Journal articles: 'Sequences of MOTUs'

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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 (MOTUs), namely the distance-based Barcode Index Number (BIN) System, Generalized Mixed Yule Coalescent (GMYC), a Java program that uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Assemble Species by Automatic Partitioning (ASAP), and Bayesian implementation of the Poisson Tree Processes model (bPTP). All species, except Hierodula chinensis Werner, 1929, were recovered as monophyletic on the neighbor-joining (NJ) tree. For the final dataset, 379 COI-5P barcode sequences were assigned to 68 BINs. Fifty-five out of 68 BINs obtained were new to BOLD. The low level of BIN overlap with other nations highlights the importance of constructing a regional DNA barcode reference library. The algorithms ASAP, jMOTU, bPTP, and GMYC clustered barcode sequences into 32, 58, 68, and 60 MOTUs, respectively. All species delimitation algorithms (except ASAP analysis) split Anaxarcha sinensis Beier, 1933, Anaxarcha zhengi Ren & Wang, 1994, H. chinensis, Spilomantis occipitalis (Westwood, 1889), Titanodula formosana Giglio-Tos, 1912 into more than one MOTUs. All algorithms merged Hierodula sp. BCM-2019 and H. chinensis into the same MOTU, as for Tenodera aridifolia Stoll, 1813 and Tenodera sinensis Saussure, 1871. More accurate identification results need to be supplemented by detailed morphological classification.

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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.

Full text

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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 (MOTUs), namely the distance-based Barcode Index Number (BIN) System, Generalized Mixed Yule Coalescent (GMYC), a Java program that uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Assemble Species by Automatic Partitioning (ASAP), and Bayesian implementation of the Poisson Tree Processes model (bPTP). All species, except Hierodula chinensis Werner, 1929, were recovered as monophyletic on the neighbor-joining (NJ) tree. For the final dataset, 379 COI-5P barcode sequences were assigned to 68 BINs. Fifty-five out of 68 BINs obtained were new to BOLD. The low level of BIN overlap with other nations highlights the importance of constructing a regional DNA barcode reference library. The algorithms ASAP, jMOTU, bPTP, and GMYC clustered barcode sequences into 32, 58, 68, and 60 MOTUs, respectively. All species delimitation algorithms (except ASAP analysis) split Anaxarcha sinensis Beier, 1933, Anaxarcha zhengi Ren & Wang, 1994, H. chinensis, Spilomantis occipitalis (Westwood, 1889), Titanodula formosana Giglio-Tos, 1912 into more than one MOTUs. All algorithms merged Hierodula sp. BCM-2019 and H. chinensis into the same MOTU, as for Tenodera aridifolia Stoll, 1813 and Tenodera sinensis Saussure, 1871. More accurate identification results need to be supplemented by detailed morphological classification.

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ROSERO-GARCÍA, DORIS, SARA A. BICKERSMITH, JUAN DAVID SUAZA-VASCO, et al. "Molecular operational taxonomic units of mosquitoes (Diptera: Culicidae) collected in high Andean mountain ecosystems of Antioquia, Colombia." Zootaxa 4277, no. 3 (2017): 369. http://dx.doi.org/10.11646/zootaxa.4277.3.3.

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Accurate taxonomic identification of highland mosquito species may be complicated because of the lack of comprehensive regional morphological keys and taxonomic specialists, particularly for mosquitoes of medical or ecological importance. We applied a multi-locus approach to explore the diversity of genera/species collected, to define the Molecular Operational Taxonomic Units (MOTUs) and to perform phylogenetic clustering. Twenty MOTUs and three single sequences were revealed from 78 concatenated cox1 + ITS2 sequences, and the species name was allocated for five of these. This study provides molecular taxonomic information of culicid fauna present in high Andean mountain ecosystems in Antioquia, Colombia. However, future morphological and integrative taxonomic studies should be conducted to achieve the specific identity of all detected MOTUs.

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Jaszczyńska, Aleksandra, Jozef Grego, Sebastian Hofman, and Andrzej Falniowski. "Phylogeography and species distinction in Bythinella (Caenogastropoda: Truncatelloidea: Bythinellidae) in Central Europe and the Balkans." Folia Malacologica 33, no. 1 (2025): 1–46. https://doi.org/10.12657/folmal.033.001.

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Genus Bythinella Moquin-Tandon, 1856 is represented by over 250 nominal species of minute snails, inhabiting springs of Europe and Asia Minor. Wide variability and eco-plasticity of the shell, coupled with not necessarily justified assumptions of complete isolation of the populations inhabiting particular springs, has resulted in chaos in species-level systematics. The aim of the study is to complete and interpret these data, considering the populations from Central Europe and West Balkans not studied so far. Mitochondrial cytochrome c oxidase subunit I (COI) as well as five nuclear fragments: histone 3 (H3), ribosomal Internal Transcribed Spacer 1 (ITS-1), ribosomal Internal Transcribed Spacer 2 (ITS-2), 18S ribosomal RNA (18S) and 28S ribosomal RNA (28S) were sequenced. For COI the phylogenetic analysis included all the sequences from GenBank to infer the pattern of evolution as well as species distinction. The specimens were collected at 84 localities in Central and South Europe. For COI 151 specimens were sequenced, 92 of them also for the five nuclear fragments. Together with sequences obtained from GenBank, a total of 1,437 COI sequences from Bythinella were used. There were 206 polymorphic sites, and 360 haplotypes. Among the three techniques for species delimitation used, ABGD and ASAP gave the most conservative result: 86 mOTUs, grouped in 19 clades (A–T). New sequences were classified in nine clades. Sympatric occurrence of two mOTUs or even clades was found in as many as 16 springs and even of three mOTUs in two springs. The sympatric occurrence of Bythinella species is thus not exceptional. The morphology of clades was compared based on: shells, radulae, renal and pallial section of the female reproductive organs and penis with the tubular accessory gland. In general, the morphostatic character of evolution was confirmed.

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Xi, Rui, Wanru Gao, Xin Wang, and Yingchun Xing. "Species diversity of coral reef fishes around the West Island of Sanya City, South China Sea, based on environmental DNA." Biodiversity Data Journal 10 (September 30, 2022): e89685. https://doi.org/10.3897/BDJ.10.e89685.

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West Island is the second largest island in the Hainan Province, China and its surrounding sea area has a well-preserved coral reef ecosystem and high species diversity of coral reef fishes. Undoubtedly, coral reef fishes and coral reefs have complex symbiotic relationships and fish species diversity should reflect the healthy status of coral reef ecosystems. Environmental DNA (eDNA) is a useful and sensitive tool to detect fish species and causes less environmental damage than traditional fish survey methods. This paper investigated coral reef fish species of West Island, Hainan Province, China, based on eDNA and provided scientific data for understanding and protection of the coral reef ecosystem of the South China Sea.The sea area surrounding West Island is the most important component of the coral reef ecosystem in the northern part of the South China Sea, which is also an essential part of the largest National Coral Reef Reserve in China. However, complete data of fish species distributed in this region have been a long-term gap. This study provides information on 41 fish species belonging to 28 genera, 16 families and three orders in this sea area and is the first complete record of coral reef fishes surrounding the West Island. In addition, the information of Molecular Operational Taxonomic Units (MOTUs) for taxon identification were also provided and it could contribute to building specific eDNA taxonomy database of coral reef fishes of the South China Sea. The study includes three datasets, with aspects of fish taxon-occurrences, MOTUs sequences and information of environmental indicators surrounding West Island, Hainan Province, China. The "fish taxon occurrences" dataset presents records involving taxonomic, distribution, habitat condition, latitude and longitude of 41 coral reef fish species detected, based on eDNA, the "MOTUs sequences" dataset provides MOTUs sequences and their abundance of 31 species detected and the "information of environmental indicators" dataset presents records of transparency, temperature, water pressure, dissolved oxygen, electrical conductivity, hydrogen and redox potential measured from five sampling localities.

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Karabanov, Dmitry P., Alexey A. Kotov, Elena A. Borovikova, Yulia V. Kodukhova, and Xiaowei Zhang. "Comparison of the Efficiency of Single-Locus Species Delimitation Methods: A Case Study of a Single Lake Fish Population in Comparison against the Barcodes from International Databases." Water 15, no. 10 (2023): 1851. http://dx.doi.org/10.3390/w15101851.

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To date, a rather large set of both mathematical theories for species delimitation, based on single-locus genetic data, and their implementations as software products, has been accumulated. Comparison of the efficiencies of different delineation methods in the task of accumulating and analyzing data with reference to different taxa in different regions, is vital. The aim of this study was to compare the efficiency of fifteen single-locus species delimitation methods using the example of a fish species found in a single lake in European Russia (Lake Plescheyevo) with reference to other sequences of revealed taxa deposited in international databases. We analyzed 186 original COI sequences belonging to 24 haplotypes, and 101 other sequences previously deposited in GenBank and BOLD. Comparison of all 15 alternative taxonomies demonstrated that all methods adequately separate only the genera, while the number of delimited mOTUs differed from 16 (locMin) to 43 (HwM/CoMa). We can assume that the effectiveness of each method is correlated with the number of matches based on Ctax and MatchRatio criteria. The most comparable results were provided by bGMYC, mPTP, STACEY, KoT and ASAP and the most synchronous results were obtained from bGMYC, mPTP, STACEY and ASAP. We believe that these results are maximally realistic in the number of revealed mOTUs. A high genetic diversity, resulting in the existence of several mOTUs and phylogenetic lineages within many species, demonstrates the usefulness of the “polymorphic species” concept, which does not underestimate species richness and does not prevent the rational use and protection of biodiversity.

