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Journal articles on the topic 'GMYC analysis'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Bergsten, Johannes, Elisabeth Weingartner, and Jiří Hájek. "Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae)." ZooKeys 678 (June 6, 2017): 73–96. https://doi.org/10.3897/zookeys.678.12886.

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The species status of Hyphydrus anatolicus Guignot, 1957 and H. sanctus Sharp, 1882, previously often confused with the widespread H. ovatus (Linnaeus, 1760), are tested with molecular and morphological characters. Cytochrome c oxidase subunit 1 (CO1) was sequenced for 32 specimens of all three species. Gene-trees were inferred with parsimony, time-free bayesian and strict clock bayesian analyses. The GMYC model was used to estimate species limits. All three species were reciprocally monophyletic with CO1 and highly supported. The GMYC species delimitation analysis unequivocally delimited the

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2

Bai, Qikun, Lili Wang, Zongqing Wang, Nathan Lo, and Yanli Che. "Exploring the diversity of Asian Cryptocercus (Blattodea : Cryptocercidae): species delimitation based on chromosome numbers, morphology and molecular analysis." Invertebrate Systematics 32, no. 1 (2018): 69. http://dx.doi.org/10.1071/is17003.

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Woodroaches from the genus Cryptocercus Scudder, 1862 are known to display low levels of morphological divergence, yet significant genetic divergence and variability in chromosome number. Compared with Cryptocercus taxa from North America, the diversity of the genus in Asia has received relatively little attention. We performed morphological and karyotypic examinations of multiple taxa from several previously unsampled mountainous areas of central and south-western China, and identified nine candidate species primarily on the basis of chromosome number. We then investigated diversity across al

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HRIVNIAK, ĽUBOŠ, PAVEL SROKA, GENCER TÜRKMEN, ROMAN J. GODUNKO, and NİLGÜN KAZANCI. "A new Epeorus (Caucasiron) (Ephemeroptera: Heptageniidae) species from Turkey based on molecular and morphological evidence." Zootaxa 4550, no. 1 (2019): 58. http://dx.doi.org/10.11646/zootaxa.4550.1.2.

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Epeorus (Caucasiron) turcicus sp. nov. is described based on larvae from NE Turkey. The new species can be distinguished from other Caucasiron by a unique combination of several diagnostic characters: the presence of a rounded hypodermal medial femur spot, colouration of abdominal terga and sterna, narrow gill plate VII, fine hair-like setae on the surface of abdominal terga, and absence of postero-lateral projections on tergum X. In addition to morphological analysis, two single-locus analytical approaches are employed for delimiting the new species using COI sequences (Automatic Barcode Gap

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4

Yuan, Jiao Jiao, Dan Chen, and Xia Wan. "A multilocus assessment reveals two new synonymies for East Asian Cyclommatus stag beetles (Coleoptera, Lucanidae)." ZooKeys 1021 (March 2, 2021): 65–79. http://dx.doi.org/10.3897/zookeys.1021.58832.

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Cyclommatus scutellaris Möllenkamp, 1912, Cyclommatus elsae Kriesche, 1921 and Cyclommatus tamdaoensis Fujita, 2010 are East Asian stag beetle species with long-debated taxonomic relationships due to high intraspecific morphological variability. In this study, we applied multilocus phylogenetic analyses to reassess their relationships. Two mitochondrial genes (16S rDNA, COI) and two nuclear genes (28S rDNA, Wingless) were used to reconstruct the phylogeny through the Bayesian inference (BI) and Maximum Likelihood (ML) methods. Both topologies supported two clades: the clade C. scutellaris was

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Wang, X. B., J. Deng, J. T. Zhang, Q. S. Zhou, Y. Z. Zhang, and S. A. Wu. "DNA barcoding of common soft scales (Hemiptera: Coccoidea: Coccidae) in China." Bulletin of Entomological Research 105, no. 5 (2015): 545–54. http://dx.doi.org/10.1017/s0007485315000413.

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AbstractThe soft scales (Hemiptera: Coccoidea: Coccidae) are a group of sap-sucking plant parasites, many of which are notorious agricultural pests. The quarantine and economic importance of soft scales necessitates rapid and reliable identification of these taxa. Nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene (barcoding region) and 28S rDNA were generated from 340 individuals of 36 common soft scales in China. Distance-based [(best match, Automated Barcode Gap Discovery (ABGD)], tree-based (neighbor-joining, Bayesian inference), Klee diagrams, and general

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Payo, Dioli Ann, Frederik Leliaert, Heroen Verbruggen, Sofie D'hondt, Hilconida P. Calumpong, and Olivier De Clerck. "Extensive cryptic species diversity and fine-scale endemism in the marine red alga Portieria in the Philippines." Proceedings of the Royal Society B: Biological Sciences 280, no. 1753 (2013): 20122660. http://dx.doi.org/10.1098/rspb.2012.2660.

