References
Antonelli, A. (2021). The rise and fall of Neotropical biodiversity.Botanical Journal of the Linnean Society , 199 (1), 8–24. https://doi.org/10.1093/botlinnean/boab061
Antonelli, A., Ariza, M., Albert, J., Andermann, T., Azevedo, J., Bacon, C., Faurby, S., Guedes, T., Hoorn, C., Lohmann, L. G., Matos-Maraví, P., Ritter, C. D., Sanmartín, I., Silvestro, D., Tejedor, M., ter Steege, H., Tuomisto, H., Werneck, F. P., Zizka, A., & Edwards, S.V. (2018). Conceptual and empirical advances in Neotropical biodiversity research.PeerJ., (6), e5644.
Antonelli, A., & Sanmartín, I. (2011). Why are there so many plant species in the Neotropics? Taxon , 60, 403–414.
Barnosky, A. D., Matzke, N., Tomiya, S., Wogan, G. O., Swartz, B., Quental, T. B., Marshall, C., McGuire, J. L, Lindsey, E.L., Maguire, K. C., Mersey, B., & Ferrer, E. A. (2011). Has the Earth’s sixth mass extinction already arrived? Nature , 471, 51–57.
Bidawid, N., & Fittkau, E. J. (1995). Zur Kenntnis der neotropischen Arten der Gattung Polypedilum Kieffer, 1912. Teil I. (Diptera, Chironomidae). Entomofauna , 16(11), 465–536.
Bidawid-Kafka, N. (1996). Zur Kenntnis der neotropischen Arten der Gattung Polypedilum Kieffer, 1912. Teil II. (Diptera, Chironomidae). Entomofauna , 17(11), 165–240.
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., de Maio, N., Matschiner, M., Mendes, F. K., Müller, N. F., Ogilvie, H. A., du Plessis, L., Popinga, A., Rambaut, A., Rasmussen, D., Siveroni, I., Suchard, M. A., Wu, C., Xie, D., Zhang, C., Stadler, T., & Drummond, A. J. (2019). Beast 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology , 15(4), e1006650.
Bradshaw, C. J., Sodhi, N. S., & Brook, B. W. (2009). Tropical turmoil: a biodiversity tragedy in progress. Frontiers in Ecology and the Environment , 7, 79–87.
Ceccarelli, F. S., Sharkey, M. J., & Zaldívar-Riverón, A. (2012). Species identification in the taxonomically neglected, highly diverse, neotropical parasitoid wasp genus Notiospathius (Braconidae: Doryctinae) based on an integrative molecular and morphological approach. Molecular Phylogenetics and Evolution , 62(1), 485–495.
Coscaron, M. C., Melo, M. C., Coddington, J., & Corronca, J. (2009). Estimating biodiversity: a case study on true bugs in Argentinian wetlands. Biodiversity and Conservation , 18, 1491–1507.
Cotoras, D. D., & Zumbad, M. A. (2020). Aerial plankton from the Eastern Tropical Pacific. Revista de Biología Tropical , 68, 155–162.
da Silva, R., Peloso, P. L. V., Sturaro, M. J., Veneza, I., Sampaio, I., Schneider, H., & Gomes, G. (2018). Comparative analyses of species delimitation methods with molecular data in snappers (Perciformes: Lutjaninae). Mitochondrial DNA Part A , 29(7), 1108–1114.
Darwin, C. (1859). On the Origin of Species by Means of Natural Selection . London, UK: John Murray, London. 502 pp.
Dellicour, S., & Flot, J. F. (2015). Delimiting species-poor data sets using single molecular markers: A study of barcode gaps, haplowebs and GMYC. Systematic Biology , 64, 900–908.
Dellicour, S., & Flot, J. F. (2018). The hitchhiker’s guide to single-locus species delimitation. Molecular EcologyResources , 18(6), 1234–46.
Deng, C., Daley, T., & Smith, A. D. (2015). Applications of species accumulation curves in large-scale biological data analysis.Quantitative Biology , 3(3),135–144.
Dopheide, A., Tooman, L. K., Grosser, S., Agabiti, B., Rhode, B., Xie, D., Stevens, M. I., Nelson, N., Buckley, T. R., Drummond, A. J., & Newcomb, R. D. (2019). Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data. Ecological Applications , 29(4), e01877.
Drummond, A. J., Nicholls, G. K., Rodrigo, A. G., & Solomon, W. (2002). Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics , 161(3), 1307–1320.
Drummond, A. J., Suchard M. A., Xie, D. & Rambaut, A. (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution , 22(8), 1185–1192.
Dupuis, J. R., Roe, A. D., & Sperling, F. A. H. (2012). Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Molecular Ecology , (21), 4422–4436.
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research , (32), 1792–1797.
