scholarly journals Systematics of the Arboreal Neotropical ‘thorellii’ Clade of Centruroides Bark Scorpions (Buthidae) and the Efficacy of Mini-Barcodes for Museum Specimens

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 441
Author(s):  
Aaron M. Goodman ◽  
Lorenzo Prendini ◽  
Lauren A. Esposito
Keyword(s):  
Molecular Phylogenetics ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Species Level ◽  
Degraded Dna ◽  
Coi Gene ◽  
Museum Specimens ◽  
Base Pairs ◽  
Representative Species ◽  
Level Identification

Fragmented and degraded DNA is pervasive among museum specimens, hindering molecular phylogenetics and species identification. Mini-barcodes, 200–300-base-pair (bp) fragments of barcoding genes, have proven effective for species-level identification of specimens from which complete barcodes cannot be obtained in many groups, but have yet to be tested in arachnids. The present study investigated the efficacy of mini-barcodes combined with longer sequences of the Cytochrome c Oxidase Subunit I (COI) gene in the systematics of the arboreal Neotropical ‘thorellii’ clade of Centruroides Marx, 1890 bark scorpions (Buthidae, C.L. Koch 1837), the species of which have proven to be difficult to identify and delimit due to their similar morphology. The phylogeny of 53 terminals, representing all nine species of the clade and representative species belonging to related clades of Centruroides, rooted on Heteroctenus junceus (Herbst, 1800) and based on up to 1078 base pairs of COI and 112 morphological characters, is presented to test the monophyly of the clade and the limits of its component species. The results support the recognition of nine species of the ‘thorellii’ clade, in accordance with a recent taxonomic revision, and highlight the efficacy of mini-barcodes for identifying morphologically similar cryptic species using specimens of variable age and preservation.

scholarly journals The DNA Barcoding of Several Commercial Fish from Simeulue Islands Coast of Aceh Using Cytochrome Oxidase Sub Unit I (COI) Gene Marker

2019 ◽  
Vol 1 (1) ◽  
pp. 62-70
Author(s):  
Edwarsyah Edwarsyah ◽  
Muhammad Nasir ◽  
Muhammad Banda Selamat
Keyword(s):  
Dna Barcoding ◽  
Species Level ◽  
Dna Bases ◽  
Coi Gene ◽  
Gene Marker ◽  
Base Pairs ◽  
Commercial Fish ◽  
Morphological Approach ◽  
Mitochodrial Dna ◽  
The Right

Simeulue is a cluster of islands that rich of commercial fisheries in Aceh waters. Management of the fisheries products is highly related to species identification in order to ascertain the appropriate steps to manage the resources sustainably. Identification using DNA barcoding tools is the right answer for the problem that have not been able to be resolved even by morphological approach. Some of 11 individual samples were taken from 6 sampling points based on lobster’s catchment and cultivation areas. All of the samples were identified using COI mitochodrial DNA resulting 6 species including Scomber scombus, Scomberomorus plurilineatus, Octopus cyanea, Taeniura Lymna, Sympterygia bonapartii and Panulirus versicolor. The DNA bases were aligned using MEGA application and Neigbour- Joining method, Kimura 2 parameters resulting a 690 base pairs nucleotides. Reconstruction of philogenetic tree shows that the species of Simeulue were conjoined into one clade with the sequences downloaded from genebank. It shows that those species were closely related genetically indicating by the bootstrap value of Scomber scombus (100), Scomberomorus plurilineatus (100), Octopus cyanea (100). The results of the study shows that the DNA barcoding tools can explicate not only the identification up to the species level but also the genetic relationship that can be seen from the interspecies bases composition.

