scholarly journals Assessing Temporal Patterns and Species Composition of Glass Eel (Anguilla spp.) Cohorts in Sumatra and Java Using DNA Barcodes

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 193
Author(s):  
Arif Wibowo ◽  
Nicolas Hubert ◽  
Hadi Dahruddin ◽  
Dirk Steinke ◽  
Rezki Antoni Suhaimi ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Economic Value ◽  
Species Conservation ◽  
Dna Barcode ◽  
Temporal Patterns ◽  
Molecular Classification ◽  
Dna Barcodes ◽  
Glass Eel ◽  
Silver Eels ◽  
Glass Eels

Anguillid eels are widely acknowledged for their ecological and socio-economic value in many countries. Yet, knowledge regarding their biodiversity, distribution and abundance remains superficial—particularly in tropical countries such as Indonesia, where demand for anguillid eels is steadily increasing along with the threat imposed by river infrastructure developments. We investigated the diversity of anguillid eels on the western Indonesian islands of Sumatra and Java using automated molecular classification and genetic species delimitation methods to explore temporal patterns of glass eel cohorts entering inland waters. A total of 278 glass eels were collected from monthly samplings along the west coast of Sumatra and the south coast of Java between March 2017 and February 2018. An automated, DNA-based glass eel identification was performed using a DNA barcode reference library consisting of 64 newly generated DNA barcodes and 117 DNA barcodes retrieved from BOLD for all nine Anguilla species known to occur in Indonesia. Species delimitation methods converged in delineating eight Molecular Operational Taxonomic Units (MOTUs), with A. nebolusa and A. bengalensis being undistinguishable by DNA barcodes. A total of four MOTUs were detected within the glass eel samples, corresponding to Anguilla bicolor, A. interioris, A. marmorata, and A. nebulosa/A. bengalensis. Monthly captures indicated that glass eel recruitment peaks in June, during the onset of the dry season, and that A. bicolor is the most prevalent species. Comparing indices of mitochondrial genetic diversity between yellow/silver eels, originating from several sites across the species range distribution, and glass eels, collected in West Sumatra and Java, indicated a marked difference. Glass eels displayed a much lower diversity than yellow/silver eels. Implications for the management of glass eel fisheries and species conservation are discussed.

scholarly journals Revision of the genus Megacraspedus Zeller, 1839, a challenging taxonomic tightrope of species delimitation (Lepidoptera, Gelechiidae)

ZooKeys ◽  
2018 ◽  
Vol 800 ◽  
pp. 1-278 ◽  
Author(s):  
Peter Huemer ◽  
Ole Karsholt
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Dna Barcode ◽  
Single Species ◽  
Dna Barcodes ◽  
Female Adult ◽  
Phylogeographic History ◽  
Species Groups ◽  
Male Sex ◽  
Taxonomic Approach