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Bidondo, L. Fernández, R. P. Colombo, M. Recchi, et al. "Detection of arbuscular mycorrhizal fungi associated with pecan (Carya illinoinensis) trees by molecular and morphological approaches." MycoKeys 42 (November 30, 2018): 73–88. http://dx.doi.org/10.3897/mycokeys.42.26118.

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Arbuscular mycorrhizal (AM) fungal community associated with pecan (Caryaillinoinensis) roots and rhizospheric soils was assessed by spore isolation and morphological characterisation and by pyrosequencing of AM molecular markers. The AM fungal community associated with pecan growing in the field, was always more diverse than that associated with pecan growing in containers. This was not observed when AM richness was studied, suggesting that soil disturbance by a reduction in host plant richness leads to a less equitable distribution of AM fungal species, in contrast to natural soils. The chosen primers (AMV4.5F/AMDGR) for pyrosequencing showed high AM fungal specificity. Based on 97% sequence similarity, 49 operational taxonomic units (MOTUs) were obtained and, amongst these, 41 MOTUs corresponded to the Glomeromycotaphylum. The number of obtained AM sequences ranged from 2164, associated with field samples, to 5572 obtained from pecan trap pot culture samples, defining 30 and 29 MOTUs, respectively. Richness estimated by conventional species identification was 6 and 9 AM fungal species in soil and pot samples, respectively. Claroideoglomuslamellosum, Funneliformismosseae and Entrophosporainfrequens were the only taxa detected using both techniques. Predominant sequences in the pecan rhizosphere samples, such as Rhizoglomusirregulare and other less abundant (Dominikiairanica, Dominikiaindica, Sclerocystissinuosa, Paraglomuslaccatum), were detected only by pyrosequencing. Detection of AM fungal species based on spore morphology, in combination with molecular approaches, provides a more comprehensive estimate of fungal community composition.

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Dahruddin, Hadi, Arni Sholihah, Tedjo Sukmono, et al. "Revisiting the Diversity of Barbonymus (Cypriniformes, Cyprinidae) in Sundaland Using DNA-Based Species Delimitation Methods." Diversity 13, no. 7 (2021): 283. http://dx.doi.org/10.3390/d13070283.

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Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of Java, Sumatra, Borneo, and Peninsular Malaysia, is one of those. With more than 900 species, its freshwater ichthyofauna includes a large number of medium- to large-size species, which are targeted by inland fisheries. Stock assessment requires accurate taxonomy; however, several species groups targeted by inland fisheries are still poorly known. One of those cases is the cyprinid genus Barbonymus. For this study, we assembled a consolidated DNA barcode reference library for Barbonymus spp. of Sundaland, consisting of mined sequences from BOLD, as well as newly generated sequences for hitherto under-sampled islands such as Borneo. A total of 173 sequences were analyzed using several DNA-based species delimitation methods. We unambiguously detected a total of 6 Molecular Operational Taxonomic Units (MOTUs) and were able to resolve several conflicting assignments to the species level. Furthermore, we clarified the identity of MOTUs occurring in Java.

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Wang, Chongzhao, Zhenhua Ma, Kun Cao, et al. "Species diversity of fish at the Wuzhizhou Island, South China Sea, based on environmental DNA." Biodiversity Data Journal 12 (June 14, 2024): e127120. https://doi.org/10.3897/BDJ.12.e127120.

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Wuzhizhou Island (WZZ) is located in Haitang Bay in the northern region of Sanya, Hainan Island. The sea area surrounding WZZ represents a typical tropical marine ecosystem, characterised by diverse and complex habitats. Therefore, there is a rich variety of marine fish species at WZZ. The marine ecosystem of WZZ was seriously destroyed initially in the 1970s-1980s and recovered in the 1990s, then constructed as the first national tropical marine ranch demonstration area of China in 2019. As fish is an important high trophic vertebrate in the marine ecosystem, understanding the composition and distribution of fish species could help us to recognise the status of the ecosystem of WZZ and supply scientific data for construction of the national marine ranch demonstration area. This study used eDNA technology to investigate the composition of fish community surrounding WZZ and provided a scientific basis for realising and protecting the marine ecosystem of the South China Sea.The WZZ is an offshore island in the South China Sea, harbouring abundant marine fish resources. Although previous research investigated fish species of WZZ, the data were, however, still incomplete due to limitation of sampling methods and survey seasons. In this study, we intended to take advantage of eDNA and supplement data of fish species at WZZ as much as possible. Based on eDNA, this study provided the data on 188 fish species (including nine undetermined species denoted by genus sp.) belonging to 17 orders, 63 families and 124 genera and they were the more comprehensive records of fish species surrounding WZZ. In addition, the information on Molecular Operational Taxonomic Units (MOTUs) for taxon identification was also provided, aiming to contribute to the establishment of a specific eDNA taxon database for fish of the South China Sea. This study included two datasets, which were occurrences of fish taxa at WZZ, as well as MOTUs sequences and geographical coordinate information of sampling sites. The "fish taxon occurrences" dataset presented records on taxonomic, distribution and habitat conditions of 188 fish species detected using eDNA, as well as the latitude and longitude information of the sampling sites, the "MOTUs information" dataset provided the MOTUs sequences, source of sequences, abundance of sequences for 188 fish species, also included the species matched in NCBI and the best NCBI BLAST sequence similarity.

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Adamo, Martino, Samuele Voyron, Matteo Chialva, Roland Marmeisse, and Mariangela Girlanda. "Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats." PLOS ONE 15, no. 12 (2020): e0244682. http://dx.doi.org/10.1371/journal.pone.0244682.

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In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.

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Bidondo, L. Fernández, R. P. Colombo, M. Recchi, et al. "Detection of arbuscular mycorrhizal fungi associated with pecan (Carya illinoinensis) trees by molecular and morphological approaches." MycoKeys 42 (November 30, 2018): 73–88. https://doi.org/10.3897/mycokeys.42.26118.

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Arbuscular mycorrhizal (AM) fungal community associated with pecan (Carya illinoinensis) roots and rhizospheric soils was assessed by spore isolation and morphological characterisation and by pyrosequencing of AM molecular markers. The AM fungal community associated with pecan growing in the field, was always more diverse than that associated with pecan growing in containers. This was not observed when AM richness was studied, suggesting that soil disturbance by a reduction in host plant richness leads to a less equitable distribution of AM fungal species, in contrast to natural soils. The chosen primers (AMV4.5F/AMDGR) for pyrosequencing showed high AM fungal specificity. Based on 97% sequence similarity, 49 operational taxonomic units (MOTUs) were obtained and, amongst these, 41 MOTUs corresponded to the Glomeromycota phylum. The number of obtained AM sequences ranged from 2164, associated with field samples, to 5572 obtained from pecan trap pot culture samples, defining 30 and 29 MOTUs, respectively. Richness estimated by conventional species identification was 6 and 9 AM fungal species in soil and pot samples, respectively. Claroideoglomus lamellosum, Funneliformis mosseae and Entrophospora infrequens were the only taxa detected using both techniques. Predominant sequences in the pecan rhizosphere samples, such as Rhizoglomus irregulare and other less abundant (Dominikia iranica, Dominikia indica, Sclerocystis sinuosa, Paraglomus laccatum), were detected only by pyrosequencing. Detection of AM fungal species based on spore morphology, in combination with molecular approaches, provides a more comprehensive estimate of fungal community composition.

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Ouvrard, Pierre, Damien M. Hicks, Molly Mouland, et al. "Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae: Meligethinae), and the population structure of Brassicogethes aeneus." Genome 59, no. 12 (2016): 1101–16. http://dx.doi.org/10.1139/gen-2016-0020.

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Pollen beetles (Nitidulidae: Meligethinae) are among the most abundant flower-visiting insects in Europe. While some species damage millions of hectares of crops annually, the biology of many species is little known. We assessed the utility of a 797 base pair fragment of the cytochrome oxidase 1 gene to resolve molecular operational taxonomic units (MOTUs) in 750 adult pollen beetles sampled from flowers of 63 plant species sampled across the UK and continental Europe. We used the same locus to analyse region-scale patterns in population structure and demography in an economically important pest, Brassicogethes aeneus. We identified 44 Meligethinae at ∼2% divergence, 35 of which contained published sequences. A few specimens could not be identified because the MOTUs containing them included published sequences for multiple Linnaean species, suggesting either retention of ancestral haplotype polymorphism or identification errors in published sequences. Over 90% of UK specimens were identifiable as B. aeneus. Plant associations of adult B. aeneus were found to be far wider taxonomically than for their larvae. UK B. aeneus populations showed contrasting affiliations between the north (most similar to Scandinavia and the Baltic) and south (most similar to western continental Europe), with strong signatures of population growth in the south.

