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Journal articles on the topic 'DNA based species delimitation analysis'

Author: Grafiati

Published: 7 June 2025

Last updated: 2 August 2025

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1

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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2

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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3

Olave, Melisa, Eduard Solà, and L. Lacey Knowles. "Upstream Analyses Create Problems with DNA-Based Species Delimitation." Systematic Biology 63, no. 2 (2014): 263–71. http://dx.doi.org/10.1093/sysbio/syt106.

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4

Koohdar, Fahimeh, Neda Aram, and Masoud Sheidai. "Biosystematics, fingerprinting and DNA barcoding study of the genus Lallemantia based on SCoT and REMAP markers." Caryologia 74, no. 4 (2022): 77–83. http://dx.doi.org/10.36253/caryologia-1163.

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Lallemantia is a medicinally important plant in the world. Due to interspecific hybridization and horizontal gene transfer, spices relationship and delimitation on the genus Lallemantia is difficult based on different molecular markers. Therefore, selecting the appropriate marker can be important. Fingerprinting techniques continue to be used for genomic profiling for the characterization of germplasm and the establishment of the identity of varieties/hybrids/parental sources of aromatic and medicinal plants. For this, we need to produce detailed information on genetic diversity available in L

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5

Han, Wei, Lu Qiu, Jing Zhu, Zong-Qing Wang, and Yan-Li Che. "Exploring the diversity of Eupolyphaga Chopard, 1929 (Blattodea, Corydioidea): species delimitation based on morphology and molecular analysis." ZooKeys 1120 (September 5, 2022): 67–94. https://doi.org/10.3897/zookeys.1120.87483.

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Eupolyphaga Chopard, 1929 is a cockroach genus mainly endemic to China. In this study, the species diversity of this genus is further explored through morphology and molecular analysis. Four species are described new to science: Eupolyphaga miracidia Qiu, sp. nov., Eupolyphaga udenostyla Qiu, sp. nov., Eupolyphaga reducta Qiu, sp. nov., and Eupolyphaga simila Qiu, sp. nov. New knowledge on some known species is added, including new distribution records and characteristics of females. Forty-five COI sequences were newly sequenced and a molecular species delimitation analysis was performed using

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6

Silva, F. L., and S. Wiedenbrug. "Integrating DNA barcodes and morphology for species delimitation in theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae)." Bulletin of Entomological Research 104, no. 1 (2013): 65–78. http://dx.doi.org/10.1017/s0007485313000515.

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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 ma

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7

TOMIMORI, YUSUKE, MASAFUMI MATSUI, HIROSHI OKAWA, KANTO NISHIKAWA, SHINGO TANABE, and RYO KAMASAKA. "Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae)." Zootaxa 5293, no. 1 (2023): 145–60. http://dx.doi.org/10.11646/zootaxa.5293.1.6.

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Hynobius akiensis sensu lato has recently been split into three species based on short sequence analyses of cyt-b gene of mtDNA and without data of nuclear DNA, and strange sympatric distribution in some areas has been indicated in two species. We analyzed nuclear DNA marker (SNPs) and complete sequence of cyt-b in H. akiensis sensu lato to reassess species delimitation and genetic introgression among species. As a result, we found two lineages with discordant mitochondrial and nuclear DNA in some areas. Of H. akiensis sensu lato, each of the two contains the type locality of two species recen

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8

Van, Der Bank Herman, Dai Herbert, Richard Greenfield, and Kowiyou Yessoufou. "Revisiting species delimitation within the genus Oxystele using DNA barcoding approach." ZooKeys 365 (December 30, 2013): 337–54. https://doi.org/10.3897/zookeys.365.5356.