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We investigated species diversity and distribution patterns of the marine red alga Portieria in the Philippine archipelago. Species boundaries were tested based on mitochondrial, plastid and nuclear encoded loci, using a general mixed Yule-coalescent (GMYC) model-based approach and a Bayesian multilocus species delimitation method. The outcome of the GMYC analysis of the mitochondrial encoded cox 2-3 dataset was highly congruent with the multilocus analysis. In stark contrast with the current morphology-based assumption that the genus includes a single, widely distributed species in the Indo-W

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7

Yuan, Jiao Jiao, Dan Chen, and Xia Wan. "A multilocus assessment reveals two new synonymies for East Asian Cyclommatus stag beetles (Coleoptera, Lucanidae)." ZooKeys 1021 (March 2, 2021): 65–79. https://doi.org/10.3897/zookeys.1021.58832.

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Cyclommatus scutellaris Möllenkamp, 1912, Cyclommatus elsae Kriesche, 1921 and Cyclommatus tamdaoensis Fujita, 2010 are East Asian stag beetle species with long-debated taxonomic relationships due to high intraspecific morphological variability. In this study, we applied multilocus phylogenetic analyses to reassess their relationships. Two mitochondrial genes (16S rDNA, COI) and two nuclear genes (28S rDNA, Wingless) were used to reconstruct the phylogeny through the Bayesian inference (BI) and Maximum Likelihood (ML) methods. Both topologies supported two clades: the clade C. scutellaris was

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8

He, Jia-Jun, Du-Ting Jin, Yi-Shu Wang, Yan-Li Che, and Zong-Qing Wang. "Species delimitation of Margattea cockroaches from China, with seven new species (Blattodea, Ectobiidae, Pseudophyllodromiinae)." ZooKeys 1036 (May 10, 2021): 121–51. http://dx.doi.org/10.3897/zookeys.1036.63232.

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Nearly 450 Margattea specimens were collected from 27 locations in China and their morphology was examined. Then 68 Margattea COI sequences were obtained and used to carry out phylogenetic analyses as well as species delimitation analyses using General Mixed Yule Coalescent (GMYC), Automatic Barcode Gap Discovery (ABGD), and Poisson Tree Processes (bPTP). GMYC analysis resulted in 21 molecular operational taxonomic units (MOTUs) (confidence interval: 20–22), which was completely consistent with the result of the bPTP. There were 15 MOTUs using the ABGD method. The number of MOTUs was slightly

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He, Jia-Jun, Du-Ting Jin, Yi-Shu Wang, Yan-Li Che, and Zong-Qing Wang. "Species delimitation of Margattea cockroaches from China, with seven new species (Blattodea, Ectobiidae, Pseudophyllodromiinae)." ZooKeys 1036 (May 10, 2021): 121–51. https://doi.org/10.3897/zookeys.1036.63232.

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Nearly 450 Margattea specimens were collected from 27 locations in China and their morphology was examined. Then 68 Margattea COI sequences were obtained and used to carry out phylogenetic analyses as well as species delimitation analyses using General Mixed Yule Coalescent (GMYC), Automatic Barcode Gap Discovery (ABGD), and Poisson Tree Processes (bPTP). GMYC analysis resulted in 21 molecular operational taxonomic units (MOTUs) (confidence interval: 20–22), which was completely consistent with the result of the bPTP. There were 15 MOTUs using the ABGD method. The number of MOTUs was slightly

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10

Zhu, Xi-Chao, Jing Chen, Rui Chen, Li-Yun Jiang, and Ge-Xia Qiao. "DNA barcoding and species delimitation of Chaitophorinae (Hemiptera, Aphididae)." ZooKeys 656 (February 14, 2017): 25–50. https://doi.org/10.3897/zookeys.656.11440.

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Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process). The genetic in

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Larson, Eric R., Magalie Castelin, Bronwyn W. Williams, Julian D. Olden, and Cathryn L. Abbott. "Phylogenetic species delimitation for crayfishes of the genusPacifastacus." PeerJ 4 (April 18, 2016): e1915. http://dx.doi.org/10.7717/peerj.1915.

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Molecular genetic approaches are playing an increasing role in conservation science by identifying biodiversity that may not be evident by morphology-based taxonomy and systematics. So-called cryptic species are particularly prevalent in freshwater environments, where isolation of dispersal-limited species, such as crayfishes, within dendritic river networks often gives rise to high intra- and inter-specific genetic divergence. We apply here a multi-gene molecular approach to investigate relationships among extant species of the crayfish genusPacifastacus, representing the first comprehensive

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Yang, Rong, Zhenzhen Wang, Yanshuang Zhou, Zongqing Wang, and Yanli Che. "Establishment of six new Rhabdoblatta species (Blattodea, Blaberidae, Epilamprinae) from China." ZooKeys 851 (June 3, 2019): 27–69. http://dx.doi.org/10.3897/zookeys.851.31403.