Ekrem, T., Stur, E., Orton, M. G., & Adamowicz, S. J. (2018). DNA barcode data reveal biogeographic trends in Arctic non-biting midges.Trends in DNA Barcoding and Metabarcoding , 1(1), 787–796.
Elworth, R. A. L., Ogilvie, H. A., Zhu, J., & Nakhleh, L. (2018). Advances in computational methods for phylogenetic networks in the presence of hybridization. arXiv 1808.08662v1.
Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity.Biology Conservation, 61, 1–10.
Faith, D. P. (2008). Phylogenetic diversity and conservation . pp. 99–115 in Carroll, S. P., & Fox, C. (Eds) Conservation Biology: Evolution in Action. New York, Oxford University Press.
Farooq, Q., Shakir, M., Ejaz, F., Zafar, T., Durrani, K., & Ullah, A. (2020). Role of DNA Barcoding in Plant Biodiversity Conservation.Scholars International Journal of Biochemistry , 3(3), 48–52.
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution , 17, 368–376.
Ferrington, L. C. Jr. (2008). Global diversity of non-biting midges (Chironomidae; Insecta-Diptera) in freshwater. Hydrobiologia , 595, 447–455.
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, 294–299.
Fujisawa, T., & Barraclough, T. G. (2013). Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: A revised method and evolution on simulated data sets. Systematic Biology , 62, 707–724.
Gostel, M. R., & Kress, W. J. (2022). The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation.Diversity , 14(3), 213.
Gressitt, J. L., Leech, R. E. & O’Brien, C. W. (1960). Trapping of air-borne insects in the Antarctic area. Pacific Insects , 2, 245–250.
Havermans, C., Nagy, Z. T., Sonet, G., De Broyer, C. & Martin, P. (2011). DNA barcoding reveals new insights into the diversity of Antarctic species of Orchomene sensu lato (Crustacea: Amphipoda: Lysianassoidea). Deep-Sea Research Part II Topical Studies in Oceanography , 58(1–2), 230–241.
Hardy, A. C., & Milne, P. S. (1938). Studies in the Distribution of Insects by Aerial Currents. Journal of Animal Ecology , 7(2), 199–229.
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, 313–321.
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004). Identification of birds through DNA barcodes. PLoS Biology , 2, e312.
Hebert, P. D. N., Ratnasingham, S., Zakharov, E. V., Telfer, A. C., Levesque-Beaudin, V., Milton, M. A., Pedersen, S., Jannetta, P., & deWaard, J. R. (2016). Counting animal species with DNA barcodes: Canadian insects. Philosophical Transactions of the Royal Society B , 371, 20150333.
Hobern, D. (2021). BIOSCAN: DNA barcoding to accelerate taxonomy and biogeography for conservation and sustainability. Genome , 64, 161–164.
Hooker, J. D. (1844-47). The Botany of the Antarctic Voyage of H. M. Discovery Ships Erebus and Terror in the Years 1839–1843, under the Command of Captain Sir James Clark Ross. Flora Antarctica. London, Reeve Brothers
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.
Kapli, P., Lutteropp, S., Zhang, J. P., Kobert, K., Pavlidis, P., Stamatakis, A., & Flouri, T. (2017). Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics , 33, 1630–1638.
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. J. (2012). Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics , 28, 1647–1649.
Kekkonen, M., & Hebert, P. D. N. (2014). DNA barcode-based delineation of putative species: efficient start for taxonomic workflows.Molecular Ecology Resources , 14, 706–715.
Kimura, M. A. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.Journal of Molecular Evolution , 16(2), 111–20.
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., & Calcott, B. (2017). PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.Molecular Biology and Evolution , 34(3), 772–773.
Larsen, T. B. (1984). The Zoogeographical Composition and Distribution of the Arabian Butterflies (Lepidoptera; Rhopalocera). Journal of Biogeography , 11(2), 119–158.
Laurance, W. F. (1999). Reflections on the tropical deforestation crisis. Biological Conservation , 91, 109–117.
Lin, X. L., Stur, E., & Ekrem, T. (2015). Exploring genetic divergence in a species-rich insect genus using 2790 DNA barcodes. PLoS ONE , 10(9), e0138993.
Lundberg, J. G., Kottelat, M., Smith, G. R., Stiassny, M. L. J., & Gill, A. C. (2000). So many fishes, so little time: an overview of recent ichthyological discovery in continental waters. Annals of the Missouri Botanical Garden, 87(1), 26–62.
Marusik, Y. M., & Koponen, S. (2005). A survey of spiders (Araneae) with Holarctic distribution. Journal of Arachnology , 33, 300–305.
Meyer, C. P., & Paulay G. (2005). DNA barcoding: Error rates based on comprehensive sampling. Plos Biology , 3, 2229–2238.
Miller, M. A., Pfeiffer, W., & Schwartz, T. (2011). Creating the CIPRES Science Gateway for inference of large phylogenetic trees.Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery , 41, 1–8.