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The genus <i>Oxystele</i>, a member of the highly diverse marine gastropod superfamily Trochoidea, is endemic to southern Africa. Members of the genus include some of the most abundant molluscs on southern African shores and are important components of littoral biodiversity in rocky intertidal habitats. Species delimitation within the genus is still controversial, especially regarding the complex <i>O. impervia</i> / <i>O. variegata</i>. Here, we assessed species boundaries within the genus using DNA barcoding and phylogenetic tree reconstruction. We analysed 56 specimens using the mitochondri

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9

Becchimanzi, Andrea, Beata Zimowska, and Rosario Nicoletti. "Cryptic Diversity in Cladosporium cladosporioides Resulting from Sequence-Based Species Delimitation Analyses." Pathogens 10, no. 9 (2021): 1167. http://dx.doi.org/10.3390/pathogens10091167.

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Cladosporium cladosporioides is an extremely widespread fungus involved in associations ranging from mutualistic to pathogenic and is the most frequently represented Cladosporium species in sequence databases, such as Genbank. The taxonomy of Cladosporium species, currently based on the integration of molecular data with morphological and cultural characters, is in frequent need of revision. Hence, the recently developed species delimitation methods can be helpful to explore cryptic diversity in this genus. Considering a previous study that reported several hypothetical species within C. clado

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10

Ramirez, Jorge L., Luisa Simbine, Carla G. Marques, et al. "DNA Barcoding of Penaeidae (Decapoda; Crustacea): Non-Distance-Based Species Delimitation of the Most Economically Important Shrimp Family." Diversity 13, no. 10 (2021): 460. http://dx.doi.org/10.3390/d13100460.

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The Penaeidae family includes some of the most economic and ecological important marine shrimp, comprising hundreds of species. Despite this importance and diversity, the taxonomic classification for penaeid shrimp has constantly been revised, and issues related to the species identification are common. In this study, we implemented DNA barcoding analyses in addition to single-gene species delimitation analyses in order to identify molecular operational taxonomy units (MOTUs) and to generate robust molecular information for penaeid shrimp based on the cytochrome oxidase subunit I (COI) mitocho

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11

Hambleton, Sarah, Keith N. Egger, and Randolph S. Currah. "The Genus Oidiodendron: Species Delimitation and Phylogenetic Relationships Based on Nuclear Ribosomal DNA Analysis." Mycologia 90, no. 5 (1998): 854. http://dx.doi.org/10.2307/3761327.

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12

Hambleton, Sarah, Keith N. Egger, and Randolph S. Currah. "The genus Oidiodendron: species delimitation and phylogenetic relationships based on nuclear ribosomal DNA analysis." Mycologia 90, no. 5 (1998): 854–68. http://dx.doi.org/10.1080/00275514.1998.12026979.

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13

Talaga, Stanislas, Amandine Guidez, Benoît de Thoisy, et al. "A DNA barcode library for Culex mosquitoes (Diptera: Culicidae) of South America with the description of two cryptic species of subgenus Melanoconion." PLOS ONE 20, no. 2 (2025): e0310571. https://doi.org/10.1371/journal.pone.0310571.

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Among mosquitoes (Diptera: Culicidae), the genus Culex Linnaeus is one of the most diverse in the world and includes numerous known vector species of parasites and viruses to humans. Morphological identification of Culex species is notoriously difficult and relies mostly on the examination of properly dissected male genitalia which largely prevents female and immature identification during entomological, ecological or arboviral surveys. The aims of this study were (i) to establish a DNA barcode library for Culex mosquitoes of French Guiana based on the mitochondrial gene cytochrome c oxidase I

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14

Wang, Rui, Clement K. M. Tsui, and Chongjuan You. "Cryptic Species Diversity and Phylogenetic Relationship in the Rust Genus Chrysomyxa from China." Journal of Fungi 8, no. 1 (2022): 83. http://dx.doi.org/10.3390/jof8010083.

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Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chr

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15

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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16

Yusseff-Vanegas, Sohath Z., and Ingi Agnarsson. "DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region." PeerJ 5 (July 25, 2017): e3516. http://dx.doi.org/10.7717/peerj.3516.