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Rolfe, Ashley K., Allen Kurta, and Daniel L. Clemans. "Species-level analysis of diets of two mormoopid bats from Puerto Rico." Journal of Mammalogy 95, no. 3 (2014): 587–96. https://doi.org/10.5281/zenodo.14817244.

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(Uploaded by Plazi for the Bat Literature Project) Molecular approaches, such as polymerase chain reaction (PCR), allow biologists to analyze the diet of mammals in more detail than conventional techniques, by targeting DNA of prey found within feces. Diets of the Antillean ghost-faced bat (Mormoops blainvillei) and sooty mustached bat (Pteronotus quadridens) on Puerto Rico were determined via PCR, and resulting sequences of DNA were compared with those in the Barcode of Life Data Systems (BOLD). We identified 21 species consumed by M. blainvillei and 4 by P. quadridens, although an additional 12 sequences were identified to genus or family. Seven taxa in the diet of these bats were of agricultural or human-health concern. All sequences, including those that did not match a reference insect in BOLD, were collapsed into molecular operational taxonomic units (MOTUs) and used to demonstrate that dietary breadth (Levin's measure) of M. blainvillei was 18% less than that of P. quadridens and that dietary overlap (Schoener's index) between species was only 11.6% at the level of species. Use of MOTUs showed significantly greater differences in dietary breadth and less dietary overlap between these insular endemics than previous analyses based on standard fecal analysis to the level of order.

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Wangensteen, Owen S., Creu Palacín, Magdalena Guardiola, and Xavier Turon. "DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers." PeerJ 6 (May 4, 2018): e4705. http://dx.doi.org/10.7717/peerj.4705.

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Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrialcytochrome c oxidase(COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.

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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 mixed Yule coalescent (GMYC) models were used to evaluate barcoding success rates in the data set. Best match showed that COI and 28S sequences could provide 100 and 95.52% correct identification, respectively. The average interspecific divergences were 19.81% for COI data and 20.38% for 28S data, and mean intraspecific divergences were 0.56 and 0.07%, respectively. For COI data, multiple methods (ABGD, Klee, and tree-based methods) resulted in general congruence with morphological identifications. However, GMYC analysis tended to provide more molecular operational taxonomic units (MOTUs). Twelve MOTUs derived from five morphospecies (Rhodococcus sariuoni, Pulvinaria vitis, Pulvinaria aurantii, Parasaissetia nigra, and Ceroplastes rubens) were observed using the GMYC approach. In addition, tree-based methods showed that 28S sequences could be used for species-level identification (except for Ceroplastes ceriferus – Ceroplastes pseudoceriferus), even with low genetic variation (<1%). This report demonstrates the robustness of DNA barcoding for species discrimination of soft scales with two molecular markers (COI and 28S) and provides a reliable barcode library and rapid diagnostic tool for common soft scales in China.

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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) mitochondrial gene. Our final data set includes COI sequences from 112 taxa distributed in 23 genera of penaeids. We employed the general mixed Yule coalescent (GMYC) model, the Poisson tree processes (PTP), and the Bayesian PTP model (bPTP) for MOTUs delimitation. Intraspecific and interspecific genetic distances were also calculated. Our findings evidenced a high level of hidden diversity, showing 143 MOTUs, with 27 nominal species not agreeing with the genetic delimitation obtained here. These data represent potential new species or highly structured populations, showing the importance of including a non-distance-based species delimitation approach in biodiversity studies. The results raised by this study shed light on the Penaeidae biodiversity, addressing important issues about taxonomy and mislabeling in databases and contributing to a better comprehension of the group, which can certainly help management policies for shrimp fishery activity in addition to conservation programs.

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Pérez-Enríquez, Ricardo, Alejandra Arciniega, Noé Díaz-Viloria, and Salvador E. Lluch-Cota. "Diversity of planktonic gastropods from western Baja California Peninsula assessed by 18S rDNA sequences." Revista Mexicana de Biodiversidad 94 (May 24, 2023): e944968. http://dx.doi.org/10.22201/ib.20078706e.2023.94.4968.

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The study of planktonic mollusks is a relevant element to understand the dynamics of the benthic communities under present and future environmental conditions. We present the description of the biodiversity of planktonic gastropods at 2 sampling sites on the Pacific coast of the Baja California Peninsula, Mexico. Organisms collected from plankton tows at 2 locations (Cabo Tosco, n = 89 and La Bocana, n = 213) were sequenced for a portion of the 18S rDNA gene. High diversity was registered, with 71 Molecular Operational Taxonomic Units (MOTUs), which contrasts with the low phenotypic diversity of stereoscopic images. Differences in community composition between and within sampling sites indicate that planktonic gastropod distribution is not random but probably modulated by micro-environmental processes such as currents or biological events. The presence of non-gastropod sequences within some shells (n = 6) suggests their use as carriers of eggs or larvae of other taxa.

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Teixeira, Marcos A. L., Arne Nygren, Ascensão Ravara, Pedro E. Vieira, José Carlos Hernández, and Filipe O. Costa. "The small polychaete Platynereis dumerilii revealed as a large species complex with fourteen MOTUs in European marine habitats." ARPHA Conference Abstracts 4 (March 4, 2021): e64937. https://doi.org/10.3897/aca.4.e64937.

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Recent studies reporting complexes of cryptic or pseudo-cryptic species with narrow geographic distributions have been challenging the cosmopolitan status of a fair number of marine benthic invertebrates. Morphologically similar species are often overlooked but molecular techniques have been extremely effective in signalling potential hidden diversity which, complemented with further detailed examination, might reveal unique morphological and ecological features.Evidence of morphological stasis, where no clear and stable morphological differences are apparent, can be exemplified by the annelids Platynereis dumerilii (Audouin & Milne Edwards, 1833) and Platynereis massiliensis (Moquin-Tandon, 1869). These sibling species, usually found among algae in marine intertidal and subtidal habitats, can only be distinguished by their different reproductive strategies and life histories. The former is gonochoric, with a single reproductive event in life (semelparous) transforming into a pelagic epitokous form called heteronereis, has free spawning synchronized by lunar periodicity and a larval stage with planktotrophic development; while the latter shows no epitokous transformation and is a protandrous hermaphrodite, characterized by egg brooding and lecithotrophic larval stages with a semi-direct development.In order to verify the possible existence of additional hidden Platynereis species within the P. dumerilii morphotype, we used a multi-locus approach to investigate 26 populations along Europe from the NE Atlantic and the Macaronesia islands (Azores, Madeira and Canaries) to the Western and Eastern Mediterranean Sea.We concatenated the mtDNA COI-5P, rDNA 16S and 28S-D2 sequences and performed a phylogenetic analysis through Bayesian inference (BI). To depict Molecular Operational Taxonomic Units (MOTUs), we applied three delimitation methods (ABGD, bPTP and GYMC) to the concatenated alignment, except for COI where we also applied the Barcode Index Number (BIN), implemented in BOLD, which is exclusive to this locus. Consensus MOTUs were defined based on the majority rule and, in case of draw, the most conservative MOTUs were chosen.We detected at least 14 MOTUs with 23.1% COI mean K2P distance (6.6 - 32.6%). The BI tree is split into three major clades (Clade A: MOTUs 1-3, Clade B: MOTUs 4-9 and Clade C: MOTUs 10-14), with MOTU 3 appearing to represent P. dumerilii sensu stricto and MOTU 9 P. massiliensis. This assumption is based on data from the Type locality and a previous study by Wage et al. (2017), which combined phylogeographic (COI barcode region), reproductive biology and life-history observations on some selected Platynereis populations thriving in the vent areas from the Italian islands of Ischia and Vulcano. Major Cade C seems to be pseudo-cryptic as some visible differences can be found in the specimens, as for example, the size of the tentacular cirri and lack of dorsal pigmentation, in contrast with Clades A and B, where only differences in pigmentation types were found so far.The Spanish archipelago of the Canary Islands and the whole Mediterranean Sea seem to be a cryptic hotspot. Five MOTUs are unique to the Macaronesia and five sympatric MOTUs are present in the Gran Canaria and La Palma islands alone. Additionally, three lineages were present exclusively in the Mediterranean with four sympatric MOTUs spotted in the southeast of Spain (Calpe) and the Greek island of Crete. Three out of four NE Atlantic MOTUs are shared with the Mediterranean with one exclusive to this part of the continent.Failure to recognise this hidden biodiversity may compromise the accuracy and the interpretation of biomonitoring data or other relevant ecological studies. Integrative taxonomy is thus essential to solve these uncertainties and to allow naming the involved undescribed species. Otherwise, most molecular data providing enough support for species hypothesis will continue to be unused, and large fractions of biodiversity will persist unnoticed.

