Tests of conspecificity for closely related black fly (Diptera: Simuliidae) species of the Simulium striatum group in Thailand

Zootaxa â—˝  
2017 â—˝  
Vol 4231 (3) â—˝  
pp. 421 â—˝  
Author(s):  
SIRINAPA PANGJANDA â—˝  
PAIROT PRAMUAL
Keyword(s):  
Dna Sequences â—˝  
Developmental Stages â—˝  
Species Group â—˝  
Biological Species â—˝  
Larval Habitat â—˝  
Habitat Characteristics â—˝  
Elongation Complex â—˝  
Morphological Examination â—˝  
Black Fly â—˝  
Gill Filaments

Four black fly species of the Simulium striatum species group have been recorded in Thailand. These species are morphologically highly similar in all developmental stages except for the number and arrangement of the pupal gill filaments. In this study, we used multiple characters sources, including morphology, cytology, molecular biology and ecology, to test the hypothesis of conspecificity for S. quinquestriatum (Shiraki), S. nakhonense Takaoka & Suzuki and S. chiangmaiense Takaoka & Suzuki. A molecular study based on the cytochrome c oxidase subunit I (COI) was unable to separate these taxa. In contrast, the elongation complex protein 1 (ECP1) sequences clearly differentiate S. quinquestriatum from S. chiangmaiense and S. nakhonense. However, the latter two taxa could not be differentiated based on molecular DNA sequences. Simulium chiangmaiense and S. nakhonense are also similar in the larval habitat characteristics and have undifferentiated polytene chromosome banding patterns. Morphological examination of the number and arrangement of the pupal gill filaments found a number of intermediate forms. Therefore, S. chiangmaiense and S. nakhonense are apparently the same biological species that is polymorphic for the number and arrangement of gill filaments. Thus, we synonymized S. chiangmaiense with S. nakhonense. 

A new species of black fly (Diptera: Simuliidae) in the Simulium (Simulium) multistriatum species-group from Thailand

Zootaxa â—˝  
2019 â—˝  
Vol 4586 (3) â—˝  
pp. 461 â—˝  
Author(s):  
JIRAPORN THAIJARERN â—˝  
KOMGRIT WONGPAKAM â—˝  
ANONGRIT KANGRANG â—˝  
PAIROT PRAMUAL
Keyword(s):  
New Species â—˝  
Genetic Distance â—˝  
Dna Sequences â—˝  
Phylogenetic Analyses â—˝  
Strong Support â—˝  
Pupal Stage â—˝  
Species Group â—˝  
Mountainous Area â—˝  
Black Fly â—˝  
Interspecific Genetic Distance

A new black fly species of the Simulium multistriatum species-group of the subgenus Simulium Latreille is described from the mountainous area in northeastern Thailand, based on morphology and mitochondrial DNA sequences. The new species is morphologically similar to S. laui Takaoka and Sofian-Azirun and S. lacduongense Takaoka and Ya’cob originally described from Vietnam, S. fenestratum Edwards originally described from Indonesia and S. chaliowae Takaoka and Boonkemtong originally described from Thailand, but can be distinguished in the adult stage by the number of upper eye facets and globular shape of the spermatheca and in the pupal stage by the cocoon and shape of thoracic tubercles. Genetic distance and phylogenetic analyses of mitochondrial cytochrome c oxidase I sequences differentiated the new species from other members of S. multistriatum species-group. All specimens of the new species formed a monophyletic clade with strong support in all phylogenetic analyses. The minimum interspecific genetic distance of 4.9% is considerably greater than the new species maximum intraspecific genetic distance (2.7%). 