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Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic

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17

Pešić, Vladimir, and Clemens Grosser. "Dina serbica, a new species of leeches (Annelida: Hirudinea: Erpobdellidae) from Serbia, based on morphological and molecular evidence." Ecologica Montenegrina 51 (February 10, 2022): 1–14. http://dx.doi.org/10.37828/em.2022.51.1.

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In the present study we used an integrative taxonomic approach that combines morphological and DNA barcoding data to describe a new species, Dina serbica sp. nov. from a spring in western Serbia. The average K2P-distance between DNA-barcode sequences of D. serbica sp. nov. and its closest relative D. minuoculata was estimated at 11.96±1.39%. Moreover, the ASAP (assemble species by automatic partitioning) species-delimitation method based on COI sequences from our study and sequences of Dina species from GenBank supported the species-status of D. serbica sp. nov. The first DNA barcoding data fo

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18

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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19

Ottoni, Felipe Polivanov, José L. O. Mattos, Axel M. Katz, and Pedro H.N. Bragança. "Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments." Zoosystematics and Evolution 95, no. (1) (2019): 49–64. https://doi.org/10.3897/zse.95.31658.

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Three distinct and independent molecular-based species delimitation analyses were performed among the species and populations included within the Australoheros autrani group, based on sequences of the mitochondrial gene Cytochrome b: a tree-based method proposed by Wiens and Penkrot (WP), a Character-based DNA Barcoding (CBB) and coalescent species delimitation method termed the Bayesian Implementation of the Poisson tree processes (bPTP). The congruence of WP and CBB delimited 11 independent lineages (species), while the bPTP delimited just nine lineages. We did not favour any of the methods,

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20

Zhang, Haiguang, and Wenjun Bu. "Exploring Large-Scale Patterns of Genetic Variation in the COI Gene among Insecta: Implications for DNA Barcoding and Threshold-Based Species Delimitation Studies." Insects 13, no. 5 (2022): 425. http://dx.doi.org/10.3390/insects13050425.

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The genetic variation in the COI gene has had a great effect on the final results of species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for the comprehensive appraisal of the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis, based on different thresholds, were also compared among 4288 genera (35,068 species). The results indicate that approximate

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KALOUSOVA, ROMANA, and LADISLAV BOCAK. "Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea." Zootaxa 4320, no. 3 (2017): 505. http://dx.doi.org/10.11646/zootaxa.4320.3.6.

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Cladophorus Guérin-Méneville, 1830 are endemic Papuan net-winged beetles which take part in highly diverse Müllerian mimicry rings. Available specimens were sequenced for cox1–tRNA-Leu–cox2 mitochondrial DNA fragment and the species delimitations were based on the genetic distance, phylogenetic analysis, and morphology. Three earlier described species were identified in the recently collected material and further 10 species are described: C. pallescens sp. nov., C. bicolor sp. nov., C. craterensis sp. nov., C. motykai sp. nov., C. mindikensis sp. nov., C. kailakiensis sp. nov., C. manokwarensi

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22

Sivaraj, Irusappan, Stalin Nithaniyal, Varadharajan Bhooma, Umapathy Senthilkumar, and Madasamy Parani. "Species delimitation of Melia dubia Cav. from Melia azedarach L. complex based on DNA barcoding." Botany 96, no. 5 (2018): 329–36. http://dx.doi.org/10.1139/cjb-2017-0148.

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The genus Melia L., which belongs to the “Mahogany” family Meliaceae, is a source of important phytochemicals with marked medicinal properties. Species identification in Melia is complex due to the existence of overlapping morphological features. Although Melia dubia Cav. is listed as a synonym of Melia azedarach L., it is not clear from the available literature whether they are the same species or different, and the species complexity still remains unresolved. In the present study, 10 accessions of M. dubia and M. azedarach were analysed by DNA barcoding using three chloroplast DNA markers (r

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23

Peng, Yu-lan, Yu Zhang, Xin-fen Gao, et al. "A phylogenetic analysis and new delimitation of Crepidiastrum (Asteraceae, tribe Cichorieae)." Phytotaxa 159, no. 4 (2014): 241. http://dx.doi.org/10.11646/phytotaxa.159.4.1.