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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. 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 different from the assigned morphospecies (16). As to the incongruence between molecular and morphological results, we checked the specimens again and made sure that most morphological differences were determined to be intraspecific differences (except the difference between M. angusta and M. mckittrickae), although a large genetic distance existed. Finally, 16 Margattea species from China were defined in this study, of which, seven new species are established, i.e. Margattea deltodonta J-J He &amp; Z-Q Wang, sp. nov., Margattea cuspidata J-J He &amp; Z-Q Wang, sp. nov., Margattea caudata J-J He &amp; Z-Q Wang, sp. nov., Margattea paratransversa J-J He &amp; Z-Q Wang, sp. nov., Margattea disparilis J-J He &amp; Z-Q Wang, sp. nov., Margattea transversa J-J He &amp; Z-Q Wang, sp. nov., and Margattea bicruris J-J He &amp; Z-Q Wang, sp. nov.

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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 different from the assigned morphospecies (16). As to the incongruence between molecular and morphological results, we checked the specimens again and made sure that most morphological differences were determined to be intraspecific differences (except the difference between M. angusta and M. mckittrickae), although a large genetic distance existed. Finally, 16 Margattea species from China were defined in this study, of which, seven new species are established, i.e. Margattea deltodonta J-J He & Z-Q Wang, sp. nov., Margattea cuspidata J-J He & Z-Q Wang, sp. nov., Margattea caudata J-J He & Z-Q Wang, sp. nov., Margattea paratransversa J-J He & Z-Q Wang, sp. nov., Margattea disparilis J-J He & Z-Q Wang, sp. nov., Margattea transversa J-J He & Z-Q Wang, sp. nov., and Margattea bicruris J-J He & Z-Q Wang, sp. nov.

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Zhao, Yizheng, Hui Wang, Huimin Huang, and Zhijun Zhou. "A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China." ZooKeys 1123 (October 5, 2022): 147–71. http://dx.doi.org/10.3897/zookeys.1123.86704.

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Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 118 BINs (Barcodes Index Numbers). Among these 90 species-level taxa, 68 corresponded with morphospecies, while the remaining 22 were identified based on reverse taxonomy using BIN assignment. Thirteen of these morphospecies were represented by a single barcode (so-called singletons), and each of 19 morphospecies were split into more than one BIN. The consensus delimitation scheme yielded 55 Molecular Operational Taxonomic Units (MOTUs). Only four morphospecies (Imax &gt; DNN) failed to be recovered as monophyletic clades (i.e., Elimaea terminalis, Phyllomimus klapperichi, Sinochlora szechwanensis and Xizicus howardi), so it is speculated that these may be species complexes. Therefore, the diversity of katydids, cave crickets, and leaf-rolling crickets in Zhejiang Province is probably slightly higher than what current taxonomy would suggest.

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Zhao, Yizheng, Hui Wang, Huimin Huang, and Zhijun Zhou. "A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China." ZooKeys 1123 (October 5, 2022): 147–71. https://doi.org/10.3897/zookeys.1123.86704.

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Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 118 BINs (Barcodes Index Numbers). Among these 90 species-level taxa, 68 corresponded with morphospecies, while the remaining 22 were identified based on reverse taxonomy using BIN assignment. Thirteen of these morphospecies were represented by a single barcode (so-called singletons), and each of 19 morphospecies were split into more than one BIN. The consensus delimitation scheme yielded 55 Molecular Operational Taxonomic Units (MOTUs). Only four morphospecies (Imax > DNN) failed to be recovered as monophyletic clades (i.e., Elimaea terminalis, Phyllomimus klapperichi, Sinochlora szechwanensis and Xizicus howardi), so it is speculated that these may be species complexes. Therefore, the diversity of katydids, cave crickets, and leaf-rolling crickets in Zhejiang Province is probably slightly higher than what current taxonomy would suggest.

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Jaquier, Mélissa, Camille Albouy, Wilhelmine Bach, et al. "Environmental DNA diffusion of reef fishes along a distance gradient from four isolated islands of the Western Indian Ocean." ARPHA Conference Abstracts 4 (March 4, 2021): e65060. https://doi.org/10.3897/aca.4.e65060.

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Islands have traditionally served as model systems to study ecological and evolutionary processes (Warren et al. 2015) and could also represent a relevant system to study environmental DNA (eDNA). Isolated island reefs that are affected by climatic threats would particularly benefit from cost- and time-efficient biodiversity surveys to set priorities for their conservation. Among time efficiency methods, eDNA has emerged as a novel molecular metabarcoding technique to detect biodiversity from simple environmental samples even in remote marine environments. However, eDNA monitoring techniques for marine environments are at a developmental phase, with a few remaining unknowns related to DNA residence time and movement. In particular, the redistribution of eDNA, via ocean currents, could blur the composition signal and its association with local environmental conditions (Goldberg et al. 2016). Here, we investigated the detection variation of eDNA along a distance gradient across four islands in the French Scattered Islands. We collected 30 L of surface water per filter at an increasing distance from the islands reefs (0m, 250m, 500m, 750m). Using a metabarcoding protocol, we used the teleo primers to target a fraction of 12S mitochondrial DNA to detect Actinopterygii and Elasmobranchii. We then applied a sequence clustering approach to generate Molecular Taxonomic Units (MOTUs), which were assigned to a taxonomic group using a reference database. By assigning eDNA sequences to species using a public reference database, we classified species according to their preferred habitat types between benthic/demersal and pelagic. Our results show no significant relationship between distance and MOTUs richness for both habitat types. By using a Joint Species Distribution Modelling approach (JSDM, Hierarchical Modelling of Species Communities), we retained the multidimensional information captured by eDNA and detect species- and family-specific responses to distance (Fig. 1). We showed that benthic MOTUs were found in closer proximity to the reef, while typical pelagic MOTUs were found at greater distances from the reef. Hence, MOTU-level analyses coupled with JSDM were more informative that when aggregating it into coarser richness. Altogether, our eDNA distance sampling gradient detected an ecological signal of habitat selection by fish species, which suggest that eDNA could help understand the behavior of species and their distribution in marine environments at a fine spatial scale.

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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 of 14 known Rhabdoblatta species are described worldwide. Our study shows that combining molecular species delimitation methods with morphological data helps to delimit species and understand cockroach biodiversity.

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Ehemann, Nicolás Roberto, Raquel Siccha-Ramirez, Junior Miranda-Romero, Francisco Javier García-Rodríguez, and José De La Cruz-Agüero. "Barcode Reveals Hidden Diversity and Cryptic Speciation among Butterfly Rays Distributed in the Americas." Taxonomy 4, no. 3 (2024): 561–73. http://dx.doi.org/10.3390/taxonomy4030027.

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The taxonomic status of butterfly rays within the genus Gymnura remains a subject of ongoing debate among researchers. Some authors recognize up to five valid species for the Americas, while others considered several to be synonyms, which has posed a persistent challenge. We aimed to shed light on this complexity by employing molecular operational taxonomic units (MOTUs) based on the mitochondrial gene cytochrome oxidase I (COI). Genetic sequences were obtained from fresh muscle tissue collected in the marine ecoregions corresponding to the type locality from all the nominal butterfly ray species distributed along the Eastern Tropical Pacific (ETP). Our results unveiled compelling findings; all the species delimitation models used consistently identified seven MOTUs for the American continent and an extra G. altavela MOTU restricted to Africa. In addition, our results and models exceeded the worldwide accepted interspecific threshold of 2.0%. Remarkably, our results support the taxonomic reinstatement of Gymnura afuerae (Hildebrand, 1946) as a valid species, with a range expanding into the ETP in the Southern Hemisphere. Similarly, our data support the recent suggestion of resurrecting Gymnura valenciennii (Duméril, 1865) as a valid species in the western Atlantic. These findings urge a reassessment of the conservation status and a comprehensive taxonomic revision of American butterfly rays.

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Limeira Filho, Daniel, Elidy Rayane de Rezende França, Dalton Kaynnan de Prado Costa, et al. "Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae)." Biology 13, no. 3 (2024): 162. http://dx.doi.org/10.3390/biology13030162.

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Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.

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Alberdi, Antton, Inazio Garin, Ostaizka Aizpurua, Joxerra Aihartza, and Brock Fenton. "The Foraging Ecology of the Mountain Long-Eared Bat Plecotus macrobullaris Revealed with DNA Mini-Barcodes." PLoS ONE 7, no. 4 (2012): e35692. https://doi.org/10.5281/zenodo.14821329.

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(Uploaded by Plazi for the Bat Literature Project) Molecular analysis of diet overcomes the considerable limitations of traditional techniques for identifying prey remains in bat faeces. We collected faeces from individual Mountain Long-eared Bats Plecotus macrobullaris trapped using mist nets during the summers of 2009 and 2010 in the Pyrenees. We analysed their diet using DNA mini-barcodes to identify prey species. In addition, we inferred some basic features of the bat's foraging ecology that had not yet been addressed. P. macrobullaris fed almost exclusively on moths (97.8%). As prey we detected one dipteran genus (Tipulidae) and 29 moth taxa: 28 were identified at species level (23 Noctuidae, 1 Crambidae, 1 Geometridae, 1 Pyralidae, 1 Sphingidae, 1 Tortricidae), and one at genus level (Rhyacia sp., Noctuidae). Known ecological information about the prey species allowed us to determine that bats had foraged at elevations between 1,500 and 2,500 m amsl (above mean sea level), mostly in subalpine meadows, followed by other open habitats such as orophilous grasslands and alpine meadows. No forest prey species were identified in the diet. As 96.4% of identified prey species were tympanate moths and no evidence of gleaning behaviour was revealed, we suggest P. macrobullaris probably forages by aerial hawking using faint echolocation pulses to avoid detection by hearing moths. As we could identify 87.8% of the analysed sequences (64.1% of the MOTUs, Molecular Operational Taxonomic Units) at species level, we conclude that DNA mini-barcodes are a very useful tool to analyse the diet of mothspecialist bats.