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This study examined 504 Rhabdoblatta specimens sampled from China, of which, 86 Rhabdoblatta specimens were used for COI sequencing. A phylogenetic analysis using the ML method and MOTUs estimations by ABGD and GMYC based on COI sequences was performed. Eighteen Rhabdoblatta species were identified when these data were combined with morphological data. Six new species were established among these samples, i.e., Rh.similsinuatasp. n., Rh.densimaculatasp. n., Rh.gyroflexasp. n., Rh.chaulformissp. n., Rh.maculatasp. n., and Rh.ecarinatasp. n. For the first time, females including female genitalia

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13

Zhou, Li Yang, Zhi Hong Zhan, Xue Li Zhu, and Xia Wan. "Multilocus phylogeny and species delimitation suggest synonymies of two Lucanus Scopoli, 1763 (Coleoptera, Lucanidae) species names." ZooKeys 1135 (December 14, 2022): 139–55. https://doi.org/10.3897/zookeys.1135.89257.

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Phylogenetic relationsships of four nominal Lucanus Scopoli, 1763 species, L. swinhoei Parry, 1874, L. continentalis Zilioli, 1998, L. liuyei Huang & Chen, 2010, and L. wuyishanensis Schenk, 1999, are assessed based on mitochondrial (16S rDNA, COI) and nuclear (28S rDNA, Wingless) genes. The genetic distance is 0.0072 between L. swinhoei and L. continentalis, and 0.0094 between L. wuyishanensis and L. liuyei. Three species-delimitation approaches (ABGD, PTP, and GMYC) consistently showed L. swinhoei + L. continentalis and L. wuyishanensis + L. liuyei as two MOTUs. A new synonymy, L. liuyei

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Yang, Rong, Zhenzhen Wang, Yanshuang Zhou, Zongqing Wang, and Yanli Che. "Establishment of six new Rhabdoblatta species (Blattodea, Blaberidae, Epilamprinae) from China." ZooKeys 851 (June 3, 2019): 27–69. https://doi.org/10.3897/zookeys.851.31403.

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This study examined 504 Rhabdoblatta specimens sampled from China, of which, 86 Rhabdoblatta specimens were used for COI sequencing. A phylogenetic analysis using the ML method and MOTUs estimations by ABGD and GMYC based on COI sequences was performed. Eighteen Rhabdoblatta species were identified when these data were combined with morphological data. Six new species were established among these samples, i.e., Rh. similsinuata sp. n., Rh. densimaculata sp. n., Rh. gyroflexa sp. n., Rh. chaulformis sp. n., Rh. maculata sp. n., and Rh. ecarinata sp. n. For the first time, females including fema

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15

Zhou, Haoyue, Ding Yang, and Xuankun Li. "Integrated Taxonomy Discovers Four New Species of Grypoctonus Speiser, 1928 (Diptera: Asilidae) from China." Insects 16, no. 7 (2025): 722. https://doi.org/10.3390/insects16070722.

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The genus Grypoctonus Speiser, 1928 (Diptera: Asilidae) is a fuzzy-looking assassin fly, and adults have only been observed in autumn and winter. Currently containing four described species, this genus is readily distinguished from other Chinese asilids by the presence of two r-m crossveins. Through integrative taxonomic analysis of over 200 specimens from multiple Chinese provinces, we combined morphological assessment with DNA barcoding and four species delimitation methods (ABGD, ASAP, mPTP, and GMYC). Four species are newly described: G. aureus sp. nov., G. sagittatus sp. nov., G. solarius

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Luna-Ramirez, Karen, Adam D. Miller, and Gordana Rašić. "Genetic and morphological analyses indicate that the Australian endemic scorpionUrodacus yaschenkoi(Scorpiones: Urodacidae) is a species complex." PeerJ 5 (January 17, 2017): e2759. http://dx.doi.org/10.7717/peerj.2759.

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BackgroundAustralian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpionUrodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom.MethodsWe employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using uniqu

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KULLANDER, SVEN, MICHAEL NORÉN, MD MIZANUR RAHMAN, and ABDUR ROB MOLLAH. "Chameleonfishes in Bangladesh: hipshot taxonomy, sibling species, elusive species, and limits of species delimitation (Teleostei: Badidae)." Zootaxa 4586, no. 2 (2019): 301. http://dx.doi.org/10.11646/zootaxa.4586.2.7.

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Five species of Badidae are reported from Bangladesh, with morphological diagnoses and mitochondrial DNA sequences (cytochrome b, cytb; and cytochrome c oxidase subunit I, coi). Dario kajal is recorded from Bangladesh for the first time with a precise locality. Badis badis is reported from several localities in central Bangladesh. Badis chittagongis is redescribed on the basis of samples from the region of Cox′s Bazar, including Maheskhali Island. Badis pallidus, new species, is described from the Sangu and Karnafuli River drainages in Bangladesh. It is most similar to B. chittagongis, but dif

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Yang, Guangju, Wenjing Wang, Yuwei Tong, and Zhijun Zhou. "Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera)." ZooKeys 1229 (February 24, 2025): 25–42. https://doi.org/10.3897/zookeys.1229.129123.