A new black fly species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from Taiwan, with keys to all 13 species of the Simulium varicorne species-group

Zootaxa â—˝  
2017 â—˝  
Vol 4312 (3) â—˝  
pp. 438
Author(s):  
HIROYUKI TAKAOKA â—˝  
YAO-TE HUANG
Keyword(s):  
New Species â—˝  
New Record â—˝  
Species Group â—˝  
Outer Margin â—˝  
Black Fly â—˝  
Oriental Region â—˝  
Gill Filaments

Simulium (Gomphostilbia) huangi sp. nov. is described from female, male, pupal and larval specimens collected from Taiwan. This new species is placed in the Simulium burtoni subgroup of the Simulium varicorne species-group of the subgenus Gomphostilbia, one of the two largest subgenera of the genus Simulium in the Oriental Region. This species also represents a new record of the S. varicorne species-group from Taiwan. It is characterized in the adults by the antenna with eight flagellomeres almost uniformly darkened, in the pupa by gill filaments arranged as [(1+2) +(1+2)] + 2, and a pair of terminal hooks much widened, each with a serrated outer margin, and in the larva by the medium-long postgenal cleft. Taxonomic notes to distinguish this new species from four other known species of the S. burtoni subgroup from other countries are provided. Revised keys to all the 13 species of the S. varicorne species-group are given. 

scholarly journals Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

BMC Biology â—˝  
2019 â—˝  
Vol 17 (1) â—˝  
Author(s):  
Amrita Srivathsan â—˝  
Emily Hartop â—˝  
Jayanthi Puniamoorthy â—˝  
Wan Ting Lee â—˝  
Sujatha Narayanan Kutty â—˝  
...  
Keyword(s):  
Dna Sequences â—˝  
Large Scale â—˝  
Low Cost â—˝  
Small Body â—˝  
Small Subset â—˝  
Similar Species â—˝  
Large Species â—˝  
Morphological Examination â—˝  
Species Discovery â—˝  
Short Period

Abstract Background More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such “molecular operational taxonomic units” (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries. Results We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered > 650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; > 99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.). Conclusions We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

10.1093/isd/ixab006 â—˝  
2021 â—˝  
Vol 5 (2) â—˝  
Author(s):  
Olivia M Gearner â—˝  
Marcin J Kamiński â—˝  
Kojun Kanda â—˝  
Kali Swichtenberg â—˝  
Aaron D Smith
Keyword(s):  
Dna Sequences â—˝  
Species Group â—˝  
Phylogenetic Placement â—˝  
Darkling Beetles â—˝  
Species Groups â—˝  
Taxonomic Groups â—˝  
Inference Methods â—˝  
A New Species â—˝  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

scholarly journals The application of drones for mosquito larval habitat identification in rural environments: a practical approach for malaria control?

Malaria Journal â—˝  
2021 â—˝  
Vol 20 (1) â—˝  
Author(s):  
Michelle C. Stanton â—˝  
Patrick Kalonde â—˝  
Kennedy Zembere â—˝  
Remy Hoek Spaans â—˝  
Christopher M. Jones
Keyword(s):  
Image Analysis â—˝  
Malaria Control â—˝  
Rural Areas â—˝  
Near Infrared â—˝  
Aquatic Vegetation â—˝  
Temporal Trends â—˝  
Scale Up â—˝  
Larval Habitat â—˝  
Habitat Characteristics â—˝  
Rural Environments

Abstract Background Spatio-temporal trends in mosquito-borne diseases are driven by the locations and seasonality of larval habitat. One method of disease control is to decrease the mosquito population by modifying larval habitat, known as larval source management (LSM). In malaria control, LSM is currently considered impractical in rural areas due to perceived difficulties in identifying target areas. High resolution drone mapping is being considered as a practical solution to address this barrier. In this paper, the authors’ experiences of drone-led larval habitat identification in Malawi were used to assess the feasibility of this approach. Methods Drone mapping and larval surveys were conducted in Kasungu district, Malawi between 2018 and 2020. Water bodies and aquatic vegetation were identified in the imagery using manual methods and geographical object-based image analysis (GeoOBIA) and the performances of the classifications were compared. Further, observations were documented on the practical aspects of capturing drone imagery for informing malaria control including cost, time, computing, and skills requirements. Larval sampling sites were characterized by biotic factors visible in drone imagery and generalized linear mixed models were used to determine their association with larval presence. Results Imagery covering an area of 8.9 km2 across eight sites was captured. Larval habitat characteristics were successfully identified using GeoOBIA on images captured by a standard camera (median accuracy = 98%) with no notable improvement observed after incorporating data from a near-infrared sensor. This approach however required greater processing time and technical skills compared to manual identification. Larval samples captured from 326 sites confirmed that drone-captured characteristics, including aquatic vegetation presence and type, were significantly associated with larval presence. Conclusions This study demonstrates the potential for drone-acquired imagery to support mosquito larval habitat identification in rural, malaria-endemic areas, although technical challenges were identified which may hinder the scale up of this approach. Potential solutions have however been identified, including strengthening linkages with the flourishing drone industry in countries such as Malawi. Further consultations are therefore needed between experts in the fields of drones, image analysis and vector control are needed to develop more detailed guidance on how this technology can be most effectively exploited in malaria control.