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Oliveira, Pablo Viana, Alexandre Rosa dos Santos, Emily Lopes Olive, et al. "Molecular Species Delimitation Using COI Barcodes of Mealybugs (Hemiptera: Pseudococcidae) from Coffee Plants in Espírito Santo, Brazil." Diversity 15, no. 2 (2023): 305. http://dx.doi.org/10.3390/d15020305.

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Mealybugs are insects belonging to the family Pseudococcidae. This family includes many plant-pest species with similar morphologies, which may lead to errors in mealybug identification and delimitation. In the present study, we employed molecular-species-delimitation approaches based on distance (ASAP) and coalescence (GMYC and mPTP) methods to identify mealybugs collected from coffee and other plant hosts in the states of Espírito Santo, Bahia, Minas Gerais, and Pernambuco, Brazil. We obtained 171 new COI sequences, and 565 from the BOLD Systems database, representing 26 candidate species of Pseudococcidae. The MOTUs estimated were not congruent across different methods (ASAP-25; GMYC-30; mPTP-22). Misidentifications were revealed in the sequences from the BOLD Systems database involving Phenacoccus solani × Ph. solenopsis, Ph. tucumanus × Ph. baccharidis, and Planacoccus citri × Pl. minor species. Ten mealybug species were collected from coffee plants in Espírito Santo. Due to the incorrect labeling of the species sequences, the COI barcode library of the dataset from the database needs to be carefully analyzed to avoid the misidentification of species. The systematics and taxonomy of mealybugs may be improved by integrative taxonomy which may facilitate the integrated pest management of these pests.

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Pinto, Israel de Souza, Bruno Leite Rodrigues, Thais de Araujo-Pereira, et al. "DNA barcoding of sand flies (Diptera, Psychodidae, Phlebotominae) from the western Brazilian Amazon." PLOS ONE 18, no. 2 (2023): e0281289. http://dx.doi.org/10.1371/journal.pone.0281289.

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The subfamily Phlebotominae comprises important insects for public health. The use of complementary tools such as molecular taxonomy is necessary for interspecific delimitation and/or discovery of cryptic species. Here, we evaluated the DNA barcoding tool to identify different species in the southwestern Brazilian Amazon. For this, we collected sand flies in forest fragments along the highway BR-317, in the municipality of Brasiléia, state of Acre, Brazil. The specimens were DNA-barcoded using a fragment of the cytochrome c oxidase subunit I (COI) gene. The sequences were analyzed to generate K2P pairwise genetic distances and a Neighbour-joining tree. The sand fly barcodes were also clustered into Molecular Operation Taxonomic Units (MOTU) using Automatic Barcode Gap Discovery (ABGD) approach. A total of 59 COI sequences comprising 22 nominal species and ten genera were generated. Of these, 11 species had not been sequenced before, thus being new COI sequences to science. Intraspecific genetic distances ranged between 0 and 4.9%, with Pintomyia serrana presenting the highest values of genetic distance, in addition to having been partitioned into three MOTUs. Regarding the distances to the nearest neighbour, all species present higher values in relation to the maximum intraspecific distance, in addition to forming well supported clusters in the neighbour-joining analysis. The DNA barcoding approach is useful for the molecular identification of sand flies from Brasiléia, state of Acre, and was efficient in detecting cryptic diversity of five species which can be confirmed in future studies using an integrative approach. We also generated new COI barcodes for Trichophoromyia auraensis, Nyssomyia shawi, and Psychodopygus paraensis, which may play a role in the transmission of Leishmania spp. in the Brazilian Amazon.

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Nascimento, Maria Histelle Sousa, Deborah Gaído Aragão, Jordânia Leticia Nascimento Silva, et al. "The DNA barcode reveals cryptic diversity and a new record for the genus Leporinus (Characiformes, Anostomidae) in the hydrographic basins of central northern Brazil." PeerJ 11 (May 25, 2023): e15184. http://dx.doi.org/10.7717/peerj.15184.

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Leporinus is one of the most speciose genera of the order Characiformes, with 81 valid species distributed throughout much of Central and South America. The considerable diversity of this genus has generated extensive debate on its classification and internal arrangement. In the present study, we investigated the species diversity of the genus Leporinus in central northern Brazil, and conclude that six valid species—Leporinus maculatus, Leporinus unitaeniatus, Leporinus affinis, Leporinus venerei, Leporinus cf. friderici, and Leporinus piau—are found in the hydrographic basins of the Brazilian states of Maranhão, Piauí, and Tocantins. We analyzed 182 sequences of the Cytochrome Oxidase subunit I gene, of which, 157 were obtained from Leporinus specimens collected from the basins of the Itapecuru, Mearim, Turiaçu, Pericumã, Periá, Preguiças, Parnaíba, and Tocantins rivers. The species delimitation analyses, based on the ABGD, ASAP, mPTP, bPTP, and GMYC methods, revealed the presence of four distinct molecular operational taxonomic units (MOTUs), identified as L. maculatus, L. unitaeniatus, L. affinis, and L. piau (from the Parnaíba River). The bPTP method restricted L. venerei to a single MOTU, and confirmed the occurrence of this species in the rivers of Maranhão for the first time. The separation of L. cf. friderici into two clades and the subsequent formation of different operational taxonomic units was consistent with polyphyly in this species, which indicates the existence of cryptic diversity. The arrangement of L. cf. friderici and L. piau in two different clades supports the conclusion that the L. piau specimens from Maranhão were misidentified, based on their morphological traits, reflecting the taxonomic inconsistencies that exist among morphologically similar species. Overall, then, the species delimitation methods employed in the present study indicated the presence of six MOTUs—L. maculatus, L. unitaenitus, L. affinis, L. cf. friderici, L. venerei, and L. piau. In the case of two other MOTUs identified in the present study, one (L. venerei) is a new record for the state of Maranhão, and we believe that the other represents a population of L. piau from the basin of the Parnaíba River.

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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 female genitalia of 14 known Rhabdoblatta species are described worldwide. Our study shows that combining molecular species delimitation methods with morphological data helps to delimit species and understand cockroach biodiversity.

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Ferreira, Flavien, Paul Oliver, Fred Kraus, et al. "Molecular and acoustic evidence for large-scale underestimation of frog species diversity on New Guinea." Frontiers of Biogeography 18 (May 8, 2025): e137988. https://doi.org/10.21425/fob.18.137988.

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Species are fundamental units in biology; however, information on species diversity and distribution remain scarce for most taxonomic groups, especially in tropical rainforests. Such knowledge gaps are particularly acute in amphibians, the most threatened group of vertebrates, in which new species continue to be described at a high rate. Herein, using molecular-based approaches, we provide estimates for species diversity of frogs (Anura) in New Guinea and nearby islands, one of the biologically most diverse regions of the world. We first characterised taxonomic and geographic sampling for all available mitochondrial DNA sequences from native frog species. This led us to identify important molecular sampling gaps in the western half of New Guinea that we partially filled by adding 534 new sequences (16S rRNA). Large territories remain uncharted, particularly in the westernmost part of the central cordillera of New Guinea. Using our 16S rRNA dataset, we then delimited Molecular Operational Taxonomic Units (MOTUs), a subset of which was bioacoustically analysed. From a total of 369 delimited MOTUs, we found that 190 could not be assigned to any taxon. Amongst these, 123 are represented by specimens collected in the western half of New Guinea and 19 were supported as distinct by bioacoustics, confirming that this portion of the island is home to many unrecognised species. Based on the estimated level of undescribed diversity in taxa and areas for which data are available, we extrapolate that New Guinea and neighbouring islands could host 800–1,200 frog species, with only 560 species described to date. Highlights We assembled the most comprehensive molecular dataset to date (16S rRNA) for frogs from New Guinea and neighbouring islands. We delimited 190 candidate species, of which 19 are supported by available bioacoustic data. We estimated the actual number of frog species on New Guinea and neighbouring islands to be between 800 and 1,200. Parts of New Guinea exhibit species-diversity levels comparable to similarly sized regions in Amazonia and Madagascar. Most unrecognised frog taxa in the region are likely confined to restricted geographical areas and, thus, likely sensitive to both land use and climate change.

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Burgar, Joanna M., Daithi C. Murray, Michael D. Craig, et al. "Who's for dinner? High‐throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed." Molecular Ecology 23, no. 15 (2014): 3605–17. https://doi.org/10.5281/zenodo.14820662.