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The systematic position of Paraixeris humifusa (Asteraceae) is hard to define, because the circumscription of Paraixeris, Youngia and Crepidiastrum, three closely related genera in subtribe Crepidinae (Cichorieae), is not clear. This paper reports on the relationships between 30 species in subtribe Crepidinae, based on an analysis of nucleotides from one nuclear (ITS) and three chloroplast DNA regions ( trnL-F, rps16 and atpB-rbcL). The phylogenetic analyses used maximum parsimony with maximum likelihood inference. The monophyly of Crepidiastrum in the most recent generic classification of Shi

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24

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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26

Ahmed, Hanan I. Sayed, Abdelfattah Badr, Hanaa H. El-Shazly, Linda Watson, Ahmed S. Fuoad, and Faten Y. Ellmouni. "Molecular Phylogeny of Trifolium L. Section Trifolium with Reference to Chromosome Number and Subsections Delimitation." Plants 10, no. 10 (2021): 1985. http://dx.doi.org/10.3390/plants10101985.

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The genus Trifolium is one of the largest genera of the legume family Fabaceae with ca. 255 species. The genus is divided into eight sections; the section Trifolium is a major section of the genus, comprising 73 species mainly distributed in the Mediterranean region. We used nuclear ribosomal DNA internal transcribed spacer (ITS) and morphological variation to reconsider the delimitation and phylogenetic relationships of species in the section Trifolium with reference to chromosomal variations. Bayesian analysis of ITS data delimited the species as three clades based on the analysis of ITS seq

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27

Yang, Qiuxia, Jason Hollinger, Steven D. Leavitt, and Xinli Wei. "Two New Species and Two New Records of the Lichen-Forming Fungal Genus Peltula (Ascomycota: Peltulaceae) from China." Biology 11, no. 10 (2022): 1518. http://dx.doi.org/10.3390/biology11101518.

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In this study, two new species, Peltula confusa Q.X. Yang & X.L. Wei, sp. nov., growing in a dry microenvironment within a semi-humid area, and Peltula subpatellata Q.X. Yang & X.L. Wei, sp. nov., occurring in arid and semi-arid regions, are described. In addition, two species, P. polyspora (Tuck.) Wetmore and P. obscuratula (Nyl.) Poelt ex Egea, are recorded for the first time in China. All four species are described based on morphological, anatomical and molecular data. Peltula confusa is characterized by a lighter, brighter, and more yellowish upper surface than other species of thi

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Ottoni, Felipe Polivanov, José L. O. Mattos, Axel M. Katz, and Pedro H. N. Bragança. "Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments." Zoosystematics and Evolution 95, no. 1 (2019): 49–64. http://dx.doi.org/10.3897/zse.95.31658.

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Three distinct and independent molecular-based species delimitation analyses were performed among the species and populations included within theAustraloherosautranigroup, based on sequences of the mitochondrial gene Cytochrome b: a tree-based method proposed by Wiens and Penkrot (WP), a Character-based DNA Barcoding (CBB) and coalescent species delimitation method termed the Bayesian Implementation of the Poisson tree processes (bPTP). The congruence of WP and CBB delimited 11 independent lineages (species), while the bPTP delimited just nine lineages. We did not favour any of the methods, an

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29

Pedraza-Marrón, Carmen del R., Raimundo Silva, Jonathan Deeds, et al. "Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation." Proceedings of the Royal Society B: Biological Sciences 286, no. 1900 (2019): 20182924. http://dx.doi.org/10.1098/rspb.2018.2924.