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DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5’ end of the mitochondrial cytochrome c oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Units (MO

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Yang, Guangju, Wenjing Wang, Yuwei Tong, and Zhijun Zhou. "Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera)." ZooKeys 1229 (February 24, 2025): 25–42. https://doi.org/10.3897/zookeys.1229.129123.

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DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5' end of the mitochondrial cytochrome <i>c</i> oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Un

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Scheffrahn, Rudolf H., and Tiago F. Carrijo. "Three new species of Rugitermes (Isoptera, Kalotermitidae) from Peru and Bolivia." ZooKeys 1000 (December 3, 2020): 31–44. https://doi.org/10.3897/zookeys.1000.59219.

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The soldier of Rugitermes aridus sp. nov. is described from a xeric, termite-depauperate region of central Peru. Rugitermes rufus sp. nov. and R. volcanensis sp. nov. are described from soldiers and dealated imagos collected in a mesic forest of Amboró National Park in western Bolivia. The imago of R. rufus is unique among all described Rugitermes species in that the head capsule is reddish orange and the pronotum is brown. The imago head and pronotum are both brown in R. volcanensis. A phylogenetic and GMYC barcode analyses were performed with the COI gene. These analyses confirmed the three

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Pino-Bodas, Raquel, Alberto Herrero, André Aptroot, Ulrik Søchting, Richard Troy McMullin, and Ana Rosa Burgaz. "Phylogenetic study of the Cladonia cervicornis group (Cladoniaceae, Lecanorales) discloses a new species, Cladonia teuvoana." Lichenologist 56, no. 5 (2024): 237–58. https://doi.org/10.1017/s0024282924000276.

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AbstractThe Cladonia cervicornis group comprises lichen-forming fungi characterized by having scyphi with central proliferations. It includes c. 20 species globally. The taxonomy of this group is poorly resolved, with many species not thoroughly disentangled. The focus of this study is the European species in the C. cervicornis group. In order to estimate the phylogenetic relationships of these species, six loci were used: ITS rDNA, IGS rDNA, RPB1, RPB2, ef1α and cox1. Species delimitation methods (ASAP, PTP and GMYC) were used to infer the species boundaries based on four loci, ITS rDNA, IGS

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Khodami, Sahar, Pedro Martinez Arbizu, Sabine Stöhr, and Silke Laakmann. "Molecular Species Delimitation of Icelandic Brittle Stars (Ophiuroidea)." Polish Polar Research 35, no. 2 (2014): 243–60. http://dx.doi.org/10.2478/popore-2014-0011.

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Abstract Brittle stars (Echinodermata: Ophiuroidea) comprise over 2, 000 species, all of which inhabit marine environments and can be abundant in the deep sea. Morphological plasticity in number and shape of skeletal parts, as well as variable colors, can complicate correct species identification. Consequently, DNA sequence analysis can play an important role in species identification. In this study we compared the genetic variability of the mitochondrial cytochrome c subunit I gene (COI) and the nuclear small subunit ribosomal DNA (SSU, 18S rDNA) to morphological identification of 66 specimen

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Ekimova, Irina, Yury Deart, Tatiana Antokhina, Anna Mikhlina, and Dimitry Schepetov. "Stripes Matter: Integrative Systematics of Coryphellina rubrolineata Species Complex (Gastropoda: Nudibranchia) from Vietnam." Diversity 14, no. 4 (2022): 294. http://dx.doi.org/10.3390/d14040294.

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Coryphellina rubrolineata (Gastropoda: Nudibranchia: Flabellinidae) was believed to be a widespread tropical species demonstrating high diversity in external and internal morphological traits. In this paper, we perform an integrative analysis of the C. rubrolineata species complex based on samples collected in Vietnam waters, combined with available data from other localities of the Indo-West Pacific. The methods of the study include morphological analysis of external and internal traits using light and scanning electron microscopy and the molecular analysis of four markers (COI, 16S, H3, and

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Palasio, Raquel Gardini Sanches, Marisa Cristina de Almeida Guimarães, Fernanda Pires Ohlweiler, and Roseli Tuan. "Molecular and morphological identification of Biomphalaria species from the state of São Paulo, Brazil." ZooKeys 668 (April 12, 2017): 11–32. https://doi.org/10.3897/zookeys.668.10562.