Elimination of micronuclear specific DNA sequences early in anlagen development

1985 â—˝  
Vol 5 (1) â—˝  
pp. 93-98
Author(s):  
C F Brunk â—˝  
R K Conover
Keyword(s):  
Developmental Stage â—˝  
Dna Sequences â—˝  
Developmental Stages â—˝  
Tetrahymena Thermophila â—˝  
Southern Analysis â—˝  
Limited Sequence

After conjugation in Tetrahymena thermophila, the old macronuclei degenerate, and new macronuclei (anlagen) develop. During anlagen development a number of DNA sequences found in the micronuclear genome (micronuclear limited sequences) are eliminated from the anlagen. A cloned copy of a repetitive micronuclear limited sequence has been used to determine the developmental stage at which micronuclear limited sequences are eliminated. DNAs from anlagen of various developmental stages were examined by Southern analysis. It was found that micronuclear limited sequences are present in 4C anlagen and essentially absent in 8C and 16C anlagen. The precipitous loss of these sequences in the 8C anlagen rules out under-replication as the mechanism for the loss and suggests that these sequences are specifically degraded early during anlagen development.

scholarly journals A DNA investigation into the mysterious disappearance of the Rocky Mountain grasshopper, mega-pest of the 1800s

2017 â—˝  
Author(s):  
W. Chapco â—˝  
G. Litzenberger
Keyword(s):  
Dna Sequences â—˝  
Nucleotide Diversity â—˝  
Rocky Mountain â—˝  
Species Group â—˝  
Pest Species â—˝  
History Of Agriculture â—˝  
Extant Species â—˝  
Remarkable Event â—˝  
History Of â—˝  
Major Pest

The mysterious extinction of the Rocky Mountain Grasshopper, Melanoplus spretus, a major pest species on the prairies and plains of the 1800s, is truly a remarkable event in the history of agriculture. Recently, we obtained specimens of M. spretus from museums and from 400-year-old glacial deposits in Wyoming. We report success in obtaining mitochondrial DNA sequences from both sources. This permitted us to examine two issues surrounding the species’ disappearance. First, a long-standing view that M. spretus and the extant species Melanoplus sanguinipes are (if not phase transforms of one another) sister taxa, is disputed, but cannot be rejected with certainty. Interestingly, there is some evidence that suggests there may be a closer affinity with another member of the Mexicanus species-group, Melanoplus bruneri. Second, because M. spretus still possesses considerable nucleotide diversity (1.15 ± 0.19%), a depletion of variation cannot be considered a factor contributing to its demise.

scholarly journals DNA-based diversity assessment reveals a new coral barnacle, Cantellius alveoporae sp. nov. (Balanomorpha: Pyrgomatidae) exclusively associated with the high latitude coral Alveopora japonica in the waters of southern Korea

PeerJ â—˝  
10.7717/peerj.11284 â—˝  
2021 â—˝  
Vol 9 â—˝  
pp. e11284
Author(s):  
Hyun Kyong Kim â—˝  
Benny K.K. Chan â—˝  
Sung Joon Song â—˝  
Jong Seong Khim
Keyword(s):  
Cryptic Species â—˝  
Dna Sequences â—˝  
Distinct Species â—˝  
Andaman Sea â—˝  
Morphological Examination â—˝  
Species Identity â—˝  
Diversity Assessment â—˝  
Molecular Studies â—˝  
Southern Korea â—˝  
Specialist Species