Taxonomic revision of the Colombian Tityus (Archaeotityus) (Scorpiones, Buthidae) species: a morphological and morphometric approach, with a description of a new species

Zootaxa ◽  
2019 ◽  
Vol 4660 (1) ◽  
pp. 1-94
Author(s):  
JAIRO A. MORENO-GONZÁLEZ ◽  
RANULFO GONZÁLEZ O. ◽  
EDUARDO FLÓREZ D.
Keyword(s):  
Principal Component Analysis ◽  
New Species ◽  
New Records ◽  
Principal Component ◽  
Taxonomic Revision ◽  
Component Analysis ◽  
Morphological Characters ◽  
Species Level ◽  
Qualitative And Quantitative ◽  
A New Species

We present a taxonomic revision of the Colombian Tityus (Archaeotityus) species based on morphological and morphometric evidence. We examined more than 385 specimens and evaluated new and previously used qualitative and quantitative morphological characters. We redescribe the Colombian species and present morphological characters for both sexes and an emended diagnosis for the subgenus Tityus (Archaeotityus). We describe a new species Tityus guane sp. nov. from Santander department, Colombia, Tityus betschi Lourenço 1992 is synonymized with Tityus parvulus Kraepelin, 1914, and Tityus wayuu Rojas-Runjaic & Armas, 2007 is synonymized with Tityus tayrona Lourenço, 1991. We measured 186 specimens and performed a multivariate principal component analysis (PCA) for 34 selected morphometric ratios for each sex. We found that a few morphological ratios support species level distinctions within the Colombian species. We provide updated distributional maps with new records and an identification key for both sexes. Furthermore, we provide an updated checklist for the subgenus and a discussion about the character systems used within Tityus (Archaeotityus). The new morphological characters proposed and the traditional morphometry examined with a PCA are useful for studying Tityus (Archaeotityus) taxonomy.

scholarly journals Cave shrimps Troglocaris s. str. (Dormitzer, 1853), taxonomic revision and description of new taxa after phylogenetic and morphometric studies

Zootaxa ◽  
2012 ◽  
Vol 3421 (1) ◽  
pp. 1 ◽  
Author(s):  
JURE JUGOVIC ◽  
BRANKO JALŽIĆ ◽  
SIMONA PREVORČNIK ◽  
BORIS SKET
Keyword(s):  
Type Species ◽  
Morphological Variability ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Molecular Data ◽  
Coi Gene ◽  
Distribution Area ◽  
Molecular Analyses ◽  
Morphometric Analyses ◽  
Morphological Distinction

Within the Dinaric genus Troglocaris cave shrimps from the subgenus Troglocaris s. str. (Dormitzer, 1853) (Crustacea:Decapoda: Atyidae), have the widest distribution area. The recent molecular analyses have revealed significant, crypticdiversity in the subgenus. The aim of the subsequent detailed morphometric analyses was the provision of the appropriatediagnosable characters for the discovered lineages, i.e. taking care of their taxonomical visibility. We herein designate aneotype and provide a detailed description for the polytipic type species of the genus T. (T.) anophthalmus (Kollar, 1848), toenable its morphological distinction from the erroneously described T. (T.) planinensis Birštejn, 1948. Considering acombination of morphological, geographical and molecular data, we describe four new subspecies: T. (T.) a. ocellata ssp. nov.,T. (T.) a. periadriatica ssp. nov., T. (T.) a. legovici ssp. nov. and T. (T.) a. sontica ssp. nov., apart from the extant T. (T.) a.intermedia Babić, 1922. Due to a considerable morphological variability and no easily observable diagnostic morphological characters, the GenBank accession numbers for the COI gene are added in all mentioned taxa.

A taxonomic revision of the Canthon subgenus Pseudepilissus Martínez, 1954 (Coleoptera: Scarabaeidae: Scarabaeinae)

2020 ◽  
Vol 51 (4) ◽  
pp. 696-752
Author(s):  
Marcelli K. Vieira ◽  
Fernando Z. Vaz-de-Mello ◽  
Fernando A. B. Silva
Keyword(s):  
New Species ◽  
Literature Review ◽  
Geographic Distribution ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Species Level ◽  
Valid Species ◽  
Incertae Sedis ◽  
Number Of Species