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Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species ( L. campechanu

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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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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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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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Song, Chao, Le Wang, Teng Lei, and Xin Qi. "New Color-Patterned Species of Microtendipes Kieffer, 1913 (Diptera: Chironomidae) and a Deep Intraspecific Divergence of Species by DNA Barcodes." Insects 14, no. 3 (2023): 227. http://dx.doi.org/10.3390/insects14030227.

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The genus Microtendipes Kieffer (Diptera: Chironomidae) has a nearly worldwide distribution, comprising more than 60 species, which are further divided into two species groups based on larval stage. However, species delimitation and identification among the adults of this genus are controversial and uncertain. For instance, previous studies have provided many synonymies based on conspecific color pattern variations in Microtendipes species. Here, we used DNA barcode data to address Microtendipes species delimitation as well as to test whether color pattern variations can be diagnostic characte

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Murphy, Nicholas P., Rachael A. King, and Steven Delean. "Species, ESUs or populations? Delimiting and describing morphologically cryptic diversity in Australian desert spring amphipods." Invertebrate Systematics 29, no. 5 (2015): 457. http://dx.doi.org/10.1071/is14036.

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Cryptic species are frequently being discovered in refugial habitats, such as desert springs and groundwater systems. Unfortunately, many of these taxa remain as unnamed entities years after their initial discovery. Recent advances in the use of molecular data and coalescent analyses allow DNA-based delimitation of species to move from single locus, tree-based methods to multilocus coalescent analyses. This study compares two DNA-based approaches to delimit species of putatively cryptic freshwater amphipods (Chiltoniidae) from desert springs in central Australia. In addition, a morphometric an

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Koffi, K., Myriam Heuertz, Charles Doumenge, Jean Onana, Frederick Gavory, and Olivier Hardy. "A combined analysis of morphological traits, chloroplast and nuclear DNA sequences within Santiria trimera (Burseraceae) suggests several species following the Biological Species Concept." Plant Ecology and Evolution 143, no. (2) (2010): 160–69. https://doi.org/10.5091/plecevo.2010.433.

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<b>Background and aims</b> – Species delimitation remains a difficult task in many groups of organisms. Even widespread and conspicuous tropical trees make no exception. <i>Santiria trimera</i>, an African rainforest tree, displays substantial morphological variability. While classical analysis of historical herbarium samples lead to the recognition of a single species, two morphotypes of <i>S. trimera</i> are regularly collected in Gabon and Equatorial Guinea, sometimes in sympatry: one form with stilt roots (SR) and another form without stilt roots (NSR). <b>Methods</b> – To assess whether t

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Kölsch, Gregor, Bo Vest Pedersen, and Olof Biström. "Species delimitation in the leaf beetle genus Macroplea (Coleoptera, Chrysomelidae) based on mitochondrial DNA, and phylogeographic considerations." Insect Systematics & Evolution 37, no. 4 (2006): 467–79. http://dx.doi.org/10.1163/187631206788831443.

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AbstractThe genus Macroplea Samouelle, 1819 is a group of highly specialized aquatic leaf beetles occurring in the Palaearctic. Since the members of this genus are morphologically very similar, we addressed the question of species identification and delimitation by analysing the second half of the mitochondrial gene coding for the cytochrome oxidase I (COI) subunit. Species limits are inferred from the multimodal frequency distribution of genetic distances between specimens: low genetic distances within a species are clearly set apart from distances between species. The species status of the h

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Le, Ngoc Hoan, Helen F. Nahrung, Jess A. T. Morgan, and Simon A. Lawson. "Multivariate ratio analysis and DNA markers reveal a new Australian species and three synonymies in eucalypt-gall-associated Megastigmus (Hymenoptera: Megastigmidae)." Bulletin of Entomological Research 110, no. 6 (2020): 709–24. http://dx.doi.org/10.1017/s000748532000022x.

