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.

A new species of cat-eyed snake (Serpentes: Dipsadinae: Leptodeirini) from the Andes of southern Ecuador

Zootaxa ◽  
2020 ◽  
Vol 4895 (3) ◽  
pp. 357-380
Author(s):  
OMAR TORRES-CARVAJAL ◽  
JUAN C. SÁNCHEZ-NIVICELA ◽  
VALENTINA POSSE ◽  
ELVIS CELI ◽  
CLAUDIA KOCH
Keyword(s):  
New Species ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Molecular Data ◽  
Genetic Distances ◽  
Dna Sequence Data ◽  
The Andes ◽  
Southern Ecuador ◽  
Morphological And Molecular Data ◽  
A New Species

Leptodeira is one of the most widespread and taxonomically problematic snake taxa in the Americas. Here we describe a new species of Leptodeira from the Andes of southern Ecuador based on morphological and molecular data. The new species is geographically close and morphologically similar to L. ornata and L. larcorum, from which it can be distinguished by having smaller dorsal body blotches, a longer tail, and shorter spines on the hemipenial body. The shortest genetic distances between the new species and its congeners are 0.02 (16S), 0.05 (cytb), and 0.18 (ND4). The new species is restricted to the Jubones River Basin in southern Ecuador, an area of endemism for other reptile species. Our phylogenetic analysis based on mitochondrial and nuclear DNA sequence data also supports recognition of the names L. larcorum (restricted to Peru) for “L. septentrionalis larcorum”, and L. ornata for populations of “L. s. ornata” from central and eastern Panama, western Colombia, and western Ecuador. However, some samples of “L. s. ornata” from Panama and Costa Rica, as well as the new species described herein, are not included within or more closely related to L. ornata, which is sister to the clade (L. bakeri, L. ashmeadii). 

scholarly journals Revision of the genus Emphylica Turner, 1913 based on morphology and molecular data (Lepidoptera, Crambidae, Pyraustinae)

ZooKeys ◽  
2019 ◽  
Vol 836 ◽  
pp. 113-133 ◽  
Author(s):  
Kai Chen ◽  
Qingming Liu ◽  
Jianhua Jin ◽  
Dandan Zhang
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Sequence Data ◽  
Southern China ◽  
Molecular Data ◽  
28S Rrna ◽  
New Combinations ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework ◽  
A New Species

Moths of the genus Emphylica Turner, 1913 resemble species of Achyra Guenée, 1849, Loxostege Hübner, 1825 and Sitochroa Hübner, 1825 in having a conical frons. In order to examine the monophyly of Emphylica, and its relationship to other genera with a conical frons, a molecular phylogenetic framework is reconstructed based on sequence data of COI, 16S rRNA, 28S rRNA, EF-1α and Wg gene regions. The results robustly support the monophyly of Emphylica. Achyra + (Loxostege + Sitochroa) is in a sister position to Emphylica. A new species, E.crassihamatasp. n., is described from Southern China and two new combinations, E.diaphana (Caradja & Meyrick, 1934), comb. n. and E.cruoralis (Warren, 1895), comb. n., are proposed. An identification key based on males is provided for all Emphylica species. The adult habitus and genitalia of all species are figured.

A cladistic analysis of Diopsidae (Diptera) based on morphological and DNA sequence data

2002 ◽  
Vol 33 (3) ◽  
pp. 325-336 ◽  
Author(s):  
Richard Baker ◽  
Rudolf Meier
Keyword(s):  
Sensitivity Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Dna Sequence Data ◽  
Character Weighting ◽  
Character Matrix

