DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao

La pérdida de biodiversidad está ocurriendo a gran escala y la necesidad de monitorearla es cada vez más necesaria. El uso de técnicas morfológicas se puede mejorar con el uso de herramientas moleculares para ayudar a resolver los vacíos en el conocimiento de la diversidad y la historia evolutiva de...

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2023
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Universidad del Rosario
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Repositorio EdocUR - U. Rosario
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spa
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oai:repository.urosario.edu.co:10336/42298
Acceso en línea:
https://doi.org/10.48713/10336_38266
https://repository.urosario.edu.co/handle/10336/42298
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Códigos de barras de ADN
COI
Cacao
Ceratopogonidae
Filogenias
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Attribution-NonCommercial-ShareAlike 4.0 International
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network_acronym_str EDOCUR2
network_name_str Repositorio EdocUR - U. Rosario
repository_id_str
dc.title.none.fl_str_mv DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao
title DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao
spellingShingle DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao
Códigos de barras de ADN
COI
Cacao
Ceratopogonidae
Filogenias
title_short DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao
title_full DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao
title_fullStr DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao
title_full_unstemmed DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao
title_sort DNA barcoding for identification and phylogenetic inference of (Diptera; Ceratopogonidae) pollinators of cacao
dc.contributor.advisor.none.fl_str_mv Richardson, James Edward
Sánchez Andrade, Adriana
Salazar Clavijo, Camilo Andrés
Yockteng, Roxana
dc.subject.none.fl_str_mv Códigos de barras de ADN
COI
Cacao
Ceratopogonidae
Filogenias
topic Códigos de barras de ADN
COI
Cacao
Ceratopogonidae
Filogenias
description La pérdida de biodiversidad está ocurriendo a gran escala y la necesidad de monitorearla es cada vez más necesaria. El uso de técnicas morfológicas se puede mejorar con el uso de herramientas moleculares para ayudar a resolver los vacíos en el conocimiento de la diversidad y la historia evolutiva de las especies. El objetivo de esta investigación fue evaluar el uso del gen mitocondrial citocromo c oxidasa 1 (COI) como marcador de código de barras de ADN para caracterizar mosquitos como posibles polinizadores en cultivos de cacao colombianos. El estudio se implementó en los departamentos del Meta y Norte de Santander. Los taxones muestreados directamente de las flores se analizaron para evaluar su diversidad y relación filogenética utilizando la máxima verosimilitud (ML) y la inferencia bayesiana (BI). Generamos secuencias de aproximadamente 656 pb para 25 individuos Culicomorpha, 13 del Meta y 12 del Norte de Santander y descargamos 388 secuencias de las familias Ceratopogonidae y Chironomidae de GenBank. El análisis de las secuencias COI revela que nuestras secuencias se ubicaron en tres grupos de linajes de Ceratopogonidae (Forcipomyia, Dasyhelea y Stilobezzia) y cinco linajes no resueltos de Chironomidae. También encontramos que las especies que visitaron las flores de cacao en las plantaciones de Meta y Norte de Santander representaban dos grupos separados, que pueden estar influenciados por los procesos orogénicos de las montañas de los Andes. La reconstrucción filogenética indicó que la mayoría (n=17) de nuestras secuencias se resolvieron en el grupo Forcipomyia. Adicionalmente, ninguna de nuestras secuencias fue idéntica a las secuencias de GenBank, lo que refleja un sesgo de investigación para las regiones templadas del norte y la necesidad de más estudios sobre especies tropicales. Nuestros datos ofrecen nuevas secuencias moleculares de Ceratopogonidae colombianos para el desarrollo de un inventario global de especies polinizadoras de plantas de interés económico, como el cacao. Se sugiere también la necesidad de seguir muestreando taxones tropicales para esclarecer la historia evolutiva de estas familias de moscas.