The subgenus Canthon (Pseudepilissus) Martínez, 1954 is revised. Four valid species are redescribed: Canthon (Pseudepilissus) muticus Harold, 1867; C. (P.) lunatus Schmidt, 1922; C. (P.) planus Lucas, 1857 and C. (P.) reichei Felsche, 1910. Three species assigned to other groups are transferred in the subgenus: C. (P.) quadratus Blanchard, 1843 [previously Canthon “incertae sedis”]; C. (P.) edentulus Harold, 1868 [previously Canthon “incertae sedis”] and C. (P.) seminulus Harold, 1867 comb. nov. [previously Vulcanocanthon]. The genus Vulcanocanthon Pereira & Martínez, 1960 syn. nov. is synonymized with Canthon (Pseudepilissus). Three subspecies are raised to species level: C. (P.) tibialis Schmidt, 1922 stat. nov. [previously C. (P.) lunatus tibialis]; C. (P.) granuliceps Felsche, 1910 stat. nov. [previously C. edentulus granuliceps] and C. (P.) hendrichsi Halffter & Martínez, 1968 stat. nov. [previously C. (P.) muticus hendrichsi]. C. (P.) honsi Balthasar, 1939 syn. nov. is synonymized with C. (P.) reichei Felsche, 1910. Four new species are described: Canthon (P.) arriagadai sp. nov., Canthon (P.) bonaerensis sp. nov., Canthon (P.) vidaurrei sp. nov. and Canthon (P.) ziggy sp. nov., bringing the number of species in the subgenus to 14. Lectotypes are designated for six species C. (P.) muticus Harold, 1867; C. (P.) reichei Felsche, 1910; C. (P.) planus Lucas, 1857; C. (P.) seminulus Harold, 1867; C. (P.) granuliceps Felsche, 1910 and C. (P.) quadratus Blanchard, 1843. A detailed literature review, synonymies, description, illustration of key morphological characters, data on the studied material and geographic distribution are provided for each species.

Molecular identification and characterization of Trichinella spiralis from a leopard in India

2019 ◽  
Author(s):  
Anil Kumar Nehra ◽  
Hira Ram ◽  
P. S. Banerjee ◽  
Rajat Garg ◽  
M. Karikalan ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Genetic Markers ◽  
Trichinella Spiralis ◽  
Ribosomal Subunit ◽  
Species Level ◽  
Homology Search ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Level Identification

TPresent study describes species level identification of Trichinella spiralis of leopard origin from India using multiplex PCR and molecular characterization of the parasite based on sequencing of multiple genetic markers viz. 5S ribosomal DNA intergenic spacer region (5S ISR), partial mitochondrial large ribosomal subunit (Mt-lsr) and partial mitochondrial cytochrome c oxidase I (COI) genes. A single amplicons of 173 bp, indicative of T. spiralis was obtained in multiplex PCR. Further, specific PCR amplifications viz. 750 bp (5S ISR), 445 bp (Mt-lsr) and 850 bp (COI) were obtained for selected genetic markers. Homology search analysis of 5S-ISR, Mt-lsr gene and COI gene showed highest 99.6% identity with sequences originating from China (KT894074, T. spiralis), 98.6% similarity with T. spiralis China isolates (GU339127, GU339147) and 99.8% sequence homology with T. spiralis sequences originating from Belarus (MH119334), respectively. In the phylogenetic analysis, sequences of each selected genetic marker clustered together with published T. spiralis isolates only, which further confirmed species level identification of detected larvae as T. spiralis, although very few differences were noted with reference to relative positions. This is the first study from India, which provide molecular evidence on circulation of T. spiralis in wild animals.

scholarly journals Illuminating species diversity of nudibranch in Indonesian coral reef ecosystem using molecular identification

2021 ◽  
Vol 944 (1) ◽  
pp. 012033
Author(s):  
I G W D Dharmawan ◽  
D G Bengen ◽  
I Setyobudiandi ◽  
B Subhan ◽  
I Verawati ◽  
...  
Keyword(s):  
Species Diversity ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Morphological Characters ◽  
Species Level ◽  
Coi Gene ◽  
Interspecific Genetic Distance ◽  
The Difference ◽  
Source Of Information

