scholarly journals A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

ZooKeys ◽  
2018 ◽  
Vol 760 ◽  
pp. 1-36 ◽  
Author(s):  
Shahan Derkarabetian ◽  
James Starrett ◽  
Nobuo Tsurusaki ◽  
Darrell Ubick ◽  
Stephanie Castillo ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Phylogenetic Position ◽  
Diagnostic Features ◽  
Ultraconserved Elements ◽  
New Family ◽  
South Central ◽  
Tarsal Claw ◽  
Phylogenetic Resolution

Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe. This clade has had a challenging taxonomic history, but the current classification consists of ~77 species in three families, the Travuniidae, Paranonychidae, and Nippononychidae. Travunioidea classification has traditionally been based on structure of the tarsal claws of the hind legs. However, it is now clear that tarsal claw structure is a poor taxonomic character due to homoplasy at all taxonomic levels. Here, we utilize DNA sequences derived from capture of ultraconserved elements (UCEs) to reconstruct travunioid relationships. Data matrices consisting of 317–677 loci were used in maximum likelihood, Bayesian, and species tree analyses. Resulting phylogenies recover four consistent and highly supported clades; the phylogenetic position and taxonomic status of the enigmatic genusYuriais less certain. Based on the resulting phylogenies, a revision of Travunioidea is proposed, now consisting of the Travuniidae, Cladonychiidae, Paranonychidae (Nippononychidae is synonymized), and the new family Cryptomastridae Derkarabetian & Hedin,fam. n., diagnosed here. The phylogenetic utility and diagnostic features of the intestinal complex and male genitalia are discussed in light of phylogenomic results, and the inappropriateness of the tarsal claw in diagnosing higher-level taxa is further corroborated.

Molecular phylogenetic position of Haplometroides intercaecalis (Digenea, Plagiorchiidae)

2018 ◽  
Vol 63 (3) ◽  
pp. 522-526 ◽  
Author(s):  
Maria Isabel Müller ◽  
Drausio Honorio Morais ◽  
Reinaldo José da Silva
Keyword(s):  
Dna Sequences ◽  
Additional Data ◽  
Ribosomal Gene ◽  
Valid Species ◽  
Phylogenetic Position ◽  
Systematic Analysis ◽  
Future Studies ◽  
New Family ◽  
Molecular Phylogenetic ◽  
Morphological Differences

Abstract Three valid species of Haplometroides Odhner, 1910 parasitise snakes and amphisbaenians from South America. This study provides additional data on morphometric and molecular phylogenetic position inferred from the nuclear ribosomal gene 28S (partial). DNA sequences were isolated from Haplometroides intercaecalis Silva, Ferreira and Strüssmann, 2007 found in one specimen of Phalotris matogrossensis Lema, D’Agostini and Cappellari, 2005. Five digenean specimens were recovered from the esophagus of this snake, and four specimens were used for morphometrical studies and one specimen for molecular analysis. Phylogenetic analysis using maximum likelihood and Bayesian methods was conducted with sequences available for the order Plagiorchiida and its phylogenetic position places H. intercaecalis among the brachycoeliids Brachycoelium (Dujardin, 1845) Stiles and Hassall, 1898 and Parabrachycoelium Pérez-Ponce de León, Mendoza-Garfias, Razo-Mendivil and Parra-Olea, 2011, and the mesocoeliid Mesocoelium Odhner, 1910, not closely related to plagiorchids as expected. Due to morphological differences among these families, it may be necessary to create a new family to accommodate Haplometroides spp. However, more genera/taxa as well as other molecular markers should be added in future studies to confirm our results and resolve this matter. This is the first phylogenetic positioning of digeneans of the genus Haplometroides, contributing to the systematic analysis of the helminthological biodiversity of Neotropical snakes.

scholarly journals Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Zhang ◽  
Yupei Zhou ◽  
Wei Sun ◽  
Lili Zhao ◽  
D. Pavlic-Zupanc ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Type Specimens ◽  
Natural Classification ◽  
Dna Sequence Data