publishDate 2023
dc.date.created.none.fl_str_mv 2023
dc.date.accessioned.none.fl_str_mv 2024-02-27T17:24:23Z
dc.date.available.none.fl_str_mv 2024-02-27T17:24:23Z
dc.date.embargoEnd.none.fl_str_mv info:eu-repo/date/embargoEnd/2025-03-24
dc.type.none.fl_str_mv bachelorThesis
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_7a1f
dc.type.document.none.fl_str_mv Trabajo de grado
dc.type.spa.none.fl_str_mv Trabajo de grado
dc.identifier.doi.none.fl_str_mv https://doi.org/10.48713/10336_38266
dc.identifier.uri.none.fl_str_mv https://repository.urosario.edu.co/handle/10336/42298
url https://doi.org/10.48713/10336_38266
https://repository.urosario.edu.co/handle/10336/42298
dc.language.iso.none.fl_str_mv spa
language spa
dc.rights.*.fl_str_mv Attribution-NonCommercial-ShareAlike 4.0 International
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dc.rights.acceso.none.fl_str_mv Restringido (Temporalmente bloqueado)
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rights_invalid_str_mv Attribution-NonCommercial-ShareAlike 4.0 International
Restringido (Temporalmente bloqueado)
http://creativecommons.org/licenses/by-nc-sa/4.0/
http://purl.org/coar/access_right/c_f1cf
dc.format.extent.none.fl_str_mv 22 pp
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universidad del Rosario
dc.publisher.department.none.fl_str_mv Facultad de Ciencias Naturales
dc.publisher.program.none.fl_str_mv Biología
publisher.none.fl_str_mv Universidad del Rosario
institution Universidad del Rosario
dc.source.bibliographicCitation.none.fl_str_mv Adachi, J., & Hasegawa, M. (1996). Model of amino acid substitution in proteins encoded by mitochondrial DNA. Journal of Molecular Evolution, 42(4), 459-468. https://doi.org/10.1007/BF02498640
Anisimova, M., Gil, M., Dufayard, J.-F., Dessimoz, C. & Gascuel, O. (2011). Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihoodbased approximation schemes. Systematic Biology, 60(5), 685-699. https://doi.org/10.1093/sysbio/syr041
Bartley, B. G. D. (Ed.). (2005). The genetic diversity of cacao and its utilization. CABI. https://doi.org/10.1079/9780851996196.0000
Beckenbach, A. T., & Borkent, A. (2003). Molecular analysis of the biting midges (Diptera: Ceratopogonidae), based on mitochondrial cytochrome oxidase subunit 2. Molecular Phylogenetics and Evolution, 27(1), 21-35. https://doi.org/10.1016/s1055-7903(02)00395-0
Borkent, A. (1991). The Ceratopogonidae (Diptera) of the Galápagos Islands, Ecuador with a discussion of their phylogenetic relationships and zoogeographic origins. Insect Systematics & Evolution, 22(1), 97-122. https://doi.org/10.1163/187631291X00336
Borkent, A. (2001). Leptoconops (Diptera: Ceratopogonidae), the Earliest Extant Lineage of Biting Midge, Discovered in 120–122 Million-Year-Old Lebanese Amber. American Museum Novitates, 2001(3328), 1-12. https://doi.org/10.1206/0003- 0082(2001)328<0001:LDCTEE>2.0.CO;2
Borkent, A. (2014). The pupae of the biting midges of the world (Diptera: Ceratopogonidae), with a generic key and analysis of the phylogenetic relationships between genera. Zootaxa, 3879, 1-327. https://doi.org/10.11646/zootaxa.3879.1.1
Borkent, A. & G. R. Spinelli. (2007). Neotropical Ceratopogonidae (Diptera: Insecta). In: Adis, J., J. R. Arias, G. Rueda-Delgado & K. M. Wattzen (Eds): Aquatic Biodiversity in Latin America (ABLA). Vol 4. Pensoft Publishers, Sofia-Moscow, 198 pp. Revista de La Sociedad Entomológica Argentina, 67(1-2), Art. 1-2. https://www.biotaxa.org/RSEA/article/view/31038
Borkent, A., & Dominiak, P. (2020). Catalog of the Biting Midges of the World (Diptera: Ceratopogonidae). Zootaxa, 4787(1), zootaxa.4787.1.1. https://doi.org/10.11646/zootaxa.4787.1.1
Bourguignon, T., Tang, Q., Ho, S. Y. W., Juna, F., Wang, Z., Arab, D. A., Cameron, S. L., Walker, J., Rentz, D., Evans, T. A., & Lo, N. (2018). Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics. Molecular Biology and Evolution, 35(4), 970-983. https://doi.org/10.1093/molbev/msy013
Branco, S. M. de J., Silva, D. V. da, Lopes, U. V. & Corrêa, R. X. (2018). Characterization of the Sexual Self- and Cross-Compatibility in Genotypes of Cacao. American Journal of Plant Sciences, 9(9), Art. 9. https://doi.org/10.4236/ajps.2018.99131