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(Uploaded by Plazi for the Bat Literature Project) Effective management and conservation of biodiversity requires understanding of predator–prey relationships to ensure the continued existence of both predator and prey populations. Gathering dietary data from predatory species, such as insectivorous bats, often presents logistical challenges, further exacerbated in biodiversity hot spots because prey items are highly speciose, yet their taxonomy is largely undescribed. We used high-throughput sequencing (HTS) and bioinformatic analyses to phylogenetically group DNA sequences into molecular operational taxonomic units (MOTUs) to examine predator–prey dynamics of three sympatric insectivorous bat species in the biodiversity hotspot of south-western Australia. We could only assign between 4% and 20% of MOTUs to known genera or species, depending on the method used, underscoring the importance of examining dietary diversity irrespective of taxonomic knowledge in areas lacking a comprehensive genetic reference database. MOTU analysis confirmed that resource partitioning occurred, with dietary divergence positively related to the ecomorphological divergence of the three bat species. We predicted that bat species' diets would converge during times of high energetic requirements, that is, the maternity season for females and the mating season for males. There was an interactive effect of season on female, but not male, bat species' diets, although small sample sizes may have limited our findings. Contrary to our predictions, females of two ecomorphologically similar species showed dietary convergence during the mating season rather than the maternity season. HTS-based approaches can help elucidate complex predator–prey relationships in highly speciose regions, which should facilitate the conservation of biodiversity in genetically uncharacterized areas, such as biodiversity hotspots.

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Czechowski, Paul, Chester J. Sands, Byron J. Adams, et al. "Antarctic Tardigrada: a first step in understanding molecular operational taxonomic units (MOTUs) and biogeography of cryptic meiofauna." Invertebrate Systematics 26, no. 6 (2012): 526. http://dx.doi.org/10.1071/is12034.

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Recent studies have suggested that some resident Antarctic biota are of ancient origin and may have been isolated for millions of years. The phylum Tardigrada, which is part of the Antarctic terrestrial meiofauna, is of particular interest due to an impressive array of biochemical abilities to withstand harsh environmental conditions. Tardigrades are one of the few widespread Antarctic terrestrial animals that have the potential to be used as a model for evolution and biogeography on the Antarctic continent. We isolated 126 individual tardigrades from four geographically isolated soil samples from two remote nunataks in the Sør Rondane Mountains, Dronning Maud Land, Antarctica. We examined genetic variation among individuals utilising three gene regions: cytochrome c oxidase subunit I gene (COI), 18S rDNA (18S), and the wingless (Wg) gene. Comparison of sequences from worldwide and Antarctic tardigrades indicated long-term survival and isolation over glacially dominated periods in ice-free habitats in the Sør Rondane Mountains.

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Grabowski, Michał, Tomasz Mamos, Karolina Bącela-Spychalska, Tomasz Rewicz, and Remi A. Wattier. "Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod." PeerJ 5 (February 28, 2017): e3016. http://dx.doi.org/10.7717/peerj.3016.

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BackgroundThe Balkans are a major biodiversity and endemism hotspot, worldwide. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification inGammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; (3) given thatG. roeseliithrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; (4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification ofG. roeselii.Material and MethodsDNA was extracted from 177 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors’ occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes.ResultsWe revealed thatG. roeseliiincludes at least 13 cryptic species or molecular operational taxonomic units (MOTUs), mostly of Miocene origin. A substantial Pleistocene diversification within-MOTUs was observed in several cases. We evidenced secondary contacts between very divergent MOTUs and introgression of nDNA. The Miocene ancestors could live in either lacustrine or riverine habitats yet their presumed geographic localisations overlapped with those of the Neogene lakes. Several extant riverine populations had Pleistocene lacustrine ancestors.DiscussionNeogene divergence of lineages resulting in substantial cryptic diversity may be a common phenomenon in extant freshwater benthic crustaceans occupying areas that were not glaciated during the Pleistocene. Evolution ofG. roeseliicould be associated with gradual deterioration of the paleolakes. The within-MOTU diversification might be driven by fragmentation of river systems during the Pleistocene. Extant ancient lakes could serve as local microrefugia during that time.

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Moore, Matthew R., Elijah J. Talamas, Jonathan S. Bremer, et al. "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs." NeoBiota 88 (October 26, 2023): 169–210. http://dx.doi.org/10.3897/neobiota.88.106326.

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In the past decade, several species of platygastroid wasps were found to be adventive in North America and Europe while under evaluation in quarantine as biological control agents of invasive pests. The scope and relative risk of this phenomenon is not fully known, but it is clearly a trend with implications for classical biological control. As a means of assessing the issue and to provide a global baseline, we implemented a data-mining approach with DNA sequences in the Barcode of Life Database, yielding 201 platygastroid BINs with intercontinental and island distributions. At least fifty-five BINs displayed exact COI barcode matches across continents, with many more BINs scored as inconclusive due to sequence length variation. These intercontinental and island BINs include biocontrol agents known to be adventive, as well as many species identified only to genus with uncertain geographic origins. We provide 2,500 identifications for platygastroid BOLD BINs, 88% to genus, to encourage additional research on this distributional phenomenon. The intercontinental BOLD BINs were compared to literature records and GBIF occurrences of cosmopolitan species to identify gaps and discordance across data sources. Smaller COI barcode datasets from localities in Florida and Germany, including topotypical specimens, revealed more intercontinental matches. We analyzed COI sequences in BOLD for the entirety of Insecta and Araneae to assess this phenomenon more broadly and because these taxa contain many hosts for platygastroid wasps. This method revealed that the intercontinental distribution phenomenon is widespread with implications for assessing biological diversity, taxonomic methodology and regulatory frameworks.

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Moore, Matthew R., Elijah J. Talamas, Jonathan S. Bremer, et al. "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs." NeoBiota 88 (October 26, 2023): 169–210. https://doi.org/10.3897/neobiota.88.106326.

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In the past decade, several species of platygastroid wasps were found to be adventive in North America and Europe while under evaluation in quarantine as biological control agents of invasive pests. The scope and relative risk of this phenomenon is not fully known, but it is clearly a trend with implications for classical biological control. As a means of assessing the issue and to provide a global baseline, we implemented a data-mining approach with DNA sequences in the Barcode of Life Database, yielding 201 platygastroid BINs with intercontinental and island distributions. At least fifty-five BINs displayed exact COI barcode matches across continents, with many more BINs scored as inconclusive due to sequence length variation. These intercontinental and island BINs include biocontrol agents known to be adventive, as well as many species identified only to genus with uncertain geographic origins. We provide 2,500 identifications for platygastroid BOLD BINs, 88% to genus, to encourage additional research on this distributional phenomenon. The intercontinental BOLD BINs were compared to literature records and GBIF occurrences of cosmopolitan species to identify gaps and discordance across data sources. Smaller COI barcode datasets from localities in Florida and Germany, including topotypical specimens, revealed more intercontinental matches. We analyzed COI sequences in BOLD for the entirety of Insecta and Araneae to assess this phenomenon more broadly and because these taxa contain many hosts for platygastroid wasps. This method revealed that the intercontinental distribution phenomenon is widespread with implications for assessing biological diversity, taxonomic methodology and regulatory frameworks.

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Bik, Holly. "Complexity matters: Evaluating the impact of bioinformatics parameters on eukaryotic MOTU delimitation and taxonomy assignment." ARPHA Conference Abstracts 4 (March 4, 2021): e65374. https://doi.org/10.3897/aca.4.e65374.

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Microbial metazoans (e.g. nematodes, copepods, tardigrades and other 'minor' animal phyla < 1mm in size) are ubiquitous and abundant across most ecosystems on earth. In marine sediment habitats, microbial metazoa exhibit high biodiversity but suffer from poor taxonomy and an ongoing lack of reference DNA sequences in public databases. Environmental DNA metabarcoding thus represents an increasingly critical tool for rapidly assessing the global biodiversity and phylogeographic patterns of such neglected metazoan groups. However, there are significant bioinformatics hurdles facing the study of microbial eukaryotes. Most software pipelines and databases have been designed and optimized for smaller (e.g. bacteria/archaea) or larger (e.g. vertebrate) taxa, and emphasize "standard" metabarcoding loci such as COI which are not useful for groups such as nematodes which lack universal COI primer binding regions. In addition, the sparsity of public reference barcodes for microbial metazoa often precludes accurate taxonomy assignments for unknown MOTUs in metabarcoding datasets. Here, I will present recent work focused on the refinement of bionformatics workflows for microbial metazoan groups, including efforts to account for intragenomic variation observed in rRNA loci, discrepancies in results across OTU vs. ASV generation pipelines, and biases in sequence-based taxonomhy assignment methods.

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Tang, Qian, Lei Deng, Qi Luo, Qian Duan, Xue Wang, and Renyi Zhang. "DNA Barcoding of Fish Species Diversity in Guizhou, China." Diversity 15, no. 2 (2023): 203. http://dx.doi.org/10.3390/d15020203.