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AbstractThe genus Megastigmus Dalman, 1820 (Hymenoptera: Megastigmidae) contains potential biocontrol agents of the invasive eucalypt galling chalcid Leptocybe spp. (Hymenoptera: Eulophidae), with several species reported in various parts of the world. Species discrimination is challenging due to intraspecific morphological variation, difficulty in measuring sizes of body parts, and the lack of information regarding the global distribution of parasitic Megastigmus. We used two species commonly associated with Leptocybe in its native range to review taxonomic methods and determine the most reli

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Basso, Andrea, Dimitrios Avtzis, Christian Burban, et al. "The pine processionary moth Thaumetopoea pityocampa (Notodontidae) species complex: a phylogeny-based revision." Arthropod Systematics & Phylogeny 81 (December 20, 2023): 1031–50. http://dx.doi.org/10.3897/asp.81.e102928.

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The pine processionary moth, Thaumetopoea pityocampa, is an iconic insect in the Mediterranean culture because of its economic and medical importance and the unique traits of the life history, namely the winter feeding and the construction of conspicuous silk tents by the larvae. Its taxonomic status, however, is unclear because the type material is not available and there is confusion among the several species and subspecies described in the last centuries. In the present study, a metadata analysis of morphological and molecular data of the species in the T. pityocampa complex were considered

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Basso, Andrea, Dimitrios Avtzis, Christian Burban, et al. "The pine processionary moth Thaumetopoea pityocampa (Notodontidae) species complex: a phylogeny-based revision." Arthropod Systematics & Phylogeny 81 (December 20, 2023): 1031–50. https://doi.org/10.3897/asp.81.e102928.

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The pine processionary moth, <i>Thaumetopoea pityocampa</i>, is an iconic insect in the Mediterranean culture because of its economic and medical importance and the unique traits of the life history, namely the winter feeding and the construction of conspicuous silk tents by the larvae. Its taxonomic status, however, is unclear because the type material is not available and there is confusion among the several species and subspecies described in the last centuries. In the present study, a metadata analysis of morphological and molecular data of the species in the <i>T. pityocampa</i> complex w

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Liu, Jun, Dan Cui, Hui Wang, Jiawei Chen, Helu Liu, and Haibin Zhang. "Extensive cryptic diversity of giant clams (Cardiidae: Tridacninae) revealed by DNA-sequence-based species delimitation approaches with new data from Hainan Island, South China Sea." Journal of Molluscan Studies 86, no. 1 (2020): 56–63. http://dx.doi.org/10.1093/mollus/eyz033.

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Abstract Accurate species delimitation is important, especially for endangered species. As one of the most conspicuous bivalve taxa, giant clams are threatened throughout their geographic range. Many phylogeographic studies have revealed strong population structure among giant clams in the Indo-Pacific, suggesting cryptic diversity within these species. However, less attention has been paid to their identification and delimitation. In this study, we assembled a comprehensive dataset of mitochondrial cytochrome c oxidase subunit I (COI) sequences for Tridacna species, focusing on new sequences

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WANG, QIANG, and DE-YUAN HONG. "Taxonomic revision of the genus Pseudocodon (Campanulaceae) based on character analysis and molecular phylogeny." Phytotaxa 204, no. 1 (2015): 49. http://dx.doi.org/10.11646/phytotaxa.204.1.4.

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All taxa of the newly established genus Pseudocodon (= Codonopsis subg. Pseudocodonopsis), except for Pseudocodon rosulatus, form a complicated group extremely controversial on species delimitation. In the present study, numerous field trips were made, 29 populations were observed, and over 800 specimens of the genus preserved in 18 herbaria were critically examined. Statistical analysis of the characters was carried out based on 148 samples from specimens and 16 field populations. Four fragments of chloroplast DNA (atpB, matK, rbcL, petD with petB-petD spacer) and ITS of nuclear DNA were used

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Lopardo, Lara, and Gabriele Uhl. "Testing mitochondrial marker efficacy for DNA barcoding in spiders: a test case using the dwarf spider genus Oedothorax (Araneae : Linyphiidae : Erigoninae)." Invertebrate Systematics 28, no. 5 (2014): 501. http://dx.doi.org/10.1071/is14017.