Bridgemohan, P., Singh, K., Cazoe, E., Perry, G., Mohamed, A., & Bridgemohan, R. S. (2017). Cacao floral phenology and pollination: Implications for productivity in Caribbean Islands. Journal of Plant Breeding and Crop Science, 9(7), 106-117. https://doi.org/10.5897/JPBCS2016.0598
Carpenter, S., Groschup, M. H., Garros, C., Felippe-Bauer, M. L., & Purse, B. V. (2013). Culicoides biting midges, arboviruses and public health in Europe. Antiviral Research, 100(1), 102-113. https://doi.org/10.1016/j.antiviral.2013.07.020
Choufani, J., El-Halabi, W., Azar, D., & Nel, A. (2015). First fossil insect from Lower Cretaceous Lebanese amber in Syria (Diptera: Ceratopogonidae). Cretaceous Research, 54, 106-116. https://doi.org/10.1016/j.cretres.2014.12.006
Damm, S., Schierwater, B. & Hadrys, H. (2010). An integrative approach to species discovery in odonates: From character-based DNA barcoding to ecology. Molecular Ecology, 19(18), 3881-3893. https://doi.org/10.1111/j.1365-294X.2010.04720.x
DNA Barcoding Program. (2017, agosto 22). ForestGEO. https://forestgeo.si.edu/researchprograms/dna-barcoding-program
Dellinger, A. S., Pérez-Barrales, R., Michelangeli, F. A., Penneys, D. S., FernándezFernández, D. M., & Schönenberger, J. (2021). Low bee visitation rates explain pollinator shifts to vertebrates in tropical mountains. New Phytologist, 231(2), 864-877. https://doi.org/10.1111/nph.17390
Eagles, D., Deveson, T., Walker, P. J., Zalucki, M. P., & Durr, P. (2012). Evaluation of longdistance dispersal of Culicoides midges into northern Australia using a migration model. Medical and Veterinary Entomology, 26(3), 334-340. https://doi.org/10.1111/j.1365- 2915.2011.01005.x
Erickson, B. J., Young, A. M., Strand, M. A., & Erickson, E. H. (1987). Pollination biology of Theobroma and Herrania (Sterculiaceae). International Journal of Tropical Insect Science, 8(3), 301-310. https://doi.org/10.1017/S1742758400005282
Folmer, O., Black, M., Hoeh, W., Lutz, R., & Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3(5), 294-299.
Freeman, J. A. (1945). Studies in the Distribution of Insects by Aerial Currents. Journal of Animal Ecology, 14(2), 128-154. https://doi.org/10.2307/1389
Frimpong, E. A., Gordon, I., Kwapong, P. K., & Gemmill-Herren, B. (2009). Dynamics of cacao pollination: Tools and applications for surveying and monitoring cacao pollinators. International Journal of Tropical Insect Science, 29(2), 62-69. https://doi.org/10.1017/S1742758409990117
Frimpong-Anin, K., Bosu, P., Adjaloo, M., Braimah, H. & Oduro, W. (2015). Some Facts About Cacao Pollination. Global Pollination Project-Ghana. ISBN: 9964-3-9352-0
Gostel, M. R., & Kress, W. J. (2022). The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation. Diversity, 14(3), 213. https://doi.org/10.3390/d14030213
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59(3), 307-321. https://doi.org/10.1093/sysbio/syq010
Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270(1512), 313-321. https://doi.org/10.1098/rspb.2002.2218
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018). UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35(2), 518-522. https://doi.org/10.1093/molbev/msx281
Holzapfel, E., & Harrell, J. (1968). Transoceanic dispersal studies of insects. https://www.semanticscholar.org/paper/TRANSOCEANIC-DISPERSAL-STUDIES-OFINSECTS-Holzapfel-Harrell/5e5d6cffb83ae68da4ac989c56eb6684d6c001be
Hortal, J., de Bello, F., Diniz-Filho, J. A. F., Lewinsohn, T. M., Lobo, J. M. & Ladle, R. J. (2015). Seven shortfalls that beset large-scale knowledge of biodiversity. Annual Review of Ecology, Evolution, and Systematics, 46(1), 523-549. https://doi.org/10.1146/annurevecolsys-112414-054400
Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England), 17(8), 754-755. https://doi.org/10.1093/bioinformatics/17.8.754
Katoh, K., & Standley, D. M. (2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30(4), 772-780. https://doi.org/10.1093/molbev/mst010
Kaufmann, T. (1975). Studies on the ecology and biology of a cacao pollinator, Forcipomyia squamipennis I. & M. (Diptera, Ceratopogonidae) in Ghana. Bulletin of Entomological Research, 65(2), 263-268. https://doi.org/10.1017/S0007485300005940
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., & Drummond, A. (2012). Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28(12), 1647-1649. https://doi.org/10.1093/bioinformatics/bts199
