scholarly journals A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3740 ◽  
Author(s):  
Hatsuko Noda ◽  
John Everett Parkinson ◽  
Sung-Yin Yang ◽  
James Davis Reimer
Keyword(s):  
Internal Transcribed Spacer ◽  
Environmental Variability ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Species Level ◽  
Sea Surface ◽  
Fine Scale ◽  
Clade C ◽  
Symbiotic Dinoflagellates ◽  
The Common

Symbiotic dinoflagellates (genus Symbiodinium) shape the responses of their host reef organisms to environmental variability and climate change. To date, the biogeography of Symbiodinium has been investigated primarily through phylogenetic analyses of the ribosomal internal transcribed spacer 2 region. Although the marker can approximate species-level diversity, recent work has demonstrated that faster-evolving genes can resolve otherwise hidden species and population lineages, and that this diversity is often distributed over much finer geographical and environmental scales than previously recognized. Here, we use the noncoding region of the chloroplast psbA gene (psbAncr) to examine genetic diversity among clade C Symbiodinium associating with the common reef zoantharian Palythoa tuberculosa on Okinawa-jima Island, Japan. We identify four closely related Symbiodinium psbAncr lineages including one common generalist and two potential specialists that appear to be associated with particular microhabitats. The sea surface temperature differences that distinguish these habitats are smaller than those usually investigated, suggesting that future biogeographic surveys of Symbiodinium should incorporate fine scale environmental information as well as fine scale molecular data to accurately determine species diversity and their distributions.

Species diversity and genetic differentiation of stygofauna (Syncarida:Bathynellacea) across an alluvial aquifer in north-eastern Australia

2012 ◽  
Vol 60 (3) ◽  
pp. 152 ◽  
Author(s):  
B. D. Cook ◽  
K. M. Abrams ◽  
J. Marshall ◽  
C. N. Perna ◽  
S. Choy ◽  
...  
Keyword(s):  
Species Diversity ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Alluvial Aquifer ◽  
Species Level ◽  
Coi Gene ◽  
Generic Level ◽  
Alluvial Aquifers ◽  
Eastern Australia ◽  
North Eastern

Recent research suggests that alluvial aquifers in southern and eastern Australia may contain a diverse subterranean aquatic fauna (i.e. stygofauna). However, to date only a limited number of alluvial aquifers have been studied and little molecular data are available to assess species-level diversity and spatial patterns of genetic variation within stygofaunal species. In this paper, we present the initial results of a stygofaunal survey of the Burdekin River alluvial aquifer in Queensland, extending the northern range of alluvial aquifers along the east coast of Australia that have been investigated. The survey resulted in the collection of bathynellid stygofauna (Syncarida: Bathynellacea) and genetic analyses were conducted to determine species level diversity using the mitochondrial cytochrome oxidase subunit I (COI) gene. We further investigated the phylogenetic relationships of the species with bathynellids from western and southern Australia to assess the generic status of species. Four highly divergent COI lineages within the Parabathynellidae and one lineage within the Bathynellidae were found. These lineages did not group within any described genera, and phylogenetic analyses indicated that both local radiations and the retention of a lineage that was more apical in the genealogy account for the diversity within the Parabathynellidae in the Burdekin River alluvial aquifer. Most COI lineages were sampled from only a single bore, although one taxon within the Parabathynellidae was found to be more widespread in the aquifer. Haplotypes within this taxon were not shared among bores (ΦST = 0.603, P < 0.001). Overall, the high species diversity for bathynellaceans from an alluvial aquifer reported here, and surveys of bathynellaceans in several other alluvial systems in south-eastern Australia, suggests that groundwater ecosystems of eastern Australia may contain high stygofaunal diversity by Australian and world standards, particularly at the generic level for parabathynellids.

scholarly journals Contribution to chromosome numbers and phylogeny of Turkish Vincetoxicum Wolf (Apocynaceae, Asclepiadoideae)

2019 ◽  
Author(s):  
Seher Güven ◽  
Serdar Makbul ◽  
Kamil Coşkunçelebì
Keyword(s):  
Chromosome Numbers ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Species Level ◽  
Nrdna Its ◽  
Chromosome Counts ◽  
As Species ◽  
Molecular Phylogenetic