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DNA barcoding and morphological characters were used to identify adult snails belonging to the genus Biomphalaria from 17 municipalities in the state of São Paulo, Brazil. The DNA barcode analysis also included twenty-nine sequences retrieved from GenBank. The final data set of 104 sequences of the mitochondrial cytochrome oxidase I (COI) gene was analyzed for K2P intraspecific and interspecific divergences, through tree-reconstruction methods (Neighbor-Joining, Maximum Likelihood and Bayesian inference), and by applying different models (ABGD, bPTP, GMYC) to partition the sequences according

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Polášek, Marek, Roman J. Godunko, Sereina Rutschmann, Marek Svitok, Milan Novikmec, and Světlana Zahrádková. "Integrative taxonomy of genus Electrogena (Ephemeroptera: Heptageniidae): the role of innovative morphological analyses for species delimitation." Arthropod Systematics & Phylogeny 76 (November 23, 2018): 449–62. https://doi.org/10.3897/asp.76.e31962.

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The easy, fast and correct identification of species is a crucial aspect of biology and its applications, such as biomonitoring and nature conservation. One of the groups that are common but not easily to identify are mayflies at the larval stage. In recent years, many attempts to species identification using modern and non-traditional methods have been made. Two different approaches are used in most cases: i) DNA taxonomy and ii) modern image processing and classification. In this study, we combined both to describe the intrageneric genetical and morphological variability of the Central Europ

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YING, YING, ZHI-HONG ZHAN, and XIA WAN. "New color patterns and new synonym of Odontolabis sinensis (Westwood, 1848) (Coleoptera: Lucanidae): insights from a multilocus phylogeny and species delimitation." Zootaxa 4926, no. 2 (2021): 263–75. http://dx.doi.org/10.11646/zootaxa.4926.2.6.

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Taxonomy of Odontolabis sinensis (Westwood, 1848) and Odontolabis fallaciosa Boileau, 1901 has long been a controversial issue due to their highly morphological similarity except for elytral color patterns. In the present work, we assessed their taxonomic status by combining molecular phylogeny and species delimitation based on multilocus datasets (COI, 16S rDNA, Cytb, CAD, Wingless). Phylogenetic analyses under both Maximum Likelihood inference and Bayesian inference recovered identical topologies. All the examined individuals in the clade of O. sinensis and O. fallaciosa formed into five sub

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VALDEZ-MONDRAGÓN, ALEJANDRO. "COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico." Zootaxa 4747, no. 1 (2020): 54–76. http://dx.doi.org/10.11646/zootaxa.4747.1.2.

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The spider genus Ixchela Huber 2000, is comprised of 22 species distributed from north-eastern Mexico to Central America, including the two new species described herein from Mexico: Ixchela panchovillai sp. nov. and Ixchela zapatai sp. nov., both from the state of Oaxaca and described for both sexes. DNA barcoding utilizing mitochondrial cytochrome c oxidase subunit 1 (COI) and morphology were used for species delimitation. Molecular analyses and species delimitation included four methods: 1) corrected p-distances under neighbor-joining (NJ), 2) general mixed yule coalescent model (GMYC), 3) a

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LO, YING-YUAN, REN-CHUNG CHENG, and CHUNG-PING LIN. "Species delimitation and taxonomic revision of Oxyopes (Araneae: Oxyopidae) of Taiwan, with description of two new species." Zootaxa 4927, no. 1 (2021): 58–86. http://dx.doi.org/10.11646/zootaxa.4927.1.4.

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This study revised the spider genus Oxyopes Latreille, 1804 in Taiwan and delineated the species boundaries based on morphological and molecular characters. A total of seven Oxyopes spiders were recognized, including two newly described species, O. hasta sp. nov. and O. taiwanensis sp. nov. Oxyopes fujianicus Song & Zhu 1993 from Yilan County, Nantou County, and Kaohsuing City, and O. striagatus Song 1999 from New Taipei City, Taichung City, Nantou County, and Kaohsiung City were recorded for the first time in Taiwan. An identification key and a distributional map of Taiwanese Oxyopes spec

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YAN, MINHUI, JIANGWEI BAO, MIAOQING LUO, YAO GAO, CHRISTOPHER H. DIETRICH, and YANI DUAN. "Phylogenetic analyses and species delimitation of Aconurella Ribaut (Hemiptera: Cicadellidae: Deltocephalinae: Chiasmini) in China based on molecular data." Zootaxa 5205, no. 3 (2022): 281–96. http://dx.doi.org/10.11646/zootaxa.5205.3.6.

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The grassland leafhopper genus Aconurella is widespread in the Old World. Species of this genus are difficult to identify by traditional morphological characters but the morphology-based species classification in this genus has not previously been tested using molecular data. This study analysed DNA sequence data from two mitochondrial genes (COI, 16S) and one nuclear gene (ITS2) to infer the phylogenetic relationships and status of five previously recognized Aconurella species and compare the performance of different molecular species-delimitation methods using single and multiple loci. The a

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Liu, Jing, Huixin Xu, Ziqing Wang, et al. "Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini)." Insects 15, no. 7 (2024): 508. http://dx.doi.org/10.3390/insects15070508.