Abstract Nudibranch has high species diversity with complex morphological characters and is challenging to identify at the species level. The lack of knowledge about nudibranchs makes it difficult to identify conventionally using morphological characters. This study aims to identify nudibranchs at the species level using the DNA barcoding method from the mitochondrial cytochrome oxidase 1 (CO1) gen. The results of DNA barcoding using the Cytochrome Oxidase I (COI) gene showed 18 species of 51 samples analyzed. The phylogenetic tree reconstruction revealed 11 main clades belonging to 11 genera. The genetic distance between and within species clearly shows the difference between individuals. Interspecific genetic distance shows the lowest value between species was found between Chromodoris annae and Chromodoris magnifica is 0.075, and the largest genetic distance observed between species Glossodoris rufomarginata and Tritonidae sp is 0.354. This study shows molecular analysis can be used to identify nudibranch up to species level, which will be a source of information in knowing the distribution and the genetic distance.

scholarly journals Technical Limitations Associated With Molecular Barcoding of Arthropod Bloodmeals Taken From North American Deer Species

2020 ◽  
Vol 57 (6) ◽  
pp. 2002-2006
Author(s):  
Erin M Borland ◽  
Daniel A Hartman ◽  
Matthew W Hopken ◽  
Antoinette J Piaggio ◽  
Rebekah C Kading
Keyword(s):  
Mitochondrial Gene ◽  
Blood Feeding ◽  
Species Level ◽  
Coi Gene ◽  
Cytochrome C Oxidase I ◽  
Molecular Barcoding ◽  
Deer Species ◽  
Multiple Loci ◽  
D Loop ◽  
Level Identification

Abstract Accurate species-level identification of the source of arthropod bloodmeals is important for deciphering blood feeding patterns of field-collected specimens. Cytochrome c oxidase I (COI) mitochondrial gene sequencing has been used for this purpose; however, species resolution can be difficult to obtain from certain vertebrate genera, including Odocoileus. Sanger sequencing of mitochondrial genes was employed to identify the bloodmeal source of wild-caught mosquitoes trapped in Greeley, Colorado. Initial sequencing of the COI gene of mitochondrial DNA in bloodmeals was inadequate for species-level resolution of bloodmeals from deer in the genus Odocoileus, with current databases returning low fidelity matches to multiple genera. The use of the hypervariable D loop of the control region provided species-level identification of white-tailed deer (Order: Artiodactyla, Family: Cervidae, Odocoileus virginianus); however, taxonomic identification was successful only to genus for mule (O. hemionus hemionus) and black-tailed deer (O. hemionus columbianus). We advocate the use of multiple loci for bloodmeal analysis and the buildout of available databases to include multiple mitochondrial reference genes for reliable host species identification.

scholarly journals Species-level identification of the blowfly Chrysomya megacephala and other Diptera in China by DNA barcoding

Genome ◽  
2017 ◽  
Vol 60 (2) ◽  
pp. 158-168 ◽  
Author(s):  
Deyi Qiu ◽  
Charles E. Cook ◽  
Qiaoyun Yue ◽  
Jia Hu ◽  
Xiaoya Wei ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Forensic Entomology ◽  
Species Level ◽  
Native Range ◽  
Base Pairs ◽  
Chrysomya Megacephala ◽  
Disease Vector ◽  
Anthropogenic Dispersal ◽  
Level Identification

The blowfly Chrysomya megacephala, or oriental latrine fly, is the most common human-associated fly of the oriental and Australasian regions. Chrysomya megacephala is of particular interest for its use in forensic entomology and because it is a disease vector. The larvae are economically important as feed for livestock and in traditional Chinese medicine. Identification of adults is straightforward, but larvae and fragments of adults are difficult to identify. We collected C. megacephala, its allies Chrysomya pinguis and Protophormia terraenovae, as well as flies from 11 other species from 52 locations around China, then sequenced 658 base pairs of the COI barcode region from 645 flies of all 14 species, including 208 C. megacephala, as the basis of a COI barcode library for flies in China. While C. megacephala and its closest relative C. pinguis are closely related (mean K2P divergence of 0.022), these species are completely non-overlapping in their barcode divergences, thus demonstrating the utility of the COI barcode region for the identification of C. megacephala. We combined the 208 C. megacephala sequences from China with 98 others from public databases and show that worldwide COI barcode diversity is low, with 70% of all individuals belonging to one of three haplotypes that differ by one or two substitutions from each other, reflecting recent anthropogenic dispersal from its native range in Eurasia.