AbstractThe results of a cladistic analysis based on a combined character matrix consisting of the morphological data set of Meier & Hilger (2000) and the molecular data set of Baker & al. (2001) is presented. The data set is subjected to an extensive sensitivity analysis and equal character weighting is found to perform best according to character incongruence and tree support. The sensitivity analysis also reveals a remarkable stability of the preferred tree with 25 of the 36 tree nodes supported under 16 different analysis conditions. Cyrtodiopsis is synonymized with Teleopsis and Shillito's (1971) synonymization of Trichodiopsis and Chaetodiopsis with Diasemopsis is confirmed. Morphological and DNA sequence data agree on all major clades and conflict is restricted to the placement of two species within their respective genera. Only in one case can the conflict be confidently resolved. Partitioned Bremer Support values reveal that 90% of the tree support is generated by the DNA sequence characters, although the average morphological character contributes twice the support of an average molecular character. The evolution of eye-stalk morphology and of a meiotic drive chromosome system in Teleopsis is briefly discussed in the light of the phylogenetic tree.

scholarly journals Synonymy of Idiococcobius Hayat with Coccobius Ratzeburg (Hymenoptera, Aphelinidae): evidenced by a new species from Malaysian Borneo

2020 ◽  
Vol 78 ◽  
pp. 33-40
Author(s):  
Hui Geng ◽  
Cheng-De Li ◽  
Jason Mottern ◽  
Andrew Polaszek
Keyword(s):  
New Species ◽  
Dna Sequence ◽  
Type Species ◽  
Sequence Data ◽  
Molecular Data ◽  
New Combination ◽  
Dna Sequence Data ◽  
Morphological And Molecular Data ◽  
A New Species ◽  
Malaysian Borneo

Idiococcobius Hayat, syn. nov., is synonymised with Coccobius Ratzeburg, based on morphological and molecular data from a new species of Coccobius from Malaysian Borneo. The new species is sufficiently similar morphologically to the type species of Idiococcobius to place it unambiguously within that genus, but molecular data from the new species, and a reassessment of the morphology of Idiococcobius, indicate synonymy of the two genera. Idiococcobius encarsoides Hayat is therefore transferred to Coccobius; resulting in the new combination: Coccobius encarsoides (Hayat), comb. nov.Coccobius islandicus Geng & Polaszek, sp. nov, is described from morphology and DNA sequence data.

Cymbidium shidianense (Orchidaceae: Epidendroideae), a new species from China: evidence from morphology and molecular data

Phytotaxa ◽  
2019 ◽  
Vol 399 (1) ◽  
pp. 100 ◽  
Author(s):  
GUI-ZHEN CHEN ◽  
GUO-QIANG ZHANG ◽  
JIE HUANG ◽  
MENG WANG ◽  
WEN-HUI RAO ◽  
...  
Keyword(s):  
New Species ◽  
Yunnan Province ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Orchid Species ◽  
Molecular Analyses ◽  
Dna Sequence Data ◽  
Pale Green ◽  
A New Species

A new orchid species, Cymbidium shidianense (Orchidaceae; Cymbidieae), from Yunnan Province, China, is described and illustrated based on morphological and molecular analyses. This new species is similar in morphology to C. cyperifolium, but it differs in its larger pseudobulbs, rigid leaves, broader pale green sepals, petals with darkly coloured veins and set of V-shaped blotches on the lip midlobe. A phylogenetic analyses based on nuclear ribosomal ITS and plastid (matK, rbcL) DNA sequence data support C. shidianense as related to C. cyperifolium.

scholarly journals Why morphology matters: the negative consequences of hasty descriptions of putative novelties in asexual ascomycetes

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ondřej Koukol ◽  
Gregorio Delgado
Keyword(s):  
Fungal Diversity ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Fungal Species ◽  
Negative Consequences ◽  
Dna Sequence Data ◽  
Phylogenetic Studies ◽  
Multiple Issues ◽  
Species Descriptions