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To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species

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Muñoz-Tobar, Sofía, and Michael Caterino. "Mountains as Islands: Species Delimitation and Evolutionary History of the Ant-Loving Beetle Genus Panabachia (Coleoptera, Staphylinidae) from the Northern Andes." Insects 11, no. 1 (2020): 64. http://dx.doi.org/10.3390/insects11010064.

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The ant-loving beetle genus Panabachia Park 1942 is a poorly studied beetle lineage from the new world tropics. We recently collected Panabachia from several previously unrecorded locations in the páramo biome of the high Ecuadorian Andes, with males exhibiting great morphological variation in the distribution of the foveae and depressions in the pronotum, as well as aspects of the male genitalia. Here, we employ phylogenetic and species delimitation methods with mitochondrial (COI) and nuclear protein-coding (wingless) gene sequences to examine the concordance of morphological characters and

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Novo, Marta, Rosa Fernández, Marchán Daniel Fernández, Mónica Gutiérrez, and Cosin Dario Diaz. "Compilation of morphological and molecular data, a necessity for taxonomy: The case of Hormogaster abbatissae sp. n. (Annelida, Clitellata, Hormogastridae)." ZooKeys 242 (November 15, 2012): 1–17. https://doi.org/10.3897/zookeys.242.3996.

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Conflict among data sources can be frequent in evolutionary biology, especially in cases where one character set poses limitations to resolution. Earthworm taxonomy, for example, remains a challenge because of the limited number of morphological characters taxonomically valuable. An explanation to this may be morphological convergence due to adaptation to a homogeneous habitat, resulting in high degrees of homoplasy. This sometimes impedes clear morphological diagnosis of species. Combination of morphology with molecular techniques has recently aided taxonomy in many groups difficult to delimi

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Song, Chao, Guanyu Chen, Le Wang, Teng Lei, and Xin Qi. "DNA Barcoding Supports “Color-Pattern’’-Based Species of Stictochironomus from China (Diptera: Chironomidae)." Insects 15, no. 3 (2024): 179. http://dx.doi.org/10.3390/insects15030179.

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The genus Stictochironomus (Diptera: Chironomidae) has an almost worldwide distribution, with more than 30 species. However, species delimitation and identification based on the markings on the wings and legs are controversial and uncertain. In this study, we focused on color patterns to review the adults of the genus from China, and two new species (S. trifuscipes sp. nov. and S. quadrimaculatus sp. nov.) are described and figured. DNA barcodes can accurately separate the two new species with specific color patterns. However, heterospecific individuals form a monophyletic cluster in the phylo

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Krivina, E. S., A. D. Temraleeva, and Yu S. Bukin. "Species delimitation and microalgal cryptic diversity analysis of the genus Micractinium (Chlorophyta)." Vavilov Journal of Genetics and Breeding 26, no. 1 (2022): 74–85. http://dx.doi.org/10.18699/vjgb-22-11.

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In this article, the system of the green microalgal genus Micractinium, based on morphological, physiological, ecological and molecular data, is considered. The main diagnostic species characteristics and the taxonomic placement of some taxa are also discussed. Phylogenetic analysis showed that the genus Micractinium is characterized by high cryptic diversity. The algorithms used for species delimitation had different results on the number of potentially species-level clusters allocated. The ABGD method was less “sensitive”. The tree-based approaches GMYC and PTP showed a more feasible taxonom

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Young, Robert G., Cathryn L. Abbott, Thomas W. Therriault, and Sarah J. Adamowicz. "Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda)." Genome 60, no. 2 (2017): 169–82. http://dx.doi.org/10.1139/gen-2015-0209.

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DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an o

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SOTO MEDINA, Edier, Maria PRIETO, and Mats WEDIN. "A new Bunodophoron species (Sphaerophoraceae, Lecanorales) from the Neotropics." Lichenologist 50, no. 3 (2018): 255–66. http://dx.doi.org/10.1017/s0024282917000743.

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AbstractThis is the first part of an ongoing taxonomic treatment of Bunodophoron (Sphaerophoraceae, Lecanorales) in the Neotropics, based on the molecular phylogenetic analysis of three markers together with studies of morphology and chemistry, and using the general mixed Yule coalescence (GMYC) method to delimit species boundaries. In the Neotropics, species in this genus grow on the ground or on shrubs in the páramos, and as epiphytes in the montane rainforests. We describe here a new species from the páramos of Colombia, Bunodophoron crespoae Soto, M. Prieto & Wedin sp. nov., and discus

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Polášek, Marek, Roman J. Godunko, Sereina Rutschmann, Marek Svitok, Milan Novikmec, and Světlana Zahrádková. "Integrative taxonomy of genus Electrogena (Ephemeroptera: Heptageniidae): the role of innovative morphological analyses for species delimitation." Arthropod Systematics & Phylogeny 76, no. 3 (2018): 449–62. http://dx.doi.org/10.3897/asp.76.e31962.

