Two new species of the “Heterocarpus gibbosus Bate, 1888” species group (Crustacea: Decapoda: Pandalidae) from the western Pacific and north-western Australia

Zootaxa ◽  
2010 ◽  
Vol 2372 (1) ◽  
pp. 206-220 ◽  
Author(s):  
CHIEN-HUI YANG ◽  
TIN-YAM CHAN ◽  
KA HOU CHU
Keyword(s):  
Molecular Genetic ◽  
Distinct Species ◽  
Species Group ◽  
Molecular Genetic Analysis ◽  
Western Pacific ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Western Coast ◽  
The Western Pacific ◽  
Very High

The widely distributed deep-sea caridean shrimp Heterocarpus gibbosus Bate, 1888 was previously believed to exhibit considerable variations in the development of the basal rostral crest. Based on the comparison of abundant material from the western Pacific, combined with a molecular genetic analysis using partial sequences of the mitochondrial COI and 16S rRNA genes, three distinct species could be recognized. The true H. gibbosus has a moderately high basal rostral crest and appears to have a more eastern distribution from the South China Sea to the Indian Ocean. Both forms with a very low or very high basal rostral crest are currently undescribed and mainly distributed along the western coast of the Pacific from Japan to Fiji. The low basal rostral crest form, H. abulbus sp. nov., is unique in the genus by lacking a distinct abdominal boss and appears to be restricted to Japan, Taiwan and NE Philippines. The very high basal rostral crest form, H. corona sp. nov., occurs in the western Pacific down to NW Australia.

Conflict and congruence between morphological and molecular data: revision of the Merodon constans group (Diptera : Syrphidae)

2020 ◽  
Author(s):  
Ante Vujić ◽  
Snežana Radenković ◽  
Laura Likov ◽  
Andrijana Andrić ◽  
Marina Janković ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Distinct Species ◽  
Morphological Characters ◽  
Molecular Data ◽  
Species Group ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
The Status ◽  
Data Revision

We revise the Merodon constans species group of the genus Merodon Meigen, 1803 (Diptera: Syrphidae), provide morphological diagnosesand descriptions, as well as an illustrated key and a discussion on the different taxonomic characters used. In total, 15 species were studied, their geographic distributions are presented on maps, and nine new species are described. Two species are redefined and neotypes are designated, lectotypes are designated for five species, and onespeciesis reinstated as valid. Following a detailed study of type material in different entomological collections, the status of several species is revised and three new synonymies are proposed. The M. constans species group was resolved as being monophyletic within the M. albifrons lineage based on molecular analyses using COI and 28S rRNA gene sequences. Three species morphologically similar to M. constans (Rossi, 1794) but occurring outside its distributional rangewere supported as being valid and distinct species on the basis of molecular data, but they were not distinguishable based on morphological characters. By contrast, continental populations of M. analis Meigen, 1822 could not be separated from Mediterranean M. constans based on differences in COI or 28S rRNA genes. The same molecular markers could not discriminate between two other species pairs. We conclude that these molecular markers only partially resolve species within the M. constans group. Geometric morphometry of wing shape successfully separated M. analis and M. constans, as well as M. spineus Vujić, Šašić Zorić & Likov, sp. nov. in both species and population analyses.

A review of the subgenus Euprepiosaurus of Varanus (Squamata: Varanidae): morphological and molecular phylogeny, distribution and zoogeography,  with an identification key for the members of the V. indicus and  the V. prasinus species groups

Zootaxa ◽  
2007 ◽  
Vol 1472 (1) ◽  
pp. 1 ◽  
Author(s):  
THOMAS ZIEGLER ◽  
ANDREAS SCHMITZ ◽  
ANDRÉ KOCH ◽  
WOLFGANG BÖHME
Keyword(s):  
Molecular Genetic ◽  
Distinct Species ◽  
Species Group ◽  
Genetic Distances ◽  
Identification Key ◽  
Sister Species ◽  
Rrna Gene ◽  
Group V ◽  
Species Groups ◽  
Gene Data

We provide a synopsis of the currently recognized taxa within the subgenus Euprepiosaurus of Varanus, consisting of the V. indicus species group (in chronological order, V. indicus, V. doreanus, V. jobiensis, V. finschi, V. melinus, V. yuwonoi, V. caerulivirens, V. cerambonensis, V. juxtindicus, V. zugorum) and the V. prasinus species group (accordingly, V. prasinus, V. beccarii, V. kordensis, V. bogerti, V. keithhornei, V. telenesetes, V. macraei, V. boehmei, V. reisingeri). We summarize the taxonomic history of the species groups and highlight the morphology and distribution of the species in detail. Molecular genetic analyses confirm Euprepiosaurus and also the two contained species groups as monophyla. Our molecular (mitochondrial 16S rRNA gene) data further reinforce that V. beccarii, V. boehmei, V. keithhornei, and V. macraei are distinct species within the V. prasinus group. V. kordensis consistently proves to be a sister species to all remaining members of the V. prasinus species group studied by us. Comparatively low genetic distances argue for relatively recent speciation processes within the V. indicus group. The species status of V. caerulivirens and V. finschi is again corroborated. The analyses consistently place V. cerambonensis and V. melinus as sister species. It is further evident that both species groups within Euprepiosaurus still contain distinct unrecognized taxa. Finally, we discuss the phylogeny and zoogeography of Euprepiosaurus in the light of our data and provide an identification key for the species of this subgenus.

