Integrating DNA barcodes and morphology for species delimitation in theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae)

2013 ◽  
Vol 104 (1) ◽  
pp. 65-78 ◽  
Author(s):  
F.L. Silva ◽  
S. Wiedenbrug

AbstractIn this study, we use DNA barcodes for species delimitation to solve taxonomic conflicts in 86 specimens of 14 species belonging to theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae), from the Atlantic Forest, Brazil. Molecular analysis of cytochrome c-oxidase subunit I (COI) gene sequences supported 14 cohesive species groups, of which two similar groups were subsequently associated with morphological variation at the pupal stage. Eleven species previously described based on morphological criteria were linked to DNA markers. Furthermore, there is the possibility that there may be cryptic species within theCorynoneuragroup, since one group of species presented internal grouping, although no morphological divergence was observed. Our results support DNA-barcoding as an excellent tool for species delimitation in groups where taxonomy by means of morphology is difficult or even impossible.

2013 ◽  
Vol 145 (6) ◽  
pp. 589-602 ◽  
Author(s):  
Fabio Laurindo da Silva ◽  
Torbjørn Ekrem ◽  
Alaide Aparecida Fonseca-Gessner

AbstractIn this study, we analysed the applicability of DNA barcodes for delimitation of 79 specimens of 13 species of nonbiting midges in the subfamily Tanypodinae (Diptera: Chironomidae) from São Paulo State, Brazil. Our results support DNA barcoding as an excellent tool for species identification and for solving taxonomic conflicts in genusLabrundinia.Molecular analysis of cytochrome c oxidase subunit I (COI) gene sequences yielded taxon identification trees, supporting 13 cohesive species clusters, of which three similar groups were subsequently linked to morphological variation at the larval and pupal stage. Additionally, another cluster previously described by means of morphology was linked to molecular markers. We found a distinct barcode gap, and in some species substantial interspecific pairwise divergences (up to 19.3%) were observed, which permitted identification of all analysed species. The results also indicated that barcodes can be used to associate life stages of chironomids since COI was easily amplified and sequenced from different life stages with universal barcode primers.


Zootaxa ◽  
2008 ◽  
Vol 1839 (1) ◽  
pp. 1 ◽  
Author(s):  
MANUEL ELÍAS-GUTIÉRREZ ◽  
FERNANDO MARTÍNEZ JERÓNIMO ◽  
NATALIA V. IVANOVA ◽  
MARTHA VALDEZ-MORENO ◽  
PAUL D. N. HEBERT

DNA barcoding, based on sequence diversity in the mitochondrial COI gene, has proven an excellent tool for identifying species in many animal groups. Here, we report the first barcode studies for freshwater zooplankton from Mexico and Guatemala and discuss the taxonomic and biological implications of this work. Our studies examined 61 species of Cladocera and 21 of Copepoda, about 40% of the known fauna in this region. Sequence divergences among conspecific individuals of cladocerans and copepods averaged 0.82% and 0.79%, respectively, while sequence divergences among congeneric taxa were on average 15-20 times as high. Barcodes were successful in discriminating all species in our study, but sequences for Mexican Daphnia exilis overlapped with those of D. spinulata from Argentina. Our barcode data revealed evidence of many species overlooked by current classification systems —for example, based on COI genotypes the Diapahanosoma birgei group appears to include 5 species, while Ceriodaphnia cf. rigaudi, Moina cf. micrura, Mastigodiaptomus albuquerquensis and Mastigodiaptomus reidae all include 2–3 taxa. The barcode results support recent taxonomic revisions, such as recognition of the genus Leberis, and the presence of several species in the D. birgei and Chydorus sphaericus complexes. The present results indicate that DNA barcoding will provide powerful new insights into both the incidence of cryptic species and a better understanding of zooplankton distributions, aiding evaluation of the factors influencing competitive outcomes, and the colonization of aquatic environments.


ZooKeys ◽  
2018 ◽  
Vol 800 ◽  
pp. 1-278 ◽  
Author(s):  
Peter Huemer ◽  
Ole Karsholt

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.


Zootaxa ◽  
2019 ◽  
Vol 4678 (1) ◽  
pp. 1-75
Author(s):  
JIA HUANG ◽  
LU GONG ◽  
SHUN-CHERN TSAUR ◽  
LIN ZHU ◽  
KEYING AN ◽  
...  

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. 


Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 348-357 ◽  
Author(s):  
Luis M. Hernández-Triana ◽  
Fernanda Montes De Oca ◽  
Sean W.J. Prosser ◽  
Paul D.N. Hebert ◽  
T. Ryan Gregory ◽  
...  

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.