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The easy, fast and correct identification of species is a crucial aspect of biology and its applications, such as biomonitoring and nature conservation. One of the groups that are common but not easily to identify are mayflies at the larval stage. In recent years, many attempts to species identification using modern and non-traditional methods have been made. Two different approaches are used in most cases: i) DNA taxonomy and ii) modern image processing and classification. In this study, we combined both to describe the intrageneric genetical and morphological variability of the Central Europ

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Yang, Qiuxia, Xiangmin Cheng, Tingting Zhang, Xinzhan Liu, and Xinli Wei. "Five New Species of the Lichen-Forming Fungal Genus Peltula from China." Journal of Fungi 8, no. 2 (2022): 134. http://dx.doi.org/10.3390/jof8020134.

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The genus Peltula is an important cyanobacterial lichen group. We performed a taxonomic study on the Peltula from China using phylogenetic analysis based on three gene loci (ITS, nuSSU, nuLSU) together with additional species delimitation analyses by ABGD, bPTP and GMYC approaches and the phenotypic characteristics. Five new species (Peltula lobulata, P. polycarpa, P. polyphylla, P. pseudoboletiformis and P. submarginata) were found and described. Peltula lobulata is diagnostic in its small thallus with plenty of lobules, rolled down and irregularly lobed margins, and uneven cracked surfaces.

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Vainutis, Konstantin S., Anastasia N. Voronova, Alexander N. Mironovsky, Oksana N. Zhigileva, and Alexander E. Zhokhov. "The Species Diversity Assessment of Azygia Looss, 1899 (Digenea: Azygiidae) from the Volga, Ob, and Artyomovka Rivers Basins (Russia), with Description of A. sibirica n. sp." Diversity 15, no. 1 (2023): 119. http://dx.doi.org/10.3390/d15010119.

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This study is devoted to the investigation of Azygia (Digenea: Azygiidae) species diversity using classical morphological, recent molecular tools (28S rRNA and cox1 mtDNA for genetic-based inference) and robust statistical techniques (Principal component analysis, PCA). The analysis revealed that the genus Azygia included four valid species: A. lucii, A. longa, A. hwangtsiyui, and A. sibirica n. sp. The distribution of the type species A. lucii was confirmed in the largest Russian rivers: the Volga and the Ob. The worms isolated from Perccottus glenii were determined as the Chinese species A.

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Boluda, C. G., V. J. Rico, P. K. Divakar, et al. "Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)." Persoonia - Molecular Phylogeny and Evolution of Fungi 42, no. 1 (2019): 75–100. http://dx.doi.org/10.3767/persoonia.2019.42.04.

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In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distri

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Scarpa, Fabio, Piero Cossu, Tiziana Lai, Daria Sanna, Marco Curini-Galletti, and Marco Casu. "Meiofaunal cryptic species challenge species delimitation: the case of the Monocelis lineata (Platyhelminthes: Proseriata) species complex." Contributions to Zoology 85, no. 2 (2016): 123–45. http://dx.doi.org/10.1163/18759866-08502001.

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Given the pending biodiversity crisis, species delimitation is a critically important task in conservation biology, but its efficacy based on single lines of evidence has been questioned as it may not accurately reflect species limits and relationships. Hence, the use of multiple lines of evidence has been portrayed as a means to overcome identification issues arising from gene/species tree discordance, morphological convergence or recent adaptive radiations. Here, the integrative taxonomic approach has been used to address the study of the Monocelis lineataspecies complex. The taxonomic resol

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Canoglu, Halim, Ismail Aksu, Davut Turan, and Yusuf Bektas. "DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey." Zoosystematics and Evolution 99, no. 1 (2023): 185–94. http://dx.doi.org/10.3897/zse.99.94333.

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The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific dist

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Canoglu, Halim, Ismail Aksu, Davut Turan, and Yusuf Bektas. "DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey." Zoosystematics and Evolution 99, no. (1) (2023): 185–94. https://doi.org/10.3897/zse.99.94333.

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The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific dist

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Ragazzini, Mattia, Roy M. J. C. Kleukers, Luc Willemse, Baudewijn Ode, Lara-Sophie Dey, and Oliver Hawlitschek. "DNA barcoding and species delimitation of crickets, katydids, and grasshoppers (Orthoptera) from Central and Southern Europe, with focus on the Mediterranean Basin." Arthropod Systematics & Phylogeny 83 (June 18, 2025): 211–30. https://doi.org/10.3897/asp.83.e138238.