The taxonomy of the Palearctic genusMegacraspedusZeller, 1839 (Lepidoptera, Gelechiidae) is revised, based on external morphology, genitalia and DNA barcodes. An integrative taxonomic approach supports the existence of 85 species which are arranged in 24 species groups (disputed taxa from other faunal regions are discussed). Morphology of all species is described and figured in detail. For 35 species both sexes are described; for 46 species only the male sex is reported, in one species the male is unknown, whereas in three species the female adult and/or genitalia morphology could not be analysed due to lack of material.DNA barcode sequences of the COI barcode fragment with > 500 bp were obtained from 264 specimens representing 62 species or about three-quarters of the species. Species delimitation is particularly difficult in a few widely distributed species with high and allegedly intraspecific DNA barcode divergence of nearly 14%, and with up to 23 BINs in a single species. Deep intraspecific or geographical splits in DNA barcode are frequently not supported by morphology, thus indicating a complex phylogeographic history or other unresolved molecular problems.The following 44 new species (22 of them from Europe) are described:Megacraspedusbengtssonisp. n.(Spain),M.junnilainenisp. n.(Turkey),M.similellussp. n.(Bulgaria, Romania, Turkey),M.golestanicussp. n.(Iran),M.tokarisp. n.(Croatia),M.nelisp. n.(France, Italy),M.faunierensissp. n.(Italy),M.gredosensissp. n.(Spain),M.bidentatussp. n.(Spain),M.fuscussp. n.(Spain),M.trineaesp. n.(Portugal, Spain),M.skouisp. n.(Spain),M.spinophallussp. n.(Spain),M.occidentellussp. n.(Portugal),M.granadensissp. n.(Spain),M.heckfordisp. n.(Spain),M.tenuiuncussp. n.(France, Spain),M.devoratorsp. n.(Bulgaria, Romania),M.brachypterissp. n.(Albania, Greece, Macedonia, Montenegro),M.barcodiellussp. n.(Macedonia),M.sumpichisp. n.(Spain),M.tabellisp. n.(Morocco),M.gallicussp. n.(France, Spain),M.libycussp. n.(Libya, Morocco),M.latiuncussp. n.(Kazahkstan),M.kazakhstanicussp. n.(Kazahkstan),M.knudlarsenisp. n.(Spain),M.tenuignathossp. n.(Morocco),M.glaberipalpussp. n.(Morocco),M.nupponenisp. n.(Russia),M.pototskiisp. n.(Kyrgyzstan),M.feminensissp. n.(Kazakhstan),M.kirgizicussp. n.(Afghanistan, Kazakhstan, Kyrgyzstan),M.ibericussp. n.(Portugal, Spain),M.steinerisp. n.(Morocco),M.gibeauxisp. n.(Algeria, Tunisia),M.multipunctellussp. n.(Turkey),M.teriolensissp. n.(Croatia, Greece, Italy, Slovenia),M.korabicussp. n.(Macedonia),M.skuleisp. n.(Spain),M.longivalvellussp. n.(Morocco),M.peslierisp. n.(France, Spain),M.pacificussp. n.(Afghanistan), andM.armatophallussp. n.(Afghanistan).NevadiaCaradja, 1920,syn. n.(homonym),CauloecistaDumont, 1928,syn. n.,ReichardtiellaFilipjev, 1931,syn. n., andVadeniaCaradja, 1933,syn. n.are treated as junior synonyms ofMegacraspedus. Furthermore the following species are synonymised:M.subdolellusStaudinger, 1859,syn. n.,M.tuttiWalsingham, 1897,syn. n., andM.grossisquammellusChrétien, 1925,syn. n. ofM.lanceolellus(Zeller, 1850);M.culminicolaLe Cerf, 1932,syn. n.ofM.homochroaLe Cerf, 1932;M.separatellus(Fischer von Röslerstamm, 1843),syn. n.andM.incertellusRebel, 1930,syn. n.ofM.dolosellus(Zeller, 1839);M.mareotidellusTurati, 1924,syn. n.ofM.numidellus(Chrétien, 1915);M.litovalvellusJunnilainen, 2010,syn. n.ofM.imparellus(Fischer von Röslerstamm, 1843);M.kaszabianusPovolný, 1982,syn. n.ofM.leuca(Filipjev, 1929);M.chretienella(Dumont, 1928),syn. n.,M.halfella(Dumont, 1928),syn. n., andM.arnaldi(Turati & Krüger, 1936),syn. n.ofM.violacellum(Chrétien, 1915);M.escalerellusSchmidt, 1941,syn. n.ofM.squalidaMeyrick, 1926.Megacraspedusribbeella(Caradja, 1920),comb. n.,M.numidellus(Chrétien, 1915),comb. n.,M.albella(Amsel, 1935),comb. n.,M.violacellum(Chrétien, 1915),comb. n., andM.grisea(Filipjev, 1931),comb. n.are newly combined inMegacraspedus.