One or two species of the rare Malagasy carnivoran Eupleres (Eupleridae)? New insights from molecular data

Mammalia ◽  
2018 ◽  
Vol 82 (2) ◽  
pp. 107-112 ◽  
Author(s):  
Géraldine Veron ◽  
Steven M. Goodman
Keyword(s):  
Morphological Characters ◽  
Molecular Data ◽  
Species Level ◽  
Deciduous Forests ◽  
Monophyletic Group ◽  
Museum Specimens ◽  
Nuclear Markers ◽  
Fresh Tissue ◽  
Tissue Samples ◽  
The Family

AbstractMembers of the genusEupleresare poorly known insectivorous carnivorans belonging to the family Eupleridae (order Carnivora), which are endemic to Madagascar. Recently, using morphological characters, the two previously recognized subspecies ofEupleres goudotiiwere raised to the species level, withE. goudotiioccurring in the humid forests of the island, largely in the east, andEupleres majorin northwestern dry deciduous forests. Using some of the few museum specimens and fresh tissue samples available for this genus, we assessed differences between these two forms based on the cytochromebgene. The results show that individuals identified asE.major, based on a combination of morphological characters and collection locality, do not form a monophyletic group, and the level of polymorphism within the genus is not in agreement with the recognition of two species. Additional molecular data, in particular from nuclear markers, are needed to verify these results.

Phylogenomic re-evaluation of Triaenonychoidea (Opiliones : Laniatores), and systematics of Triaenonychidae, including new families, genera and species

2021 ◽  
Author(s):  
Shahan Derkarabetian ◽  
Caitlin M. Baker ◽  
Marshal Hedin ◽  
Carlos E. Prieto ◽  
Gonzalo Giribet
Keyword(s):  
New Zealand ◽  
New Taxa ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Species Level ◽  
Systematic Research ◽  
Ultraconserved Elements ◽  
Genus Level ◽  
Sequence Capture ◽  
Family Level

The Opiliones superfamily Triaenonychoidea currently includes two families, the monogeneric New Zealand–endemic Synthetonychiidae Forster, 1954 and Triaenonychidae Sørensen, 1886, a diverse family distributed mostly throughout the temperate Gondwanan terranes, with ~110 genera and ~500 species and subspecies currently described. Traditionally, Triaenonychidae has been divided into subfamilies diagnosed by very few morphological characters largely derived from the troublesome ‘Roewerian system’ of morphology, and classifications based on this system led to many complications. Recent research within Triaenonychoidea using morphology and traditional multilocus data has shown multiple deeply divergent lineages, non-monophyly of Triaenonychidae, and non-monophyly of subfamilies, necessitating a revision based on phylogenomic data. We used sequence capture of ultraconserved elements across 164 samples to create a 50% taxon occupancy matrix with 704 loci. Using phylogenomic and morphological examinations, we explored family-level relationships within Triaenonychoidea, including describing two new families: (1) Lomanellidae Mendes & Derkarabetian, fam. nov., consisting of Lomanella Pocock, 1903, and a newly described genus Abaddon Derkarabetian & Baker, gen. nov. with one species, A. despoliator Derkarabetian, sp. nov.; and (2) the elevation to family of Buemarinoidae Karaman, 2019, consisting of Buemarinoa Roewer, 1956, Fumontana Shear, 1977, Flavonuncia Lawrence, 1959, and a newly described genus Turonychus Derkarabetian, Prieto & Giribet, gen. nov., with one species, T. fadriquei Derkarabetian, Prieto & Giribet, sp. nov. With our dataset we also explored phylogenomic relationships within Triaenonychidae with an extensive taxon set including samples representing ~80% of the genus-level diversity. Based on our results we (1) discuss systematics of this family including the historical use of subfamilies, (2) reassess morphology in the context of our phylogeny, (3) hypothesise placement for all unsampled genera, (4) highlight lineages most in need of taxonomic revision, and (5) provide an updated species-level checklist. Aside from describing new taxa, our study provides the phylogenomic context necessary for future evolutionary and systematic research across this diverse lineage. ZooBank Registration: urn:lsid:zoobank.org:pub:81683834-98AB-43AA-B25A-C28C6A404F41

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