ABSTRACTRecent progress in the discovery of fungal diversity has been enabled by intensive mycological surveys in centres of global biodiversity. Descriptions of new fungal species have been almost routinely based on phenotypic studies coupled with single or multigene phylogenetic analyses of DNA sequence data. However, high accessibility of sequencing services together with an increasing amount of available molecular data are providing easier and less critical support for taxonomic novelties without carefully studying the phenotype, particularly morphology. As a result, the accelerated rate of species descriptions has been unfortunately accompanied by numerous cases of overlooking previously described and well documented species, some of them that have been known for more than a century. Here, we critically examined recent literature, phenotypic and molecular data, and detected multiple issues with putative novelties of asexual Ascomycota traditionally known as hyphomycetes. In order to fix these taxonomic problems, three new combinations within the genera Pleopunctum, Camposporium and Sporidesmium, and two new names in Camposporium are proposed. Moreover, three genera, Aquidictyomyces, Fusiconidium and Pseudohelminthosporium, together with nine species are reduced to synonymy. The examples outlined here clearly show the relevance of morphology in modern phylogenetic studies and the importance of more stringent ‘quality controls’ during biodiversity studies documenting the extensive fungal diversity in a speedy manner.

A new species of Philophylla Rondani (Diptera: Tephritidae: Trypetini) from New Caledonia, recognized based on female postabdominal structure and molecular sequence data

Zootaxa ◽  
2008 ◽  
Vol 1759 (1) ◽  
pp. 43 ◽  
Author(s):  
HO-YEON HAN ◽  
ALLEN L. NORRBOM
Keyword(s):  
New Species ◽  
New Caledonia ◽  
Sequence Data ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Relationship Of ◽  
A New Species

Philophylla millei, n. sp., from New Caledonia is described and its relationship analyzed. This species was recorded previously as Anastrephoides sp. based on a single female, which closely resembles the eastern Palaearctic species Anastrephoides matsumurai Shiraki. Whether this similarity reflects the close relationship of these species or a case of convergent evolution was examined using morphology and molecular data. We examined both male and female specimens of the New Caledonian trypetine species and sequenced the mitochondrial 16S ribosomal RNA gene of this species and related trypetine species. This new species is a member of the genus Philophylla Rondani based both on the female postabdominal structure as well as DNA sequence data.

A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia

Zootaxa ◽  
2020 ◽  
Vol 4766 (3) ◽  
pp. 472-484
Author(s):  
HANNAH E. SOM ◽  
L. LEE GRISMER ◽  
PERRY L. JR. WOOD ◽  
EVAN S. H. QUAH ◽  
RAFE M. BROWN ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Dna Sequence ◽  
Rare Species ◽  
Sequence Data ◽  
Peninsular Malaysia ◽  
Tropical Asia ◽  
Dna Sequence Data ◽  
A New Species ◽  
Lines Of Evidence

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12. 

Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

2021 ◽  
Author(s):  
Sara Fuentes-Soriano ◽  
Elizabeth A. Kellogg
Keyword(s):  
Sequence Data ◽  
Plastid Dna ◽  
Sister Relationship ◽  
Data Set ◽  
Woody Perennial ◽  
History Of ◽  
Nuclear Its ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

A new species of trypanosome, Trypanosoma desterrensis sp. n., isolated from South American bats

Parasitology ◽  
2003 ◽  
Vol 127 (3) ◽  
pp. 265-271 ◽  
Author(s):  
E. C. GRISARD ◽  
N. R. STURM ◽  
D. A. CAMPBELL
Keyword(s):  
New Species ◽  
Dna Sequence ◽  
Sequence Data ◽  
Rrna Gene ◽  
South American ◽  
Sequence Variability ◽  
Dna Sequence Data ◽  
Hybridization Probes ◽  
5S Rrna Gene ◽  
A New Species

Trypanosomes isolated from South American bats include the human pathogen Trypanosoma cruzi. Other Trypanosoma spp. that have been found exclusively in bats are not well characterized at the DNA sequence level and we have therefore used the SL RNA gene to differentiate and characterize kinetoplastids isolated from bats in South America. A Trypanosoma sp. isolated from bats in southern Brazil was compared with the geographically diverse isolates T. cruzi marinkellei, T. vespertilionis, and T. dionisii. Analysis of the SL RNA gene repeats revealed size and sequence variability among these bat trypanosomes. We have developed hybridization probes to separate these bat isolates and have analysed the DNA sequence data to estimate their relatedness. A new species, Trypanosoma desterrensis sp. n., is proposed, for which a 5S rRNA gene was also found within the SL RNA repeat.

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