Revision of the subgenus Phortica (sensu stricto) (Diptera, Drosophilidae) from East Asia, with assessment of species delimitation using DNA barcodes

Zootaxa ◽  
2019 ◽  
Vol 4678 (1) ◽  
pp. 1-75
Author(s):  
JIA HUANG ◽  
LU GONG ◽  
SHUN-CHERN TSAUR ◽  
LIN ZHU ◽  
KEYING AN ◽  
...  
Keyword(s):  
New Species ◽  
Cytochrome C Oxidase ◽  
Species Delimitation ◽  
Species Complex ◽  
Dna Barcode ◽  
Sensu Stricto ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Dna Barcodes ◽  
New Synonyms

A total of 50 (43 known and seven new) species in the subgenus Phortica (sensu stricto) were surveyed and (re)described from China: P. bicornuta (Chen & Toda, 1997); P. bipartita (Toda & Peng, 1992); P. biprotrusa (Chen & Toda, 1998); P. cardua (Okada, 1977); P. chi (Toda & Sidorenko, 1996); P. conifera (Okada, 1977); P. eparmata (Okada, 1977); P. eugamma (Toda & Peng, 1990); P. excrescentiosa (Toda & Peng, 1990); P. fangae (Máca, 1993); P. flexuosa (Zhang & Gan, 1986); P. foliata (Chen & Toda, 1997); P. gamma (Toda & Peng, 1990); P. gigas (Okada, 1977); P. glabtabula Chen & Gao, 2005; P. hainanensis (Chen & Toda, 1998); P. hongae (Máca, 1993); P. huazhii Cheng & Chen, 2008; P. iota (Toda & Sidorenko, 1996); P. jadete Zhu, Cao & Chen, 2018; P. kappa (Máca, 1977); P. lambda (Toda & Peng, 1990); P. latifoliacea Chen & Watabe, 2008; P. magna (Okada, 1960); P. okadai (Máca, 1977); P. omega (Okada, 1977); P. orientalis (Hendel, 1914); P. pangi Chen & Wen, 2005; P. paramagna (Okada, 1971); P. perforcipata (Máca & Lin, 1993); P. pi (Toda & Peng, 1990); P. protrusa (Zhang & Shi, 1997); P. pseudopi (Toda & Peng, 1990); P. pseudotau (Toda & Peng, 1990); P. psi (Zhang & Gan, 1986); P. rhagolobos Chen & Gao, 2008; P. saeta (Zhang & Gan, 1986); P. setitabula Chen & Gao, 2005; P. subradiata (Okada, 1977); P. tau (Toda & Peng, 1990); P. uncinata Chen & Gao, 2005; P. unipetala Chen & Wen, 2005; P. allomega Gong & Chen, sp. nov.; P. archikappa Gong & Chen, sp. nov.; P. dianzangensis Gong & Chen, sp. nov.; P. imbacilia Gong & Chen, sp. nov.; P. liukuni Gong & Chen, sp. nov.; P. tibeta Gong & Chen, sp. nov.; and P. xianfui Gong & Chen, sp. nov. In addition, seven new synonyms were recognized: P. acongruens (Zhang & Shi, 1997), syn. nov.; P. antillaria (Chen & Toda, 1997), syn. nov.; P. kukuanensis Máca, 2003, syn. nov.; P. linae (Máca & Chen, 1993), syn. nov.; P. shillongensis (Singh & Gupta, 1979), syn. nov.; P. takadai (Okada, 1977), syn. nov.; and P. watanabei (Máca & Lin, 1993), syn. nov. A key to all Asian species (except for the eparmata species complex) of this subgenus was provided. All currently available DNA barcode (partial mitochondrial cytochrome c oxidase subunit I (COI) gene) sequences of this subgenus (217 sequences of 54 species) are employed in a molecular analysis using different species delimitation methods. The results indicate that approximately 68.5% (37 of 54 spp.) of Phortica (s. str.) species could be clearly distinguished from closely related morphospecies or cryptic species. 