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Guizhou is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River basins with abundant fish species. However, fish from these regions are threatened by anthropogenic activities, including overfishing and habitat destruction. Here, we assessed the fish diversity including more than half of the species from the region using DNA barcoding (partial sequence of cytochrome c oxidase subunit I (COI) gene). We obtained 800 mitochondrial COI barcode sequences from 82 genera, 18 families and 8 orders of fishes. The average Kimura two-parameter (K2P) distances within species and genera were 0.35% and 5.44%, respectively. The average interspecific distance was 15.54 times higher than the mean intraspecific distance. Moreover, DNA barcodes revealed 175 operational taxonomic units (OTUs) based on consensus demarcation schemes. Barcoding gaps were detected in 94.81% of morphospecies. Three fish species (Schistura fasciolata, Vanmanenia pingchowensis, and Misgurnus dabryanus) have considerable intraspecific variability, and each was divided into multiple molecular operational taxonomic units (MOTUs) using molecular definition methods (Automatic Barcode Gap Discovery, Refined Single Linkage, General Mixed Yule Coalescent, and Poisson Tree Processes), possibly indicating the occurrence of cryptic species. Altogether, our study reveals the complex diversity of fish species in Guizhou Province, serving as a reference for the conservation and monitoring of fish species in this region.

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Jacobina, Uedson Pereira, Rodrigo Augusto Torres, Paulo Roberto Antunes de Mello Affonso, Ewerton Vieira dos Santos, Leonardo Luiz Calado, and Jamille de Araújo Bitencourt. "DNA barcoding reveals cryptic diversity and peculiar phylogeographic patterns in mojarras (Perciformes: Gerreidae) from the Caribbean and South-western Atlantic." Journal of the Marine Biological Association of the United Kingdom 100, no. 2 (2020): 277–83. http://dx.doi.org/10.1017/s0025315419001206.

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AbstractThe mojarras (Eucinostomus) are a widespread group of coastal fishes of controversial taxonomy because of similarities in their external morphology. In the present study, we assessed the genetic diversity of species and populations of Eucinostomus using DNA barcodes using a systematic and phylogeographic context. In total, 416 COI sequences of all valid Eucinostomus representatives were analysed based on public databases and collected specimens from the north-eastern coast of Brazil (Western South Atlantic). Several cases of misidentification were detected in the barcode dataset (E. argenteus, E. harengulus, E. gula, E. dowii and E. jonesii) that could account for the taxonomic issues in this genus. In contrast, we identified four molecular operational taxonomic units (MOTUs), with divergence above 2% in the Western Atlantic, that correspond to cryptic forms within E. argenteus, E. harengulus, E. gula and E. melanopterus. These data suggest that Plio-Pleistocene events (rise of the Panama isthmus, Amazonas outflow and sea-level fluctuations) played a major role in the diversification of mojarras. While subtle morphological differences have been used as proxies to discriminate Eucinostomus species, the genetic data proved to be efficient in differentiating them and revealing potentially undescribed taxa. Therefore, we recommend that further taxonomic studies in mojarras should incorporate DNA-based evidence.

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van Staden, Michaela, David A. Ebert, Enrico Gennari, et al. "Molecular Taxonomy of South Africa’s Catsharks: How Far Have We Come?" Diversity 15, no. 7 (2023): 828. http://dx.doi.org/10.3390/d15070828.

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The ability to correctly identify specimens at the species level is crucial for assessing and conserving biodiversity. Despite this, species-specific data are lacking for many of South Africa’s catsharks due to a high level of morphological stasis. As comprehensive and curated DNA reference libraries are required for the reliable identification of specimens from morphologically similar species, this study reviewed and contributed to the availability of cytochrome c oxidase subunit I (COI) and nicotinamide adenine dehydrogenase subunit 2 (NADH2) sequences for South Africa’s catsharks. A molecular taxonomic approach, implementing species delimitation and specimen assignment methods, was used to assess and highlight any taxonomic uncertainties and/or errors in public databases. The investigated species were summarised into 47 molecular operational taxonomic units (MOTUs), with some conflicting specimen assignments. Two Apristurus specimens sampled in this study remained unidentified, revealing the presence of previously undocumented genetic diversity. In contrast, haplotype sharing within Haploblepharus—attributed to nucleotide ambiguities—resulted in the delimitation of three congeners into a single MOTU. This study reveals that molecular taxonomy has the potential to flag undocumented species and/or misidentified specimens, and further highlights the need to implement integrated taxonomic assessments on catsharks that represent an irreplaceable component of biodiversity in the region.

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Jablonska, Aleksandra, Nicolas Navarro, Remi Laffont, et al. "DNA barcodes combined with geometric morphometry challenge species hypothesis in palaemonid shrimp." ARPHA Conference Abstracts 4 (March 4, 2021): e65363. https://doi.org/10.3897/aca.4.e65363.

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Although the Mediterranean Region is known as a hotspot for biodiversity and endemism its freshwater fauna is still greatly unexplored, and even the emblematic taxa such as decapods require in-depth integrative investigation. In our research we used integrative approach composed of various geometric morphometric and molecular methods to challenge the taxonomic status of two freshwater shrimps representing Palaemonidae: Palaemon antennarius and Palaemon minos. Basing on 352 COI sequences, three Molecular Operational Taxonomic Units (MOTUs) were defined. Two of them belonged to P. antennarius: first inhabiting Apennine Peninsula and Sicily, the second one from the Balkan Peninsula. The third MOTU corresponded to Palaemon minos from Crete. The Balkan MOTU of P. antennarius was closer to P. minos in terms of genetics, than to the other conspecific MOTU. The carapace shape variation, studied on 180 individuals, was mainly explained by the geographic distribution. Balkan and Cretan groups were clearly distinguished, while other samples were distributed along the shape gradient from Sicily and southern Apennine Peninsula to the Balkans. The results of our study showed that, either the MOTU assigned to the Apennine Peninsula and Sicily constitutes a separate species or, alternatively, P. minos should be synonymised with P. antennarius.

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Kundu, Shantanu, Piyumi S. De Alwis, Jerome D. Binarao, et al. "Mitochondrial DNA Corroborates the Genetic Variability of Clarias Catfishes (Siluriformes, Clariidae) from Cameroon." Life 13, no. 5 (2023): 1068. http://dx.doi.org/10.3390/life13051068.

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The airbreathing walking catfish (Clariidae: Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species, Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences of Clarias camerunensis and Clarias gariepinus from the Nyong River in Cameroon. Both C. camerunensis and C. gariepinus species maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with other Clarias congeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes of C. camerunensis and C. gariepinus, respectively. The TCS networks revealed distinct haplotypes of C. camerunensis and shared haplotypes of C. gariepinus in African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the two Clarias species examined, we found more than one MOTU in C. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separated C. camerunensis and C. gariepinus from other Clarias species with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation of C. camerunensis in African drainages. Further, the present study confirms the reduced genetic diversity of C. gariepinus across its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity of Clarias species in Africa and other countries.

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Cancian, de Araujo Bruno, Marcelo Tavares, Thales Renan Brotto, et al. "Accelerating the knowledge of Peruvian Chalcididae (Insecta, Hymenoptera, Chalcidoidea) with integrative taxonomy." Biodiversity Data Journal 7 (December 4, 2019): e35907. https://doi.org/10.3897/BDJ.7.e35907.

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We present the first regional inventory of the fauna of Chalcididae in the Peruvian Amazon, with a nearly 6-fold increase in the number of species recorded for the country. A total of 418 specimens of Chalcididae were collected between 2000 and 2017 at the Panguana Reserve, Peruvian Amazon, 400 of which were obtained using Malaise traps and the remaining 18 specimens by canopy fogging. The morphological analyses indicated that these specimens represent 183 species of Chalcididae in 10 different genera, with 173 new to Peru and 134 potentially new species. We submitted 268 specimens, representing 167 species, to DNA barcoding. Of these, 141 specimens yielded sequences, 136 of them with a minimum of 300 bp. Sixty specimens were assigned a BIN by the Barcode of Life Database System (BOLD), resulting in 50 BINs. A cluster analysis of 138 individuals that yielded DNA sequences longer than 100 bp revealed 118 MOTUs (molecular operative taxonomic units), all of them highly congruent with the morphological data. Prior to the present study, 37 species in 9 genera of Chalcididae were known from Peru. With our results, this number was increased to 210 species in 13 genera. The present study is the result of a joint effort between the SNSB - Zoologische Staatssammlung München, Germany (ZSM) and the Insect Biodiversity Laboratory of the Universidade Federal do Espírito Santo, Vitória, Brazil (LaBI-UFES), intending to apply an accelerated taxonomic treatment of the Chalcididae of the Panguana reserve using traditional morphological approaches in combination with DNA barcoding. The complete molecular dataset and associated voucher information is publicly available through BOLD. The new species that were discovered as part of the study are being formally described elsewhere as part of taxonomic treatments of Neotropical and world generic revisions at LaBI-UFES.

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Mager, Enno, Ronja Brockhage, Meike Piepenbring, et al. "Soil Horizons Harbor Differing Fungal Communities." Diversity 16, no. 2 (2024): 97. http://dx.doi.org/10.3390/d16020097.