scholarly journals Genome-Derived Criteria for Assigning Environmental narG and nosZ Sequences to Operational Taxonomic Units of Nitrate Reducers

2009 ◽  
Vol 75 (15) ◽  
pp. 5170-5174 ◽  
Author(s):  
Katharina Palmer ◽  
Harold L. Drake ◽  
Marcus A. Horn
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Nitrate Reducers ◽  
Multiple Copies ◽  
Tree Topologies ◽  
Gene Similarity ◽  
Very High

ABSTRACT Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of ≥97% had a narG or nosZ similarity of ≥67% or ≥80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent.

scholarly journals Phylogenetic diversity of bacteria in rock salt of the Verkhnekamskoe deposit (Perm Krai)

2021 ◽  
pp. 256-262
Author(s):  
Anna A. Pyankova ◽  
◽  
Yulia A. Beloglazova ◽  
Ekaterina S. Korsakova ◽  
Boris A. Bachurin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Rock Salt ◽  
Phylogenetic Diversity ◽  
Molecular Genetic ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sample Depth ◽  
Perm Krai ◽  
Total Dna ◽  
Type Strains

New data on the phylogenetic diversity of bacteria in the salt of the Verkhnekamskoe deposit (Perm Krai) have been obtained using molecular genetic methods. Analysis of the 16S rRNA genes of total DNA from the rock salt sample (depth intervals of 239.7-239 m) evinces the presence of bacteria belonging to the classes: Actinobacteria (closely related to the genera Rhodococcus, Demequina), Gammaproteobacteria (the genera Pseudomonas, Serratia, Shigella), Betaproteobacteria (the genus Ralstonia) and Alphaproteobacteria (the genus Phyllobacterium). In addition, we identified two phylotypes of the Alphaproteobacteria (clone 66BA (GenBank MH410136) and clone 12BA (GenBank MH410128) that show lower similarity in 16S rRNA genes (98.46%) with the closest type strains of the genus Mesorhizobium (M. alhagi CCNWXJ12-2T) and the genus Chelativorans (C. multitrophicus DSM9103T). The identified phylotypes may represent new taxonomic units.

Sargassum muticum: a taxonomic history including world-wide and western Pacific distributions

1983 ◽  
Vol 63 (3) ◽  
pp. 617-625 ◽  
Author(s):  
Alan T. Critchley
Keyword(s):  
Species Group ◽  
Sargassum Muticum ◽  
Western Pacific ◽  
Distribution Map ◽  
Western Pacific Region ◽  
Reproductive Structures ◽  
The World ◽  
Taxonomic History ◽  
History Of ◽  
The Western Pacific

Sargassum muticum(Yendo) Fensholt was first described from Japan as the formamuticus(sic.) ofS. kjellmanianumYendo. Subsequently,s. kjellmanianumandS. miyabeiYendo have been recognised as conspecific with dioecious reproductive structures.S. muticumis monoecious. The taxonomic history ofS. muticumand confusions arising are presented.The spread ofSargassum muticum to regionsof the world outside of Japan is illustrated. A distribution map ofS. kjellmanianum, S. miyabeiandS. muticumin the western Pacific is also presented with a discussion of this selected species group. Further work is required to determine the exact extent ofS. muticumin the western Pacific region.

scholarly journals Genome-based classification of three novel actinobacteria from the Karakum Desert: Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov

2020 ◽  
Vol 70 (3) ◽  
pp. 1993-2002 ◽  
Author(s):  
Hayrettin Saygin ◽  
Hilal Ay ◽  
Kiymet Guven ◽  
Nevzat Sahin
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Morphological Characteristics ◽  
Distinct Species ◽  
Diaminopimelic Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