Testing three proposed DNA barcodes for the wood identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain

Holzforschung ◽  
2016 ◽  
Vol 70 (2) ◽  
pp. 127-136 ◽  
Author(s):  
Min Yu ◽  
Kai Liu ◽  
Liang Zhou ◽  
Lei Zhao ◽  
Shengquan Liu
Keyword(s):  
Economic Value ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
First Grade ◽  
Wood Identification ◽  
Dna Barcodes ◽  
Success Rates ◽  
Interspecific Differences ◽  
Dalbergia Odorifera ◽  
Dalbergia Tonkinensis

Abstract Dalbergia odorifera T. Chen is a first-grade state protected plant in China. However, it is difficult to distinguish it from the closely related species Dalbergia tonkinensis Prain, which is less important in economic value, by wood anatomical features. In this study, three potential DNA barcode sequences, namely rpoC1, trnH-psbA and internal transcribed spacer (ITS), were used to differentiate wood of D. odorifera from D. tonkinensis. The average quantities of DNA extracts from twigs, sapwood and heartwood were 16.3, 11.5 and 6.0 ng mg-1, respectively. The success rates for polymerase chain reaction (PCR) amplification for three loci, namely ITS, trnH-psbA and rpoC1, were 62.5, 100 and 81.25%, respectively. The success rate for bidirectional sequencing of amplified products was 100% for all the three loci. The identification power of the three proposed DNA barcodes has been calculated by the BLAST, tree-based method and the TAXONDNA method. The interspecific differences of the trnH-psbA region were greater than intraspecific variations. Moreover, the identification power of trnH-psbA was higher than that of ITS and rpoC1 regions at the species level. Finally, the trnH-psbA region is proposed as a DNA barcode for wood identification between D. odorifera and D. tonkinensis.

LSU rDNA D5 region: the DNA barcode for molecular classification and identification of Demodex

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 295-304 ◽  
Author(s):  
Li Hu ◽  
Yae Zhao ◽  
Yuanjun Yang ◽  
Dongling Niu ◽  
Rui Yang
Keyword(s):  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Its Region ◽  
Molecular Classification ◽  
Ribosomal Genes ◽  
Lsu Rdna ◽  
Dna Barcodes ◽  
Barcoding Gap ◽  
Demodex Folliculorum

Whether ribosomal genes can be used as DNA barcodes for molecular identification of Demodex (Acariformes: Demodicidae) is unclear. To examine this, Demodex folliculorum, D. brevis, D. canis, and D. caprae were collected for DNA extraction, rDNA fragments amplification, sequencing, and analysis. The V2 and V4 regions of SSU rDNA; D5, D6, and D8 regions of LSU rDNA; and ITS region were obtained from the four morphospecies. BLAST analysis showed that the obtained sequences matched those of Demodex or Aplonobia (Acariformes: Tetranychidae) in Raphignathae. Phylogenetic trees derived from V2, V4, D5, D6, and D8 regions, but not from ITS region, showed that the four species of Demodex clustered independently. Sequence divergence analysis further demonstrated that D5, D6, and D8 regions had obvious barcoding gap between intraspecific and interspecific divergences, with the gap of D5 (16.91%) larger than that of D6 (11.82%) and D8 (4.66%). The V2 and V4 regions did not have a barcoding gap, as the intraspecific and interspecific divergences partially overlapped. For the ITS region, intraspecific and interspecific divergences completely overlapped. These results suggest that the D5, D6, and D8 regions of LSU rDNA, especially D5, are suitable DNA barcodes for Demodex.

DNA barcodes of Plecoptera from China: The preliminary dataset and its performance in species delimitation

Zootaxa ◽  
2020 ◽  
Vol 4751 (2) ◽  
pp. 345-356 ◽  
Author(s):  
ZHI-TENG CHEN ◽  
CHAO JIANG ◽  
YUAN-SEN-YU LI
Keyword(s):  
Species Identification ◽  
Species Delimitation ◽  
Population Genetic ◽  
Life Stage ◽  
Dna Barcode ◽  
Genetic Distances ◽  
Species Number ◽  
Dna Barcodes ◽  
Gene Trees ◽  
Genetic Studies

The DNA barcodes of Chinese Plecoptera project has a goal to promote species identification, life stage association, systematic, conservation, biodiversity, and population genetic studies for stoneflies of China. In this study, we sequenced and analyzed 19 DNA barcode sequences belonging to 19 stonefly species, increasing the Chinese barcoded stonefly species number to 53. Genetic distances were calculated and the gene trees constructed, suggesting the efficiency of delimiting Chinese stonefly species using DNA barcodes. 