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The Mediterranean Basin, recognized as a global biodiversity hotspot, harbors a remarkable diversity of grasshoppers, katydids, and crickets, many of which are endemic and potentially contain cryptic lineages. In this study, we generated a comprehensive dataset comprising 1,441 barcodes from 270 identified species within the Ensifera and Caelifera suborders. These were combined with existing data to form a dataset of 2,606 barcodes representing 351 species. We employed Maximum Likelihood (ML) topology reconstruction and applied five species delimitation methods (BIN, ABGD, ASAP, GMYC, and PTP)

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Kar, Oishik, Arka Mukherjee, Koustav Mukherjee, Debdeep Pramanik, Atanu Naskar, and Dhriti Banerjee. "Molecular identification and genetic variations of forensically significant blow flies (Diptera: Calliphoridae) from Eastern India using DNA barcoding." PLOS One 20, no. 7 (2025): e0327039. https://doi.org/10.1371/journal.pone.0327039.

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Flies, especially those from the Calliphoridae family, play a crucial role in decomposition and are the first to colonize a cadaver. Firstly, accurate species identification is a prerequisite for entomological evidence-based calculation of postmortem interval (PMI). While morphological criteria for identifying the species of adult blow flies exist, there are either absent or inadequate keys for younger stages. In all phases of blow fly development, molecular identification offers a quick and accurate procedure. It is widely known that mitochondrial cytochrome oxidase subunit I has the capacity

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Lo, Ying-Yuan, Ren-Chung Cheng, and Chung-Ping Lin. "Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan." PLOS ONE 19, no. 5 (2024): e0301776. http://dx.doi.org/10.1371/journal.pone.0301776.

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An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and

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Hurt, Carla R., Roger F. Thoma, David I. Withers, Carl E. Williams, and Robert T. R. Paine. "Extensive regional endemism and cryptic diversity in the Tennessee and Kentucky, USA populations of the burrowing crayfish Cambarus deweesae (Bouchard & Etnier, 1979) (Decapoda: Astacidea: Cambaridae) as revealed by molecular genetics." Journal of Crustacean Biology 39, no. 4 (2019): 440–49. http://dx.doi.org/10.1093/jcbiol/ruz027.

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Abstract The southeastern United States is a global hotspot for crayfish biodiversity, with more than 300 described species in the region. Some of this diversity is unfortunately being threatened by anthropogenic activities and nearly one fifth of the North American crayfish species are currently threatened with extinction. Efforts to protect crayfish species have been hindered by a lack of information regarding their taxonomy, distribution, and conservation status. Here we target populations of the burrowing valley flame crayfish, Cambarus deweesae (Bouchard & Etnier 1979) for molecular t

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Ruchiy, Yana, Daniela Nunes, Casandra Salinas, et al. "MDB-34. LITHIUM AND RADIATION REDUCE TUMOUR GROWTH IN GROUP 3 MEDULLOBLASTOMA." Neuro-Oncology 26, Supplement_4 (2024): 0. http://dx.doi.org/10.1093/neuonc/noae064.483.

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Abstract Medulloblastoma (MB) is the most common high-grade paediatric brain tumour, accounting for ~20 % of all childhood CNS tumours. It is comprised of 4 distinct molecular subtypes, with Group 3 MB having the worst prognosis with an overall survival of around 50 %. Additionally, current treatments, especially radiotherapy (RT), come at a very high cost for the developing brain and result in permanent complications, including lower IQ, slower processing speed, as well as social problems and lifelong dependency. Lithium has been shown to protect neurogenesis and cognitive functions from the

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Mercado-Salas, Nancy F., Sahar Khodami, and Pedro Martínez Arbizu. "Copepods and ostracods associated with bromeliads in the Yucatán Peninsula, Mexico." PLOS ONE 16, no. 3 (2021): e0248863. http://dx.doi.org/10.1371/journal.pone.0248863.

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A substantial fraction of the freshwater available in the Neotropical forests is enclosed within the rosettes of bromeliads that form small aquatic islands within a terrestrial landscape. These aquatic oases provide shelter, water, nutrients and resting of aggregation sites for several aquatic organisms, among them crustaceans. However, in comparison with the multitude of studies on open aquatic systems, our knowledge on crustaceans inhabiting semi-terrestrial habitats and phytotelmata is limited and their presence in such environments is poorly understood. The present study was carried out in

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Phillips, Anna J., Jason Reilly, Don Ashton, Dennis J. Richardson, Makiri Sei, and William E. Moser. "Introduced Placobdella parasitica in the lower Rogue River, Oregon: origin story." Aquatic Invasions 20, no. 2 (2025): 251–72. https://doi.org/10.3391/ai.2025.20.2.152871.

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The Common North American Turtle Leech, Placobdella parasitica, was reported in 2023 using the Northwestern Pond Turtle, Actinemys (Emys) marmorata, as a host in the Lower Rogue River, southwestern Oregon, USA. Molecular analysis and haplotype networks based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence revealed that this introduced population has very low haplotype diversity and is likely the result of a single introduction of a gravid adult, an adult brooding eggs or hatchlings, or a small number of related individuals. While we determined that the precise source po

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