Three isolates, 5K138T, 8K307T and KC603T, with typical morphological characteristics of members of the genus Jiangella were obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliations of the strains. The strains showed chemotaxonomic properties consistent with their classification as representing members of the genus Jiangella such as ll-diaminopimelic acid in the cell wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as major polar lipids as well as MK-9(H4) as a major menaquinone. Pairwise sequence comparisons of the 16S rRNA genes showed that the strains were closely related to Jiangella alba DSM 45237T, Jiangella rhizosphaerae NEAU-YY265T and Jiangella mangrovi 3SM4-07T with higher than 99 % sequence identities. However, a combination of phenotypic and phylogenetic approaches as well as genome-based comparative analyses confirmed the taxonomic positions of these strains as representing distinct species within the genus Jiangella . Therefore, strains 5K138T, 8K307T and KC603T should each be classified as representing a novel species within the genus Jiangella , for which the names Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov. are proposed, respectively. The type strains of the proposed novel species are as follows: Jiangella asiatica 5K138T (=JCM 33518T=CGMCC 4.7672T), Jiangella aurantiaca 8K307T (=JCM 33519T=CGMCC 4.7621T) and Jiangella ureilytica KC603T (=JCM 33520T=CGMCC 4.7618T).

scholarly journals New aspects upon the classification of Staphylococcus intermedins

2017 ◽  
Vol 61 (1) ◽  
pp. 57
Author(s):  
E. PETRIDOU (Ε. ΠΕΤΡΙΔΟΥ) ◽  
R. FARMAKI (Ρ. ΦΑΡΜΑΚΗ) ◽  
A. F. KOUTINAS (Α.Φ. ΚΟΥΤΙΝΑΣ)
Keyword(s):  
Normal Skin ◽  
Distinct Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Staphylococcus Intermedius ◽  
Skin Flora ◽  
Pcr Rflp ◽  
Group A ◽  
Commercial Kits ◽  
Coagulase Positive Staphylococci

In 1976, Staphylococcus intermedins was first described as being a new species isolated from pigeons, dogs, mink and horses. Until recently, the majority of coagulase-positive staphylococci originating from animals such as dogs and pigeons have been classified as S. intermedins. This species has been recognized to constitute normal skin flora of various animal species and to occasionally cause a variety of infections in dogs and cats. There have been six species of coagulase-positive staphylococci other than Staphylococcus aureus, namely S.intermedius, S.schleiferì subsp. coagulans, S.hyicus, S. lutrae, S.delphini and S. pseudintermedius. Sequence similarities of 16S rRNA genes among four of these species, except S. hyicus and S. lutrae, are 99% identical. In addition, it is very difficult to differentiate among S. intermedius, S. delphini and S. pseudintermedius phenotypically, and commercial kits are not available for the differentiation between of S. pseudintermedius and S. delphini. It has been shown that isolates phenotypically identified as Staphylococcus intermedius consist of four distinct species, including S. intermedius, Staphylococcus pseudintermedius and Staphylococcus delphini group A and B, which together represent the Staphylococcus intermedius group (SIG). Moreover, S. delphini group Β might be a novel species. In 2009, a new, rapid and inexpensive PCR-RFLP was developed and is capable of discriminating the SIG strains.

scholarly journals Relationships among streptococci from the mitis group, misidentified as Streptococcus pneumoniae

2020 ◽  
Vol 39 (10) ◽  
pp. 1865-1878 ◽  
Author(s):  
Ewa Sadowy ◽  
Agnieszka Bojarska ◽  
Alicja Kuch ◽  
Anna Skoczyńska ◽  
Keith A. Jolley ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
16S Rrna ◽  
Genome Analysis ◽  
Phylogenetic Trees ◽  
Core Genome ◽  
Distinct Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Nucleotide Position

Abstract The aim of our study was to investigate phenotypic and genotypic features of streptococci misidentified (misID) as Streptococcus pneumoniae, obtained over 20 years from hospital patients in Poland. Sixty-three isolates demonstrating microbiological features typical for pneumococci (optochin susceptibility and/or bile solubility) were investigated by phenotypic tests, lytA and 16S rRNA gene polymorphism and whole-genome sequencing (WGS). All isolates had a 6-bp deletion in the lytA 3′ terminus, characteristic for Mitis streptococc and all but two isolates lacked the pneumococcal signature cytosine at nucleotide position 203 in the 16S rRNA genes. The counterparts of psaA and ply were present in 100% and 81.0% of isolates, respectively; the spn9802 and spn9828 loci were characteristic for 49.2% and 38.1% of isolates, respectively. Phylogenetic trees and networks, based on the multilocus sequence analysis (MLSA) scheme, ribosomal multilocus sequence typing (rMLST) scheme and core-genome analysis, clearly separated investigated isolates from S. pneumoniae and demonstrated the polyclonal character of misID streptococci, associated with the Streptococcus pseudopneumoniae and Streptococcus mitis groups. While the S. pseudopneumoniae clade was relatively well defined in all three analyses, only the core-genome analysis revealed the presence of another cluster comprising a fraction of misID streptococci and a strain proposed elsewhere as a representative of a novel species in the Mitis group. Our findings point to complex phylogenetic and taxonomic relationships among S. mitis-like bacteria and support the notion that this group may in fact consist of several distinct species.

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