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The present study focusses on comparatively assessing the efficacy for DNA barcoding of the two most commonly used mitochondrial markers (cox1 and 16S) in a genus of erigonine spiders. In total, 53 specimens representing five species, including four multi-sampled species, were sampled from several European localities. Initial evaluation of species monophyly was performed through parsimony and Bayesian phylogenetic analyses. Efficacy of mitochondrial markers was tested using operational (including distance-, tree-based measures and Barcode Gap) and evolutionary criteria (using the General Mixed

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Crespo, Luís, Marc Domènech, Alba Enguídanos, et al. "A DNA barcode-assisted annotated checklist of the spider (Arachnida, Araneae) communities associated to white oak woodlands in Spanish National Parks." Biodiversity Data Journal 6 (November 29, 2018): e29443. https://doi.org/10.3897/BDJ.6.e29443.

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A large scale semi-quantitative biodiversity assessment was conducted in white oak woodlands in areas included in the Spanish Network of National Parks, as part of a project aimed at revealing biogeographic patterns and identify biodiversity drivers. The semi-quantitative COBRA sampling protocol was conducted in sixteen 1-ha plots across six national parks using a nested design. All adult specimens were identified to species level based on morphology. Uncertain delimitations and identifications due to either limited information of diagnostic characters or conflicting taxonomy were further inve

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Tavares, Valéria Da C., Alfred L. Gardner, Molly M. Mcdonough, et al. "Historical DNA of rare yellow-eared bats Vampyressa Thomas, 1900 (Chiroptera, Phyllostomidae) clarifies phylogeny and species boundaries within the genus." Systematics and Biodiversity 20, no. 1 (2022): 1–13. https://doi.org/10.5281/zenodo.13421942.

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(Uploaded by Plazi for the Bat Literature Project) Patterns of rarity, endemism, and vulnerability are known for four species of yellow-eared bats of the genus Vampyressa: V. melissa, V. voragine, V. elisabethae, and V. sinchi, the last two described based on skull and external morphology. We extracted DNA from the holotypes of V. elisabethae and V. sinchi using strict ancient DNA protocols and sequenced the complete cytochrome-b gene of the mtDNA to investigate the phylogenetic relationships within the genus and employed species-delimitation tests to evaluate the validity of all the currently

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Tavares, Valéria Da C., Alfred L. Gardner, Molly M. Mcdonough, et al. "Historical DNA of rare yellow-eared bats Vampyressa Thomas, 1900 (Chiroptera, Phyllostomidae) clarifies phylogeny and species boundaries within the genus." Systematics and Biodiversity 20, no. 1 (2022): 1–13. https://doi.org/10.5281/zenodo.13421942.

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(Uploaded by Plazi for the Bat Literature Project) Patterns of rarity, endemism, and vulnerability are known for four species of yellow-eared bats of the genus Vampyressa: V. melissa, V. voragine, V. elisabethae, and V. sinchi, the last two described based on skull and external morphology. We extracted DNA from the holotypes of V. elisabethae and V. sinchi using strict ancient DNA protocols and sequenced the complete cytochrome-b gene of the mtDNA to investigate the phylogenetic relationships within the genus and employed species-delimitation tests to evaluate the validity of all the currently

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Tavares, Valéria Da C., Alfred L. Gardner, Molly M. Mcdonough, et al. "Historical DNA of rare yellow-eared bats Vampyressa Thomas, 1900 (Chiroptera, Phyllostomidae) clarifies phylogeny and species boundaries within the genus." Systematics and Biodiversity 20, no. 1 (2022): 1–13. https://doi.org/10.5281/zenodo.13421942.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Patterns of rarity, endemism, and vulnerability are known for four species of yellow-eared bats of the genus Vampyressa: V. melissa, V. voragine, V. elisabethae, and V. sinchi, the last two described based on skull and external morphology. We extracted DNA from the holotypes of V. elisabethae and V. sinchi using strict ancient DNA protocols and sequenced the complete cytochrome-b gene of the mtDNA to investigate the phylogenetic relationships within the genus and employed species-delimitation tests to evaluate the validity of all the currently