In the present study, the Indo-Pacific coral associated barnacle Cantellius euspinulosum (Broch, 1931) was found to have cryptic species in Korea, Taiwan and other regions based on molecular studies. However, the original specimens of C. euspinulosum from Broch have not been previously described or illustrated, making it difficult to assign which cryptic species to the original C. euspinulosum. The original specimen of C. euspinulosum was examined and illustrated here, and the species identity of C. cf. euspinulosum collected from Jejudo Island in the present study and other cryptic species (based on literature illustrations) in the Indo-Pacific were evaluated.C. euspinulosum from Singapore, Java, Mergui Archipelago in Andaman Sea and Nha Trang represented the C. euspinulosum identified by Broch (1931). It is a generalist on Acropora, Favia, Favites, Leptoria, Montipora, Pachyseris and Pocillipora corals and distributed in the Indo-Pacific region. Morphological examination and DNA sequencing (COI, 12S DNA sequences) in the present study showed that C. cf. euspinulosum from Jejudo Island, Korea represents a distinct species, herein named C. alveoporae sp. nov. Cantellius alveroporae sp. nov. is a specialist species that only grows on Alveopora and also present in Palau, and Ogasawara Island in Japan. Cantellius cf. euspinuloum in Taiwan, the Moscos Island, and Australia belong to several other distinct species awaiting further morphological and molecular studies. At least five cryptic species of C. euspinulosum were identified in the present study, including both specialist and generalists.

A molecular phylogeny of the “Madascincus polleni species complex”, with description of a new species of scincid lizard from the coastal dune area of northern Madagascar

Zootaxa â—˝  
2011 â—˝  
Vol 2876 (1) â—˝  
pp. 1 â—˝  
Author(s):  
AURÉLIEN MIRALLES â—˝  
JÖRN KÖHLER â—˝  
FRANK GLAW â—˝  
MIGUEL VENCES
Keyword(s):  
Dna Sequences â—˝  
Species Complex â—˝  
Nuclear Dna â—˝  
Taxonomic Status â—˝  
Nominal Species â—˝  
Morphological Examination â—˝  
Closely Related Species â—˝  
A New Species â—˝  
Evolutionary Lineages â—˝  
Dune Area

The present paper constitutes a study on a taxonomically confusing group of closely related species belonging to the Malagasy skink genus Madascincus, currently encompassing the nominal species M. polleni, M. intermedius and M. stumpffi. Based on combined analyses of mitochondrial and nuclear DNA sequences (ND1 and RAG2 genes, respectively), and morphological examination, we provide evidence for the existence of at least four distinct evolutionary lineages within this complex: Madascincus stumpffi; Madascincus arenicola sp. nov. from northern Madagascar; and two cryptic species morphologically similar to the name-bearing types of M. polleni and M. intermedius. The two latter species, although genetically distinct, appear to be morphologically indistinguishable and their taxonomic status cannot be resolved until a better sampling will be available.

A new black fly species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from Sulawesi, Indonesia

Zootaxa â—˝  
2019 â—˝  
Vol 4651 (2) â—˝  
pp. 392-400
Author(s):  
HIROYUKI TAKAOKA â—˝  
MOHD SOFIAN-AZIRUN â—˝  
CHEE DHANG CHEN â—˝  
MUHAMMAD RASUL ABDULLAH HALIM â—˝  
KOON WENG LAU â—˝  
...  
Keyword(s):  
New Species â—˝  
Related Species â—˝  
Species Group â—˝  
Black Fly

Simulium (Gomphostilbia) marosense sp. nov. is described based on adults, pupae and mature larvae from Sulawesi, Indonesia. This new species is placed in the Simulium duolongum subgroup of the S. batoense species-group, representing the ninth member for the subgroup in Sulawesi. This new species is characterized by a narrow female frons and pupal gill with eight filaments, of which two filaments of the ventral pair are 1.9–3.0 times as long as the six other filaments. Taxonomic notes are provided to distinguish this new species from related species. 

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