Klein, A.-M., Vaissière, B. E., Cane, J. H., Steffan-Dewenter, I., Cunningham, S. A., Kremen, C., & Tscharntke, T. (2007). Importance of pollinators in changing landscapes for world crops. Proceedings of the Royal Society B: Biological Sciences, 274(1608), 303-313. https://doi.org/10.1098/rspb.2006.3721
Kobayashi, S., Denda, T., Placksanoi, J., Waengsothorn, S., Aryuthaka, C., Panha, S., & Izawa, M. (2019). The pollination system of the widely distributed mammal-pollinated Mucuna macrocarpa (Fabaceae) in the tropics. Ecology and Evolution, 9(11), 6276-6286. https://doi.org/10.1002/ece3.5201
Kress, W. J., García-Robledo, C., Uriarte, M., & Erickson, D. L. (2015). DNA barcodes for ecology, evolution, and conservation. Trends in Ecology & Evolution, 30(1), 25-35. https://doi.org/10.1016/j.tree.2014.10.008
Krosch, M. N., Baker, A. M., Mather, P. B., & Cranston, P. S. (2011). Systematics and biogeography of the Gondwanan Orthocladiinae (Diptera: Chironomidae). Molecular Phylogenetics and Evolution, 59(2), 458-468. https://doi.org/10.1016/j.ympev.2011.03.003
Kumar, N. P., Rajavel, A. R., Natarajan, R., & Jambulingam, P. (2007). DNA Barcodes Can Distinguish Species of Indian Mosquitoes (Diptera: Culicidae). Journal of Medical Entomology, 44(1), 01-07. https://doi.org/10.1093/jmedent/41.5.01
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spelling Richardson, James Edward0ac28eb4-5e07-4e05-b534-0dc0d7411868-1Sánchez Andrade, Adriana52699585600Salazar Clavijo, Camilo Andrés79873757600Yockteng, Roxana61bd6133-5271-47c6-a3c2-4ed8e5e4308d-1Tamayo Ceballos, Iván MateoBiólogoPregrado45970148-2ad1-4676-a136-927e3f1d306a-12024-02-27T17:24:23Z2024-02-27T17:24:23Z2023info:eu-repo/date/embargoEnd/2025-03-24La pérdida de biodiversidad está ocurriendo a gran escala y la necesidad de monitorearla es cada vez más necesaria. El uso de técnicas morfológicas se puede mejorar con el uso de herramientas moleculares para ayudar a resolver los vacíos en el conocimiento de la diversidad y la historia evolutiva de las especies. El objetivo de esta investigación fue evaluar el uso del gen mitocondrial citocromo c oxidasa 1 (COI) como marcador de código de barras de ADN para caracterizar mosquitos como posibles polinizadores en cultivos de cacao colombianos. El estudio se implementó en los departamentos del Meta y Norte de Santander. Los taxones muestreados directamente de las flores se analizaron para evaluar su diversidad y relación filogenética utilizando la máxima verosimilitud (ML) y la inferencia bayesiana (BI). Generamos secuencias de aproximadamente 656 pb para 25 individuos Culicomorpha, 13 del Meta y 12 del Norte de Santander y descargamos 388 secuencias de las familias Ceratopogonidae y Chironomidae de GenBank. El análisis de las secuencias COI revela que nuestras secuencias se ubicaron en tres grupos de linajes de Ceratopogonidae (Forcipomyia, Dasyhelea y Stilobezzia) y cinco linajes no resueltos de Chironomidae. También encontramos que las especies que visitaron las flores de cacao en las plantaciones de Meta y Norte de Santander representaban dos grupos separados, que pueden estar influenciados por los procesos orogénicos de las montañas de los Andes. La reconstrucción filogenética indicó que la mayoría (n=17) de nuestras secuencias se resolvieron en el grupo Forcipomyia. Adicionalmente, ninguna de nuestras secuencias fue idéntica a las secuencias de GenBank, lo que refleja un sesgo de investigación para las regiones templadas del norte y la necesidad de más estudios sobre especies tropicales. Nuestros datos ofrecen nuevas secuencias moleculares de Ceratopogonidae colombianos para el desarrollo de un inventario global de especies polinizadoras de plantas de interés económico, como el cacao. Se sugiere también la necesidad de seguir muestreando taxones tropicales para esclarecer la historia evolutiva de estas familias de moscas.Biodiversity loss is occurring on a large scale and the need to monitor it is becoming more and more necessary. The use of morphological techniques can be enhanced with the use of molecular tools to help resolve diversity and evolutionary history knowledge gaps. The objective of this research was to evaluate the use of the mitochondrial cytochrome c