We report chromosome counts for ten taxa of Vincetoxicum sensu stricto (s. str.) (Apocynaceae) from Turkey (of which two are endemic), including the first chromosome counts for V. canescens subsp. pedunculata, V. funebre, V. fuscatum subsp. boissieri, V. parviflorum and V. tmoleum. Two taxa of V. fuscatum proved to be tetraploid (2n=44) and the remaining eight taxa diploid (2n=22). Molecular phylogenetic analyses based on nrDNA (ITS) and cpDNA (trnT-trnL) (including 31 newly generated sequences) confirm the position of the Turkish Vincetoxicum in the Vincetoxicum s. str. clade. Vincetoxicum fuscatum, V. parviflorum, V. speciosum, as well as the Turkish endemic V. fuscatum subsp. boissieri, were clearly resolved as species-level clades, whereas the delimitation of the rest of the Turkish taxa was less clear based on molecular data.

scholarly journals The genus Coprinellus (Basidiomycota; Agaricales) in Pakistan with the description of four new species

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 41-61 ◽  
Author(s):  
Shah Hussain ◽  
Muhammad Usman ◽  
Najam-ul-Sehar Afshan ◽  
Habib Ahmad ◽  
Junaid Khan ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Species Level ◽  
Rdna Its ◽  
The Family ◽  
Rdna Its Region ◽  
Morphological And Molecular Data ◽  
Species Descriptions

Mushrooms with a thin-fleshed pileus that becomes plicate on opening, deliquescent lamellae and dark brown to blackish basidiospores are commonly called coprinoid mushrooms. The genusCoprinellusis one of the important lineages of coprinoid mushroom in the family Psathyrellaceae. Species-level taxonomy inCoprinellusis based mainly on the presence or absence and the structure of veil and cystidia on the pileus, of cystidia on the lamellae and on basidiospore morphology. In this study, four new species ofCoprinellus(Co.campanulatus,Co.disseminatus-similis,Co.pakistanicusandCo.tenuis) are described from Pakistan. Species descriptions are based on morphological and molecular data. Phylogenetic analyses based on nuc rDNA ITS region show that the new speciesCo.campanulatusandCo.disseminatus-similisare clustered in a clade including members of section Micacei;Co.tenuisfalls in a clade with members of section Domestici; andCo.pakistanicusrecovered in a separate clade adjacent to other recently described clades of genusCoprinellus. Morpho-anatomical descriptions of the new species and comparison with closely allied taxa are provided. With this study, the number of known species ofCoprinellusin Pakistan has reached eight.

Phylogenetic relationships among Coregonus species inferred from the DNA sequence of the first internal transcribed spacer (ITS1) of ribosomal DNA

1997 ◽  
Vol 54 (7) ◽  
pp. 1494-1503 ◽  
Author(s):  
S L Sajdak ◽  
R B Phillips
Keyword(s):  
Ribosomal Dna ◽  
North American ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Base Pairs ◽  
Phylogenetic Hypotheses ◽  
Northwestern North America ◽  
Hybridization And Introgression

Phylogenetic analyses based on morphometrics, data on protein electrophoresis, and mitochondrial DNA have given conflicting phylogenetic hypotheses for the subfamily Coregoninae (Prosopium, Coregonus, and Stenodus). To resolve these conflicts, phylogenetic analysis of 13 taxa of Coregoninae was done using a nuclear gene, the first internal transcribed spacer (ITS1) of the ribosomal DNA (rDNA). ITS1 sequences of all North American ciscoes were identical. In agreement with analyses based on other molecular data, the genus Stenodus was included in Coregonus, and there was no support for the monophyly of the ciscoes. The analysis based on rDNA also placed C. peled as the sister species to C. lavaretus, but this may represent a case of hybridization and introgression. A length polymorphism involving a repeating unit of 65-67 base pairs was found in the ITS1. All ciscoes except C. peled had one copy of the repeat. Coregonus peled, C. lavaretus, and Eurasian and Beringian C. clupeaformis had two copies of the repeat, while the other North American C. clupeaformis had three copies, suggesting that C. clupeaformis of northwestern North America is a form of C. lavaretus.

A new pratylenchid nematode, Hoplotylus japonicus n. sp. (Tylenchina: Pratylenchidae) from the rhizosphere of Japanese maple, Acer palmatum (Thumb.)

Nematology ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1131-1140
Author(s):  
Jianfeng Gu ◽  
Munawar Maria ◽  
Yiwu Fang ◽  
Majid Pedram
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Anterior Margin ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Dorsal Side ◽  
Lateral View ◽  
Molecular Phylogenetic ◽  
A New Species

Summary During quarantine inspections, a new species of Hoplotylus was detected from the rhizosphere of the Japanese maple, Acer palmatum, imported into China from Japan. Hoplotylus japonicus n. sp. is characterised by a stout 431-602 μm long body, well-developed 20.0-24.5 μm long stylet with tulip-shaped knobs having rounded sides in lateral view and a rounded anterior margin, excretory pore located slightly posterior to the hemizonid, usually empty, spermatheca, conical tail with a spike-like projection, which is distally smooth on the dorsal side, and males not found. It was morphologically compared with four currently known species of the genus, viz., H. femina, H. montanus, H. silvaticus, and H. sjacobi. In molecular phylogenetic analyses using 18S, 28S and internal transcribed spacer (ITS) ribosomal DNA sequences, the new species formed a clade with the only currently sequenced species of the genus, H. femina, in all phylogenies. This is the second species of the genus characterised by molecular data and the second species recovered from Japan.