scholarly journals KEBIJAKAN TENTANG INTEGRASI AKTIVITAS PENANGKAPAN DENGAN PEMBUDIDAYAAN UNTUK KEBERLANJUTAN SUMBERDAYA IKAN SIDAT (Anguilla spp) DI DAS POSO

2015 ◽  
Vol 7 (1) ◽  
pp. 37
Author(s):  
Navy Novy Jefry Watupongoh ◽  
Krismono Krismono
Keyword(s):  
Economic Value ◽  
Environmentally Friendly ◽  
Glass Eel ◽  
River Damming ◽  
Fishing Gears ◽  
Glass Eels

<p>Daerah Aliran Sungai (DAS) Poso merupakan salah satu daerah penangkapan ikan sidat, memiliki luas 1.101,87 km2 dan panjang ± 68,70 km. Ikan sidat di perairan Poso merupakan komoditas perikanan yang memiliki nilai ekonomis tinggi (harga Rp.100.000,-/kg) dan menjadi primadona hasil tangkapan. Ikan sidat yang hidup di DAS Poso terdapat 5 jenis, yaitu A. marmorata, A. bicolor pasific, A. celebensis, A. borneensis dan A. interioris. Saat ini telah terjadi penurunan produksi induk maupun glass eel ikan sidat di DAS Poso disebabkan oleh penangkapan yang belum memperhatikan faktor kelestarian dan keberlajutannya seperti penangkapan yang berlangsung tidak hanya pada saat induk ikan sidat yang beruaya ke laut tapi juga glas eel yang menuju ke danau. Pembangunan PLTA pada alur Sungai Poso mengganggu ruaya ikan sidat yang mengakibatkan terputusnya ruaya ikan sidat dari dan ke Danau Poso yang berakibat hilangnya ikan sidat di Danau Poso. Berkaitan dengan permasalahan ini maka populasi sumberdaya ikan sidat perlu dijaga keberlanjutannya dengan cara mengintegrasikan aktivitas penangkapan dengan pembudidayaan, oleh karena itu diperlukan kebijakan yang menetapkan peraturan terkait dengan penangkapan yang menggunakan alat tangkap ramah lingkungan serta diintegrasikan dengan pembudidayaan. Kajian kebijakan ini bertujuan untuk merumuskan kebijakan tentang integrasi aktivitas penagkapan dengan pembudidayaan untuk berkelanjutan ikan sidat di DAS Poso.</p><p> </p><p>The watershed of Poso River is one of anguillid eel fishing areas. This watershed has an area of 1,101.87 km2 and length ± 68.70 miles. The anguillid eel is a commodity that has a high economic value (IDR 100,000 / kg) and has an excellent catches. There are 5 types of eels that live in the watershed of Poso, they are: A. marmorata, A. bicolor pacific, A. celebensis, A. borneensis and A. interioris. The decreased production of anguillid parent and glass eels in the watershed of Poso is a result from the capture that had not yet noticed the preservation and sustainability factors, such as the capture that took place not only at the time of sea migration phase (the parents), but also on the lake migration phase (the glass eels), as well as Poso river damming for hydropower purpose. The decrease in the production of glass eel and parent eels in the watershed of Poso is also caused by fishing activities that have not been integrated with cultivation. There is a need of a regulation for fishing by using environmentally friendly fishing gears as well as the integration with cultivation. This paper aims to formulate policy on integration of capture and cultivation for sustainable catch of anguillid eels in the watershed of Poso.</p>

The Value of Private Non-Industrial Forestland for Wildlife Species Conservation

EDIS ◽  
2017 ◽  
Vol 2017 (3) ◽  
Author(s):  
Shelly A. Johnson ◽  
Timm Kroeger ◽  
Josh Horn ◽  
Alison E. Adams ◽  
Damian C. Adams
Keyword(s):  
Animal Species ◽  
Human Life ◽  
Economic Value ◽  
Species Conservation ◽  
Fact Sheet ◽  
Monetary Value ◽  
Wildlife Species ◽  
Wildlife Viewing ◽  
Animal Habitat