The genus Botryosphaeria includes more than 200 epithets, but only the type species, Botryosphaeria dothidea and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 “Botryosphaeria” species are reassessed to clarify their identity and phylogenetic position. nuDNA sequences of four regions, ITS, LSU, tef1-α and tub2, are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, Botryosphaeria cruenta and Botryosphaeria hamamelidis are transferred to Neofusicoccum. The generic status of Botryosphaeria aterrima and Botryosphaeria mirabile is confirmed in Botryosphaeria. Botryosphaeria berengeriana var. weigeliae and B. berengeriana var. acerina are treated synonyms of B. dothidea. Botryosphaeria mucosa is transferred to Neodeightonia as Neodeightonia mucosa, and Botryosphaeria ferruginea to Nothophoma as Nothophoma ferruginea. Botryosphaeria foliicola is reduced to synonymy with Phyllachorella micheliae. Botryosphaeria abuensis, Botryosphaeria aesculi, Botryosphaeria dasylirii, and Botryosphaeria wisteriae are tentatively kept in Botryosphaeria sensu stricto until further phylogenetic analysis is carried out on verified specimens. The ordinal status of Botryosphaeria apocyni, Botryosphaeria gaubae, and Botryosphaeria smilacinina cannot be determined, and tentatively accommodate these species in Dothideomycetes incertae sedis. The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.

scholarly journals A new species of sinistral flatfish of the genus Chascanopsetta (Teleostei: Bothidae) from off Papua New Guinea, western Pacific Ocean

Zootaxa ◽  
2018 ◽  
Vol 4476 (1) ◽  
pp. 168
Author(s):  
PAKORN TONGBOONKUA ◽  
MAO-YING LEE ◽  
WEI-JEN CHEN
Keyword(s):  
New Species ◽  
Papua New Guinea ◽  
Dna Sequences ◽  
Taxonomic Status ◽  
New Guinea ◽  
Coi Gene ◽  
Phylogenetic Position ◽  
Nominal Species ◽  
The West ◽  
West Pacific

Left-eyed flounders of the genus Chascanopsetta Alcock 1894 (Bothidae) occur in the Indian, Pacific, and Atlantic oceans at depths ranging from 120 to 1500 meters. They possess some unique features in bothid fishes including a strongly compressed and elongated body and a tremendously large mouth. Currently, nine species of Chascanopsetta are recognized, and three of them (C. micrognatha Amaoka & Yamamoto 1984, C. lugubris Alcock 1894 and C. prognatha Norman 1939) are distributed in the West Pacific. We collected 25 specimens of Chascanopsetta during 11 biodiversity expeditions carried out mainly in the West Pacific. Among them, eight specimens taken off Papua New Guinea present morphological features that differ from those of the three nominal species known in the West Pacific. In this study, we examined these eight specimens of unknown affinity and compared their morphology to that of specimens of other congeneric species. Results of these comparisons showed that these specimens represent an undescribed species of Chascanopsetta, named herein, C. novaeguineae sp. nov.. The new species resembles C. elski Foroshchuk 1991, which is known only from the Saya de Malha Bank in the western Indian Ocean, in having a high number of gill rakers (> 13). However, the combination of the following characters further distinguishes C. novaeguineae sp. nov. from C. elski: longer jaws, narrower interorbital width, and number of pseudobranches (21–25 vs. 26–27). The DNA sequences from the mitochondrial cytochrome oxidase subunit I (COI) gene from C. novaeguineae sp. nov. and other species were obtained and compared to confirm its taxonomic status and to infer its tentative phylogenetic position within the Chascanopsetta.

scholarly journals Two new species of the Macrobiotus hufelandi complex (Tardigrada: Eutardigrada: Macrobiotidae) from Australia and India, with notes on their phylogenetic position

2019 ◽  
Author(s):  
Kyle Coughlan ◽  
Daniel Stec
Keyword(s):  
Dna Sequences ◽  
18S Rrna ◽  
Taxonomic Status ◽  
Phylogenetic Position ◽  
28S Rrna ◽  
Future Studies ◽  
Mitochondrial Coi ◽  
Definition Of ◽  
Group Species ◽  
Independent Species

In this paper we describe two new tardigrade species belonging to the Macrobiotus hufelandi complex: Macrobiotus noongaris sp. nov. from Perth, Australia, and Macrobiotus kamilae sp. nov. from Mussoorie, India. Live specimens extracted from moss samples were used to establish laboratory cultures in order to obtain additional animals and eggs needed for their integrative descriptions. These descriptions are based on traditional morphological and morphometric data collected using both light and scanning electron microscopy, which, at the same time, were associated with DNA sequences of four genetic markers, three nuclear (18S rRNA, 28S rRNA and ITS-2) and one mitochondrial (COI). The use of DNA sequences allowed for a more accurate verification of the taxonomic status of M. noongaris sp. nov. and M. kamilae sp. nov as independent species of the hufelandi group. Although they both exhibit typical inverted goblet-shaped processes, they represent a recently discovered clade, which was thought to group species with modified morphology of egg processes. Thus, this contribution expands the definition of the mentioned clade and constitutes another link that will be helpful for future studies on the evolution of the M. hufelandi complex.