A new species of Tricholosporum (Agaricales, Tricholomataceae) from Liaoning Province of China

Phytotaxa ◽  
2018 ◽  
Vol 374 (1) ◽  
pp. 63 ◽  
Author(s):  
JIZE XU ◽  
CHUNLAN ZHANG ◽  
TAIGA KASUYA ◽  
ODESHNEE MOODLEY ◽  
BAO LIU ◽  
...  
Keyword(s):  
New Species ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Liaoning Province ◽  
Morphological And Molecular Data ◽  
A New Species

Tricholosporum haitangshanum sp. nov. is described as a new species from China, based on morphological and molecular data. It is morphologically characterized by a yellowish ochre pileus, cruciate basidiospores and ampullaceous cystidia. Phylogenetic analyses based on the nuc rDNA internal transcribed spacer (ITS) region supports that it belongs to Tricholosporum. Comparing it with phenotypically similar and molecular phylogenetically allied taxa concluded that it is a new species in Tricholosporum.

scholarly journals Molecular data reveal a new species of Rhopalias Stiles & Hassall, 1898 (Digenea, Echinostomatidae) in the Common opossum, Didelphis marsupialis L. (Mammalia, Didelphidae) in the Yucatán Peninsula, Mexico

ZooKeys ◽  
2019 ◽  
Vol 854 ◽  
pp. 145-163 ◽  
Author(s):  
Jorge López-Caballero ◽  
Rosario Mata-López ◽  
Gerardo Pérez-Ponce de León
Keyword(s):  
New Species ◽  
Genetic Divergence ◽  
Phylogenetic Analyses ◽  
Yucatan Peninsula ◽  
Molecular Data ◽  
Morphological Evidence ◽  
Data Set ◽  
Yucatán Peninsula ◽  
The Common ◽  
A New Species

A new species of Rhopalias Stiles &amp; Hassall, 1898 is described from the small intestine of the Common opossum, Didelphismarsupialis Linnaeus from the Yucatán Peninsula, Mexico. Rhopaliasoochisp. nov. is morphologically very similar to the type species of the genus, Rhopaliascoronatus (Rudolphi, 1819) Stiles &amp; Hassall 1898, a species widely distributed in opossums across Mexico. A molecular phylogenetic analysis using a mitochondrial gene (cox1), and the nuclear ribosomal internal transcribed spacer region (ITS1-5.8S-ITS2), of specimens of R.coronatus collected in several localities of Mexico revealed that those from the Yucatán Peninsula, originally recorded on morphological grounds as R.coronatus actually represented an independent genetic lineage. Maximum Likelihood and Bayesian Inference analyses were performed for each data set independently, and for the concatenated data set (ITS1-5.8S-ITS2 + cox1). All phylogenetic analyses showed that the specimens from Yucatán represented a monophyletic lineage, with high bootstrap support and Bayesian posterior probabilities. In addition, the genetic divergence estimated between R.oochisp. nov. and two species of Rhopalias, R.coronatus, and R.macracanthus Chandler, 1932 that also occur in Mexican marsupials ranged between 7–8% and 16–17%, for cox1, and between 0.1–0.2% and 7% for the ITS region, respectively. The molecular evidence gathered in this study (reciprocal monophyly in both phylogenetic analyses, and estimated genetic divergence) suggested that the specimens found in the intestine of D.marsupialis originally reported as R.coronatus from Yucatán, actually represent a new species. Morphological evidence was found through light and scanning electron microscopy to support the species distinction based on molecular data.

scholarly journals Morphological and molecular identification of four new resupinate species of Lyomyces (Hymenochaetales) from southern China

MycoKeys ◽  
2020 ◽  
Vol 65 ◽  
pp. 101-118
Author(s):  
Jun-Zhu Chen ◽  
Chang-Lin Zhao
Keyword(s):  
New Species ◽  
Molecular Identification ◽  
Internal Transcribed Spacer ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Fungal Species ◽  
Molecular Evidence ◽  
Thin Walled