oxidase 1 (COI) gene as a DNA barcode marker to characterize possible pollinators of Colombian cacao crops. The study was implemented in the departments of Meta and Northern Santander, Colombia. Taxa sampled directly from flowers were analyzed to assess their diversity and phylogenetic relationships using Maximum-Likelihood (ML) and Bayesian Inference (BI). We generated sequences of approximately 656 bp for 25 Culicomorpha individuals, 13 from Meta and 12 from Northern Santander and downloaded 388 sequences of the Ceratopogonidae and Chironomidae families from GenBank. Analysis of the COI sequences reveals that our sequences were placed in three Ceratopogonidae lineages (Forcipomyia, Dasyhelea and Stilobezzia) and five unresolved lineages of Chironomidae. We also found that species that visited cacao flowers in Meta and Northern Santander plantations represented two separate guilds, which could have been influenced by the orogenic processes of the Andes Mountains. Phylogenetic reconstruction indicated that most (n=17) of our sequences were resolved in the Forcipomyia group. Additionally, none of our sequences were identical to any GenBank sequences, reflecting an investigative bias towards northern temperate regions and the need for more molecular studies on tropical species. Our data offer new DNA sequences of Colombian Ceratopogonidae for the development of a global inventory of pollinating species of plants of economic interest, such as cacao. The need to continue sampling tropical taxa is also suggested in order to clarify the evolutionary history of these families of flies.22 ppapplication/pdfhttps://doi.org/10.48713/10336_38266https://repository.urosario.edu.co/handle/10336/42298spaUniversidad del RosarioFacultad de Ciencias NaturalesBiologíaAttribution-NonCommercial-ShareAlike 4.0 InternationalRestringido (Temporalmente bloqueado)EL AUTOR, manifiesta que la obra objeto de la presente autorización es original y la realizó sin violar o usurpar derechos de autor de terceros, por lo tanto la obra es de exclusiva autoría y tiene la titularidad sobre la misma.http://creativecommons.org/licenses/by-nc-sa/4.0/http://purl.org/coar/access_right/c_f1cfAdachi, J., & Hasegawa, M. (1996). Model of amino acid substitution in proteins encoded by mitochondrial DNA. Journal of Molecular Evolution, 42(4), 459-468. https://doi.org/10.1007/BF02498640Anisimova, M., Gil, M., Dufayard, J.-F., Dessimoz, C. & Gascuel, O. (2011). Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihoodbased approximation schemes. Systematic Biology, 60(5), 685-699. https://doi.org/10.1093/sysbio/syr041Bartley, B. G. D. (Ed.). (2005). The genetic diversity of cacao and its utilization. CABI. https://doi.org/10.1079/9780851996196.0000Beckenbach, A. T., & Borkent, A. (2003). Molecular analysis of the biting midges (Diptera: Ceratopogonidae), based on mitochondrial cytochrome oxidase subunit 2. Molecular Phylogenetics and Evolution, 27(1), 21-35. https://doi.org/10.1016/s1055-7903(02)00395-0Borkent, A. (1991). The Ceratopogonidae (Diptera) of the Galápagos Islands, Ecuador with a discussion of their phylogenetic relationships and zoogeographic origins. Insect Systematics & Evolution, 22(1), 97-122. https://doi.org/10.1163/187631291X00336Borkent, A. (2001). Leptoconops (Diptera: Ceratopogonidae), the Earliest Extant Lineage of Biting Midge, Discovered in 120–122 Million-Year-Old Lebanese Amber. American Museum Novitates, 2001(3328), 1-12. https://doi.org/10.1206/0003- 0082(2001)328<0001:LDCTEE>2.0.CO;2Borkent, A. (2014). The pupae of the biting midges of the world (Diptera: Ceratopogonidae), with a generic key and analysis of the phylogenetic relationships between genera. Zootaxa, 3879, 1-327. https://doi.org/10.11646/zootaxa.3879.1.1Borkent, A. & G. R. Spinelli. (2007). Neotropical Ceratopogonidae (Diptera: Insecta). In: Adis, J., J. R. Arias, G. Rueda-Delgado & K. M. Wattzen (Eds): Aquatic Biodiversity in Latin America (ABLA). Vol 4. Pensoft Publishers, Sofia-Moscow, 198 pp. Revista de La Sociedad Entomológica Argentina, 67(1-2), Art. 1-2. https://www.biotaxa.org/RSEA/article/view/31038Borkent, A., & Dominiak, P. (2020). Catalog of the Biting Midges of the World (Diptera: Ceratopogonidae). 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