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Tavares, Valéria Da C., Alfred L. Gardner, Molly M. Mcdonough, et al. "Historical DNA of rare yellow-eared bats Vampyressa Thomas, 1900 (Chiroptera, Phyllostomidae) clarifies phylogeny and species boundaries within the genus." Systematics and Biodiversity 20, no. 1 (2022): 1–13. https://doi.org/10.5281/zenodo.13421942.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Patterns of rarity, endemism, and vulnerability are known for four species of yellow-eared bats of the genus Vampyressa: V. melissa, V. voragine, V. elisabethae, and V. sinchi, the last two described based on skull and external morphology. We extracted DNA from the holotypes of V. elisabethae and V. sinchi using strict ancient DNA protocols and sequenced the complete cytochrome-b gene of the mtDNA to investigate the phylogenetic relationships within the genus and employed species-delimitation tests to evaluate the validity of all the currently

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48

Tavares, Valéria Da C., Alfred L. Gardner, Molly M. Mcdonough, et al. "Historical DNA of rare yellow-eared bats Vampyressa Thomas, 1900 (Chiroptera, Phyllostomidae) clarifies phylogeny and species boundaries within the genus." Systematics and Biodiversity 20, no. 1 (2022): 1–13. https://doi.org/10.5281/zenodo.13421942.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Patterns of rarity, endemism, and vulnerability are known for four species of yellow-eared bats of the genus Vampyressa: V. melissa, V. voragine, V. elisabethae, and V. sinchi, the last two described based on skull and external morphology. We extracted DNA from the holotypes of V. elisabethae and V. sinchi using strict ancient DNA protocols and sequenced the complete cytochrome-b gene of the mtDNA to investigate the phylogenetic relationships within the genus and employed species-delimitation tests to evaluate the validity of all the currently

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49

Tavares, Valéria Da C., Alfred L. Gardner, Molly M. Mcdonough, et al. "Historical DNA of rare yellow-eared bats Vampyressa Thomas, 1900 (Chiroptera, Phyllostomidae) clarifies phylogeny and species boundaries within the genus." Systematics and Biodiversity 20, no. 1 (2022): 1–13. https://doi.org/10.5281/zenodo.13421942.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Patterns of rarity, endemism, and vulnerability are known for four species of yellow-eared bats of the genus Vampyressa: V. melissa, V. voragine, V. elisabethae, and V. sinchi, the last two described based on skull and external morphology. We extracted DNA from the holotypes of V. elisabethae and V. sinchi using strict ancient DNA protocols and sequenced the complete cytochrome-b gene of the mtDNA to investigate the phylogenetic relationships within the genus and employed species-delimitation tests to evaluate the validity of all the currently

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Anđelić Dmitrović, Barbara, Mišel Jelić, Emilia Rota, and Lucija Šerić Jelaska. "DNA Barcoding of Invertebrates Inhabiting Olive Orchards and Vineyards Accelerates Understudied Mediterranean Biodiversity Assessment." Diversity 14, no. 3 (2022): 182. http://dx.doi.org/10.3390/d14030182.

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The Mediterranean region has a high but unevenly studied level of invertebrate diversity. Genetic-based methods, such as DNA barcoding and metabarcoding, are proposed for biodiversity assessment; however, their application is not always straightforward. The current state of data available in genetic databases limits species identification, especially in the case of certain invertebrate groups. The aim of the study was (1) to assess the diversity of seven invertebrate groups, which are potential prey for predatory arthropods, in order to facilitate the analysis of the metabarcoding of trophic i

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