Four new wood-inhabiting fungal species, Lyomyces bambusinus, L. cremeus, L. macrosporus and L. wuliangshanensis, are proposed based on a combination of morphological and molecular evidence. Lyomyces bambusinus is characterized by resupinate basidiomata with colliculose to tuberculate hymenial surface and broadly ellipsoid, hyaline, slightly thick-walled, smooth basidiospores. Lyomyces cremeus is characterised by resupinate basidiomata with smooth, cream hymenial surface and ellipsoid, hyaline, thin-walled to slightly thick-walled basidiospores. Lyomyces macrosporus is characterized by pruinose basidiomata with reticulate hymenial surface, presence of three kinds of cystidia and larger basidiospores (6.7–8.9 × 4.4–5.4 µm). Lyomyces wuliangshanensis is characterized by coriaceous basidiomata and ellipsoid, hyaline, slightly thick-walled, smooth basidiospores. The phylogenetic analyses based on molecular data of the internal transcribed spacer (ITS) region sequences revealed that the four new species belonged to Lyomyces. Lyomyces bambusinus grouped with L. sambuci. Lyomyces cremeus clade was sister to a clade comprised of L. microfasciculatus. Lyomyces macrosporus was sister to L. allantosporus. Lyomyces wuliangshanensis was closely related to L. mascarensis.

Phylogeny of the Erysiphales (powdery mildews) inferred from internal transcribed spacer ribosomal DNA sequences

1999 ◽  
Vol 77 (1) ◽  
pp. 150-168 ◽  
Author(s):  
Gregory S Saenz ◽  
John W Taylor
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Powdery Mildews ◽  
Outgroup Species ◽  
Morphological And Molecular Data ◽  
Clade 1

Phylogenetic relationships were inferred for 45 powdery mildews plus two outgroup species from internal transcribed spacer sequence data. Phylogenetic analyses revealed that the powdery mildews formed six evolutionary lineages, which corresponded well to recently revised mitosporic taxa. Clade 1 consisted of Erysiphe, Microsphaera, and Uncinula, all of which have an Oidium subgenus Pseudoidium mitosporic state. Clade 2 consisted of Erysiphe galeopsidis and Erysiphe cumminsiana, which have an Oidium subgenus Striatoidium mitosporic state. Clade 3 consisted of Erysiphe species with an Oidium subgenus Reticuloidium mitosporic state. Clade 4 consisted of Leveillula and Phyllactinia, which have Oidiopsis and Ovulariopsis mitosporic states, respectively. Clade 5 consisted of Sphaerotheca, Podosphaera, and Cystotheca, which have Oidium subgenera Fibroidium and Setoidium mitosporic states. Clade 6 consisted of Blumeria graminis, which has an Oidium subgenus Oidium mitosporic state. Seventeen morphological characters were analysed and found not to conflict with the molecular data, so the morphological and molecular data were combined. The combined data increased the overall support for the six clades.Key words: Ascomycete, Blumeria, Erysiphe, fungi, molecular evolution, plant pathogen.

scholarly journals Inter- and infraspecific relationships in the Gondwanan liverwort genus Hymenophyton (Hymenophytaceae, Hepaticophytina). Studies in austral temperate rain forest bryophytes 23

2004 ◽  
Vol 17 (4) ◽  
pp. 407 ◽  
Author(s):  
Tanja Pfeiffer ◽  
Friederike Schaumann ◽  
Gabriela G. Hässel de Menéndez ◽  
Wolfgang Frey
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Divergence ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Species Level ◽  
Morphological Examination ◽  
Temperate Rain Forest ◽  
High Bootstrap ◽  
Trnluaa Intron ◽  
Molecular Characters

Inter- and infraspecific relationships in Hymenophyton Dumort. were studied by sequencing of the cpDNA trnTUGU-trnLUAA 5′exon intergenic spacer, trnLUAA 5′exon and trnLUAA intron and nrDNA internal transcribed spacer 2 (ITS2), and by morphological examination of representative specimens. Based on the molecular data, four taxa were recognised, comprising (i) Australasian H.�flabellatum (Labill.) Dumort. ex Trevis., (ii) Chilean specimens, (iii) New Zealand H.�leptopodum (Hook.f. & Taylor) A.Evans samples and (iv) a Tasmanian H. leptopodum specimen, respectively. The former three clades are supported by high bootstrap values, while the affinities of the latter specimen remain ambiguous in the calculated trnT-trnL and ITS2 trees. The observed sequence divergence supports the existence of a distinct Hymenophyton taxon in southern South America, delimitated from H. flabellatum and H. leptopodum on species level: H.�pedicellatum Steph. This reinstated species is described in detail; differentiating morphological and molecular characters are presented. Hymenophyton taxa have a basically palaeoaustral distribution pattern. Biogeography, dispersal biology and phylogeography of the taxa are discussed.

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