Animals in Florida provide a variety of benefits to people, from recreation (fishing, hunting, or wildlife viewing) to protection of human life and property (oysters and corals provide reef structures that help protect coasts from erosion and flooding). By measuring the economic value of these benefits, we can assign a monetary value to the habitats that sustain these species and assess the value that is lost when development or other human-based activities degrade animal habitat. This 5-page fact sheet presents the results of a study that assessed the value of protecting five animal species in Florida and showed the economic value of protecting animal habitat.

DNA Barcoding and Phylogenetic Analysis Sugarcane (Saccharum officinarum L.) Based on matK ( maturase K) Gene

2020 ◽  
Vol 840 ◽  
pp. 162-170
Author(s):  
Ganies Riza Aristya ◽  
Fauzana Putri ◽  
Rina Sri Kasiamdari ◽  
Arni Musthofa
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Level ◽  
Economic Value ◽  
Saccharum Officinarum ◽  
Saccharum Spontaneum ◽  
Dna Barcodes ◽  
Pcr Method ◽  
Hybrid Cultivar ◽  
I Gene ◽  
Sequencing Process

Sugarcane (Saccharum officinarum L.) is an agricultural commodities with a great extent of diversity and high economic value. In Indonesia, the great extent of diversity of sugarcane is evidenced by a large number of cultivars cultivated. Sugarcane diversities at the molecular level can be seen using DNA barcodes, one of which is the matK. The purpose of the study was to identify and characterize matK and reconstruct the phylogenetic tree to determine the phylogeny of 24 sugarcane cultivars Indonesia. matK was amplified using the PCR method with matK F-5’ATGATTAATTAAGAGTAAGAGGAT-3’ and matK R-5’AATGCAAAAATTCGAAGGGT-3. Results showed that the matK gene was successfully amplified as many as 1531 bp. The sequencing process was done to determine the nucleotide sequence and compared with those of the GenBank database. It showed that the samples used had a similarity of 98.87%-99.44% to that of matK in Saccharum officinarum, Saccharum hybrid cultivar and Saccharum spontaneum. Reconstruction of the phylogenetic tree showed that the samples used were located in the same clade with a zero genetic distance, while all the references from NCBI were also located in the same clade. The analysis of genetic variation indicated that it had no haplotype value.

Challenges to quantifying glass eel abundance from large and dynamic estuaries

2017 ◽  
Vol 75 (2) ◽  
pp. 727-737 ◽  
Author(s):  
Sarah Walmsley ◽  
Julie Bremner ◽  
Alan Walker ◽  
Jon Barry ◽  
David Maxwell
Keyword(s):  
Large Scale ◽  
Anguilla Anguilla ◽  
Commercial Fishing ◽  
European Eel ◽  
Estuarine System ◽  
Glass Eel ◽  
The North ◽  
Adequate Sampling ◽  
South Shore ◽  
Glass Eels

Abstract European eel Anguilla anguilla recruitment into the rivers of the northeastern Atlantic has declined substantially since the 1980s. Monitoring of recruiting juveniles, or glass eels, is usually undertaken in small estuaries and rivers. Sampling of large-scale estuaries is rare, due to the size of the sampling area and the resources needed to provide adequate sampling levels. Here we describe surveys for glass eels in the UK’s largest estuarine system, the Severn Estuary/Bristol Channel. We sampled across a 20 km-wide stretch of the estuary in 2012 and 2013, using a small-meshed net deployed from a commercial fishing trawler, and the surveys yielded over 2500 glass eels. Eels were more abundant in the surface layer (0–1.4 m depth) than at depth (down to 8.4 m depth), were more abundant close to the south shore than along the north shore or middle of the estuary, and were more abundant in lower salinity water. Numbers were higher in the second year than in the first and eels were more abundant in February than April. The difficulties and logistics of sampling in such a large estuary are discussed, along with the level of resources required to provide robust estimates of glass eel abundance.

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