship, Pittasoma was strongly supported as the sister genus to Conopophaga (Conopophagidae). The remaining antpitta genera form a fully resolved and well-supported monophyletic lineage with two major subclades. The first clade consists of the genus Grallaria and supports the subgenera identified by Lowery and O'Neill (1969). The second antpitta clade has Hylopezus as the sister genus to Myrmothera, with Grallaricula as their sister genus. The results here allow for a new interpretation of the morphological characters used in previous studies.

Malformation Disease in Tabebuia rosea (Rosy Trumpet) Caused by Fusarium pseudocircinatum in Mexico

Plant Disease ◽  
2021 ◽  
Author(s):  
Amelia C. Montoya-Martínez ◽  
Kerry O’Donnell ◽  
Mark Busman ◽  
Martha M. Vaughan ◽  
Susan P. McCormick ◽  
...  
Keyword(s):  
Mating Type ◽  
Sequence Data ◽  
Fusaric Acid ◽  
Causal Agent ◽  
New Disease ◽  
Dna Sequence Data ◽  
Neotropical Tree ◽  
Multiplex Pcr Assay ◽  
Tabebuia Rosea ◽  
Relationship Of

Tabebuia rosea (rosy trumpet) is an economically important Neotropical tree in Mexico that is highly valued for the quality of its wood, which is used for furniture, crafts, and packing, and for its use as an ornamental and shade tree in parks and gardens. During surveys conducted in the lower Balsas River Basin region in the states of Guerrero and Michoacán, symptoms of floral malformation were detected in T. rosea trees. The main objectives of this study were to describe this new disease, to determine its causal agent, and to identify it using DNA sequence data. A second set of objectives was to analyze the phylogenetic relationship of the causal agent to Fusarium associated with Swietenia macrophylla trees with malformation surveyed in the same region, and to compare mycotoxin production and the mating type idiomorphs of fusaria recovered from T. rosea and S. macrophylla. Tabebuia rosea showed malformed inflorescences with multiple, tightly curled shoots, and shortened internodes. A total of 31 Fusarium isolates recovered from symptomatic T. rosea (N = 20) and S. macrophylla (N = 11) trees were identified by molecular analysis as F. pseudocircinatum. Pathogenicity tests showed that isolates of F. pseudocircinatum recovered from T. rosea, induced malformation in inoculated T. rosea seedlings. Eighteen F. pseudocircinatum isolates were tested for their ability to produce mycotoxins and other secondary metabolites. Moniliformin, fusaric acid, bikaverin, beauvericin, aurofusarin and 8-O-methylbostrycoidin were produced by at least 1 strain of the 18 isolates tested. A multiplex PCR assay for mating type idiomorph revealed that 22 F. pseudocircinatum isolates were MAT1-1 and 9 were MAT1-2. Here we report a new disease of T. rosea in Mexico caused by F. pseudocircinatum.

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