scholarly journals Inclusion of Kickxia abhaica D.A. Sutton in the genus Nanorrhinum (Plantaginaceae): Evidence from its nuclear ribosomal DNA sequences

2018 ◽  
Vol 25 (2) ◽  
pp. 209-214
Author(s):  
M. Ajmal Ali
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Discrimination Power ◽  
Molecular Phylogenetic ◽  
Endemic Taxon

The nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) sequences is extensively used in the plant molecular phylogenetics for plant taxonomic identification and DNA barcoding purposes because the nrDNA ITS gene is easy to amplify by using the universal primers, its length is shorter and thus easy to sequence, and has strong discrimination power to distinguish the taxon at the species level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved endemic taxon Kickxia abhaica D.A. Sutton (Family Plantaginaceae, tribe Antirrhineae) reported from Saudi Arabia. The analysis supports the transfer of K. abhaica under the genus Nanorrhinum.

scholarly journals Filling the Gaps in the Cyanobacterial Tree of Life—Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 389
Author(s):  
Pia Marter ◽  
Sixing Huang ◽  
Henner Brinkmann ◽  
Silke Pradella ◽  
Michael Jarek ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Morphological Diversity ◽  
Cell Types ◽  
Phylogenetic Position ◽  
Metagenome Analysis ◽  
New Family ◽  
Metagenome Sequencing ◽  
Axenic Strains ◽  
Reliable Classification ◽  
Metagenomic Assembly

Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.

Soil and litter nematode diversity of Mount Hamiguitan, the Philippines, with description of Bicirronema hamiguitanense n. sp. (Rhabditida: Bicirronematidae)

Nematology ◽  
2015 ◽  
Vol 17 (3) ◽  
pp. 325-344 ◽  
Author(s):  
Xue Qing ◽  
Wim Bert ◽  
Hanne Steel ◽  
Joeseph Quisado ◽  
Irma Tandingan De Ley
Keyword(s):  
New Species ◽  
Molecular Data ◽  
The Philippines ◽  
Phylogenetic Position ◽  
Species Status ◽  
Diagnostic Features ◽  
Lateral Field ◽  
Nematode Diversity ◽  
Common Group

The nematode diversity in soil and litter was investigated on Mount Hamiguitan, the Philippines, along four eco-habitats from elevations of 75-1600 m a.s.l. A total of 155 and 467 nematodes were identified to 39 and 62 genera from litter and soil, respectively. The nematode assemblages and diversity did not show any relation to eco-habitat or elevation. Bacterivorous nematodes were the most common group (37.5%). Acrobeloides was most abundant from the soil and Aphelenchoides from the litter. Bicirronema hamiguitanense n. sp. is herein described based on morphology, morphometrics and molecular data. The new species has the following diagnostic features: a wide lateral field one-fifth of its body diam. with four incisures forming two ornamented ridges; gubernaculum with proximal thickening; spicules (35-38 μm) and gubernaculum (18-20 μm) longer than B. caledoniense; and with 37 molecular autapomorphies supporting its new species status. The phylogenetic position of the new species within Cephalobomorpha is discussed.

Pseudoditrichum mirabile gen. et sp. nov. (Musci: Pseudoditrichaceae fam. nov.), a unique moss from Great Bear Lake, Northwest Territories

1974 ◽  
Vol 52 (4) ◽  
pp. 701-705 ◽  
Author(s):  
William Campbell Steere ◽  
Zennoske Iwatsuki
Keyword(s):  
Northwest Territories ◽  
New Genus ◽  
The Arctic ◽  
Phylogenetic Position ◽  
New Genus And Species ◽  
Arctic Circle ◽  
New Family ◽  
Bear Lake ◽  
Evolutionary Level

The name Pseudoditrichum mirabile Steere et Iwatsuki is proposed for a minute moss with leafy stem 1-3 mm high and seta 6 mm long; it was collected on calcareous silt near the Sloan River, Great Bear Lake, Northwest Territories, only a few miles south of the Arctic Circle. The gametophytic characters agree well with those of the Ditrichaceae, a relatively primitive family, but the peristome is clearly double, with the inner and outer teeth opposite, which thereby indicates a much more advanced phylogenetic position, perhaps at the evolutionary level of the Funariaceae. As the combination of gametophytic and sporophytic characteristics exhibited by this moss does not occur in any existing family of mosses, it is therefore deemed necessary to create the new family Pseudoditrichaceae for the new genus and species described here.

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