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In the present study, the mycobiomes of two soils with different ecological conditions located in Benin (West Africa) were investigated by environmental sequencing (Illumina MiSeq) of the ITS2-region of ribosomal DNA to gain information about the influence of pedological stratification on fungal diversity. For each soil depth and horizon, fungal diversity and community composition were analyzed as well as the potential impact of site characteristics, like vegetation, on these traits. The retrieved sequences revealed in all their replicates high similarities between fungal communities of samples from the same site and soil horizon, but differed within one site in their horizons. It was possible to assign a saprotrophic, symbiotrophic, or parasitic lifestyle to 24% of the recorded fungal mOTUs. Plant parasites were found in all samples in similar proportions. The presence of ectomycorrhizal fungi in one site could be linked to the presence of ectomycorrhizal trees. Overall, it was observed that fungal diversity decreased with increasing depth if only one horizon was present, whereas a deeper horizon present at one site contained communities with a distinct composition regarding the taxonomical affiliations and lifestyles of the fungi found compared to the upper layer. Hence, soil horizonation seems to drive differences in the composition of fungal communities, and should be regarded with more attention when analyzing soil mycobiomes.

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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 group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.

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Mathon, Laetitia, Virginie Marques, David Mouillot, et al. "Circumglobal distribution of fish environmental DNA in coral reefs." ARPHA Conference Abstracts 4 (March 4, 2021): e64792. https://doi.org/10.3897/aca.4.e64792.

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Coral reefs host the highest fish diversity on Earth despite covering less than 0.1% of the ocean's seafloor. At the same time they are also extremely threatened. Data syntheses over decades of surveys estimate the total number of coral reef fishes to vary from 2,400 to 8,000 species distributed among roughly 100 families. But this diversity remains largely unknown.Here, we investigated how environmental DNA (eDNA) could describe the distribution of fish diversity in coral reefs. We generated 504,457,267 raw 12S ribosomal DNA (rDNA) sequence reads from 251 samples (2,693 PCR replicates) collected at 25 sites in 145 stations covering five regions across the Indian, Pacific and Atlantic Oceans. Bioinformatic analysis clustered these sequences into 2,160 molecular operational taxonomic units (MOTUs) corresponding to distinct species (Marques 2020) We compared our results, with visual census surveys from Reef Life Survey, on 2,813 transects in tropical regions.Our outcomes demonstrate the capacity of eDNA metabarcoding from water samples to reconstruct well-known biogeographic patterns of fish diversity on coral reefs, such as species richness gradients towards the coral triangle, and family proportion stability across sites (Bellwood and Hughes 2001). Additionally, eDNA survey data documented a higher fish species (16%) and family (50%) diversity than estimates obtained with underwater visual surveys carried out on 20 times more sites. MOTU richness per family retrieved with eDNA closely matched fish species richness within families recorded in visual census data. However, eDNA revealed higher richness of reef-associated species and species from adjacent habitats, of cryptobenthic or nocturnal species, but also of pelagic and wide-ranging species. eDNA survey data showed that fish diversity is characterized by spatially heterogeneous species assemblages among regions, with more dissimilarity among adjacent coral reefs than detected with visual survey data. Unlike visual surveys, eDNA metabarcoding revealed the same prevalence of rarity as expected under the neutral theory of biodiversity, suggesting the predominance of random processes and ecological equivalence within trophic groups at large scale to explain fish biodiversity patterns on coral reefs. Our study demonstrates how sequencing eDNA from water provides a rapid and effective approach to characterize and assess coral reef diversity across large spatial scales, thereby also uncovering hidden biodiversity patterns.

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Jurado-Rivera, José A., Francesco Zapelloni, Joan Pons, Carlos Juan, and Damià Jaume. "Morphological and molecular species boundaries in the Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda)." Contributions to Zoology 89, no. 4 (2020): 353–72. http://dx.doi.org/10.1163/18759866-bja10004.

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The Hyalella species diversity in the high-altitude water bodies of the Andean Altiplano is addressed using mitochondrial cox1 sequences and implementing different molecular species delimitation criteria. We have recorded the presence of five major genetic lineages in the Altiplano, of which one seems to be exclusive to Lake Titicaca and nearby areas, whereas the rest occur also in other regions of South America. Eleven out of 36 South American entities diagnosed by molecular delimitation criteria in our study are likely endemic to the Titicaca and neighbouring water bodies. We have detected a remarkable disagreement between morphology and genetic data in the Titicacan Hyalella, with occurrence of several cases of the same morpho-species corresponding to several Molecular Operational Taxonomic Units (MOTUs), some even distantly related, and other instances where a particular MOTU is shared by a morphologically heterogeneous array of species, including species with body smooth and others with body heavily armoured. Species diversification and incongruence between morphological and molecular boundaries within this species assemblage may be associated to the sharp changes in hydrological conditions experienced by the water bodies of the Altiplano in the past, which included dramatic fluctuations in water level and salinity of Lake Titicaca. Such environmental shifts could have triggered rapid morphological changes and ecological differentiation within the Hyalella assemblage, followed by phenotypic convergence among the diverse lineages. Factors such as phenotypic plasticity, incomplete lineage sorting or admixture between divergent lineages might lie also at the root of the morphological-genetic incongruence described herein.

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Li, Hongmei, Huan Cheng, Renrong Huang, Zhenya Qiu, and Renyi Zhang. "DNA Barcoding of the Genus Discogobio (Teleostei, Cyprinidae) in China." Fishes 10, no. 4 (2025): 157. https://doi.org/10.3390/fishes10040157.

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Discogobio is a genus of small, economically important freshwater fishes that are widely distributed in Southwestern China. The species of the genus are morphologically very similar, which makes their taxonomic identification quite challenging. DNA barcoding technology can identify species at the molecular level, thus overcoming the limitations of morphological classification. In this study, we collected 16 morphological species of Discogobio from China, analyzed the mitochondrial cytochrome oxidase I subunit (COI) gene sequences of 206 samples, and applied DNA barcoding to identify the species. The COI amplicon was 651 bp in length, and the mean base contents were: (T) 28.83%, (C) 27.63%, (A) 25.97%, (G) 17.57%. The AT content (54.8%) was higher, and the base composition was biased. The intraspecific differences in the genus Discogobio were not significant, and the genetic distances were all less than 2%. The average interspecific genetic distances (3.94%) were about 18.8 times the average intraspecific genetic distances (0.21%), suggesting that there are barcode gaps among the species of the genus Discogobio. Five different species definition methods, Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), Bayesian Poisson Tree Process (bPTP), Generalized Mixed Yule Combination (GMYC), and Refined Single Linkage (RESL), were used to infer molecular operational taxonomic units (MOTU). The number of MOTUs ranged from 9 to 18. Phylogenetic analysis based on COI gene haplotypes showed that most species formed well-evolved branches on the phylogenetic tree, and the clustering among species was obvious without mixing. The results of this study provide reliable DNA barcoding information for species identification within the genus Discogobio, which is of great significance for taxonomic identification.

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Matoso, Daniele Aparecida, Hallana Cristina Menezes da Silva, Augusto Luiz Ferreira Júnior, et al. "Is there hidden genetic variability in the species of Steindachneridion Garavello, 2005 (Siluriformes: Pimelodidae)?" PeerJ 13 (March 28, 2025): e18193. https://doi.org/10.7717/peerj.18193.

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Background The genus Steindachneridion, which includes large-sized freshwater pimelodid species, is endemic to the southeastern coastal drainages of South America, specifically the Paraná River and Uruguay River basins. Methods In this study, genetic analyses of mitochondrial DNA (mtDNA) D-loop were conducted on four species within this genus across their respective distributions: Steindachneridion scriptum (from the Tibagi and Uruguay rivers), S. melanodermatum (from the Iguaçu River), S. doceanum (from the Doce River), and S. parahybae (from the Paraíba do Sul River). Zungaro zungaro and Brachyplatystoma rousseauxii were employed as outgroups, and the topology was inferred using Bayesian Inference (BI) and maximum likelihood (ML) phylogenetic reconstruction techniques. Additionally, the sequences were analyzed to assess genetic diversity levels. Results In contrast to the remaining species, which exhibited distinct species-specific clades, our data suggests that S. scriptum formed two sister clades, potentially representing distinct operational taxonomic units. Novel haplotypes were identified for each of the four species, further supporting the conclusions derived from the phylogenetic analysis. Overall, Steindachneridion species displayed high haplotype diversity paired with low nucleotide diversity, indicating a demographic expansion event after reduced effective population size. Nevertheless, genetic structure indexes were notably high. These findings suggest that the genetic diversity within these species may be underestimated, which has implications for both taxonomic classification and biological conservation strategies. Conclusion In conclusion, the study of genetic diversity in four Steindachneridion species has revealed distinct molecular operational taxonomic units (MOTUs), which highlights the necessity for conservation efforts. The detection of new haplotypes and intraspecific variability emphasizes the urgency of implementing systematic conservation measures in the face of looming extinction threats.

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Journal articles on the topic 'Sequences of MOTUs'

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