ZooKeys ◽  
2021 ◽  
Vol 1034 ◽  
pp. 1-163
Author(s):  
Jianshuang Zhang ◽  
Hao Yu ◽  
Shuqiang Li

Spiders of the genus Clubiona Latreille, 1804 from Xishuangbanna, Yunnan Province, China are studied. A total of 47 species is reported and illustrated, including 14 new species and two new synonyms. Twelve of the new species belong to four species groups: C. dengpao Yu & Li, sp. nov., C. subdidentata Yu & Li, sp. nov., C. tixing Yu & Li, sp. nov., C. xiaoci Yu & Li, sp. nov., C. xiaokong Yu & Li, sp. nov., C. yejiei Yu & Li, sp. nov., C. zhaoi Yu & Li, sp. nov. and C. zhigangi Yu & Li, sp. nov. from the C. corticalis group; C. mii Yu & Li, sp. nov. and C. subtongi Yu & Li, sp. nov. from the C. ternatensis group; C. banna Yu & Li, sp. nov. from the C. filicata group; and C. menglun Yu & Li, sp. nov. from the C. trivialis group. The remaining two new species, C. shuangsi Yu & Li, sp. nov. and C. wangchengi Yu & Li, sp. nov., are not readily assignable to any of the existing species groups. The female of C. cochlearis Yu & Li, 2019, the female of C. tiane Yu & Li, 2019, the female of C. bicornis Yu & Li, 2019, the male of C. lala Jäger & Dankittipakul, 2010 and the true female of C. suthepica Dankittipakul, 2008 are described for the first time. Two new synonyms are: C. vukomi Jäger & Dankittipakul, 2010 syn. nov. = C. circulata Zhang & Yin, 1998; C. melanothele Thorell, 1895 syn. nov. = Clubiona melanosticta Thorell, 1890. A checklist of Clubiona species from Xishuangbanna is provided. The DNA barcodes of almost all of the species were obtained for species delimitation, matching of sexes and future use.


2020 ◽  
Author(s):  
Andrea Galimberti ◽  
Giacomo Assandri ◽  
Davide Maggioni ◽  
Fausto Ramazzotti ◽  
Daniele Baroni ◽  
...  

AbstractThe Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference datasets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658 bp 5’ end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the dataset to 1294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC, bGMYC) methods were used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct Molecular Operational Units, whereas the remaining ones were classified as ‘warnings’ (i.e., showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped in three categories depending on if they showed low, high, or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic, and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.


Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1995
Author(s):  
Teresa Fernandes Silva-do-Nascimento ◽  
Jordi Sánchez-Ribas ◽  
Tatiane M. P. Oliveira ◽  
Brian Patrick Bourke ◽  
Joseli Oliveira-Ferreira ◽  
...  

Identifying the species of the subfamily Anophelinae that are Plasmodium vectors is important to vector and malaria control. Despite the increase in cases, vector mosquitoes remain poorly known in Brazilian indigenous communities. This study explores Anophelinae mosquito diversity in the following areas: (1) a Yanomami reserve in the northwestern Amazon Brazil biome and (2) the Pantanal biome in southwestern Brazil. This is carried out by analyzing cytochrome c oxidase (COI) gene data using Refined Single Linkage (RESL), Assemble Species by Automatic Partitioning (ASAP), and tree-based multi-rate Poisson tree processes (mPTP) as species delimitation approaches. A total of 216 specimens collected from the Yanomami and Pantanal regions were sequenced and combined with 547 reference sequences for species delimitation analyses. The mPTP analysis for all sequences resulted in the delimitation of 45 species groups, while the ASAP analysis provided the partition of 48 groups. RESL analysis resulted in 63 operational taxonomic units (OTUs). This study expands our scant knowledge of anopheline species in the Yanomami and Pantanal regions. At least 18 species of Anophelinae mosquitoes were found in these study areas. Additional studies are now required to determine the species that transmit Plasmodium spp. in these regions.


2018 ◽  
Vol 8 (1) ◽  
pp. 222-232 ◽  
Author(s):  
R. V. Yakovlev ◽  
N. A. Shapoval ◽  
G. N. Kuftina ◽  
A. V. Kulak ◽  
S. V. Kovalev

The Proclossiana eunomia (Esper, 1799) complex is currently composed of the several subspecies distributed throughout Palaearсtic region and North America. Despite the fact that some of the taxa have differences in wing pattern and body size, previous assumptions on taxonomy not supported by molecular data. Therefore, the identity of certain populations of this complex has remained unclear and the taxonomic status of several recently described taxa is debated. Here, we provide insights into systematics of some Palaearctic members of this group using molecular approach, based on the analysis of the barcoding fragment of the COI gene taking into account known morphological differences.


Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 290
Author(s):  
Hua-Yan Chen ◽  
Hong-Liang Li ◽  
Hong Pang ◽  
Chao-Dong Zhu ◽  
Yan-Zhou Zhang

The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is an emerging invasive insect pest in China. Hymenopteran parasitoids are the key organisms for suppressing populations of P. solenopsis in the field, and therefore could be used as biological agents. Accurate identification of the associated parasitoids is the critical step to assess their potential role in biological control. In this study, we facilitated the identification of the parasitoid composition of P. solenopsis using an integrated approach of species delimitation, combining morphology with molecular data. Eighteen Hymenoptera parasitoid species belonging to 11 genera of four families are recognized based on morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene and the 28S rDNA using the automatic barcode gap discovery (ABGD) and the Bayesian Poisson tree processes model (bPTP). Among these species, eight species are primary parasitoids with Aenasius arizonensis (Girault) (Hymenoptera: Encyrtidae) being the dominant taxon, while the other 10 species are probably hyperparasitoids, with a prevalence of Cheiloneurus nankingensis Li & Xu (Hymenoptera: Encyrtidae). These results indicate that parasitoid wasps associated with P. solenopsis from China are diverse and the integrated taxonomic approach applied in this study could enhance the accurate identification of these parasitoids that should be assessed in future biological control programs.


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