Miralles, A., & Vences, M. (2013). New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. PLoS ONE , (8) e68242.
Monaghan, M. T., Wild, R., Elliot, M., Fujisawa, T., Balke, M., Inward, D. J., Lees, D. C., Ranaivosolo, R., Eggleton, P., Barraclough, T. G., & Vogler, A. P. (2009). Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology , 58, 298–311.
Morrone, J. J., Escalante, T., Rodríguez-Tapia, G., Carmona, A., Arana, M., & Mercado-Gómez, J. D. (2022). Biogeographic regionalization of the Neotropical region: New map and shapefile. Anais da Academia Brasileira de Ciência , 4(1), e20211167.
Nzelu, C. O., Cáceres, A. G., Arrunátegui-Jiménez, M. J., Lañas-Rosas, M. F., Yañez-Trujillano, H. H., Luna-Caipo, D. V., Holguín-Mauricci, C. E., Katakura, K., Hashiguchi, Y., & Kato, H. (2015). DNA barcoding for identification of sand fly species (Diptera: Psychodidae) from leishmaniasis-endemic areas of Peru. Acta Tropica , 145, 45–51.
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Simpson, G. L., Solymos, P., Henry, M., Stevens, H., & Wagner, H. (2017). Community Ecology Package. R package version 2.4-3.http://cran.r-project.org/web/packages/vegan
O’Meara, B. (2010). New heuristic methods for joint species delimitation and species tree inference. Systematic Biology , 59, 59–73.
Oyewo, E. A., & Sæther, O. A. (2008). Revision of Polypedilum(Pentapedilum ) Kieffer and Ainuyusurika Sasa et Shirasaki (Diptera: Chironomidae). Zootaxa , 1953, 1–145.
Parslow B.A., Schwarz M. P., & Stevens M.I. (2021). Molecular diversity and species delimitation in the family Gasteruptiidae (Hymenoptera: Evanioidea). Genome , 64, 253–264.
Paz, A., & Crawford, A. J. (2012). Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.Journal of Biosciences , 37, 887–896.
Pearl, H., Ryan, T., Howard, M., Shimizu, Y., & Shapcott, A. (2022). DNA Barcoding to Enhance Conservation of Sunshine Coast Heathlands.Diversity , 14, 436.
Pinho, L. C., & Silva, F. L. (2020). Description of two new species ofPolypedilum (Asheum ) and immature stages ofPolypedilum (A .) curticaudatum (Diptera: Chironomidae). Zootaxa , 4759(2), 179–190.
Pons, J., Barraclough, T. G., Gomez-Zurita J., Cardoso, A., Duran, D. P., Hazell, S., Kamoun, S., Sumlin, W. D., & Vogler, A. P. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology , 55, 595–609.
Puillandre, N., Lambert, A., Brouillet, S., & Achaz, G. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation.Molecular Ecology , 21, 1864–1877.
Puillandre, N., Brouillet, S., & Achaz, G. (2021). ASAP: assemble species by automatic partitioning. Molecular Ecology Resources , 21, 609–620.
R Core Team. (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.https://www.R-project.org/
Rannala, B., & Yang, Z. (2020). Species Delimitation. Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas. Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book, pp. 5.5:1–5.5:18.
Rambaut, A. (2010). FigTree version 1.4.4. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh.http://tree.bio.ed.ac.uk/software/figtree/
Rambaut, A., Suchard. M. A., Xie, D., & Drummond, A. J. (2018). Tracer v1.7. Available fromhttp://beast.bio.ed.ac.uk/Tracer
Ratnasingham, S., & Hebert, P. D. N. (2013). A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One , 8, e66213.
Rodrigues, B. L., Baton, L. A., & Shimabukuro, P. H. F. (2020). Single-locus DNA barcoding and species delimitation of the sandfly subgenus Evandromyia (Aldamyia ). Medical and Veterinary Entomology , 34(4), 420–431.
Rodríguez, J., Hortal, J., & Nieto, M. (2006). An evaluation of the influence of environment and biogeography on community structure: the case of Holarctic mammals. Journal of Biogeography , 33(2), 291–303.
Rull, V. (2008). Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence. Molecular Ecology , 17, 2722–2729.
Schwarzfeld, M. D., & Sperling, F. A. H. (2015). Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae). Molecular Phylogenetics and Evolution , 93, 234–248.
Shapcott, A., Forster, P. I., Guymer, G. P., McDonald, W. J. F., Faith, D. P., Erickson, D., & Kress, W. J. (2015). Mapping biodiversity and setting conservation priorities for SE Queensland’s rainforests using DNA barcoding. PLoS ONE , 10, e0122164.
Shimabukuro, E. M., Trivinho-Strixino, S. & Lamas, C. J. E. (2019). NewPolypedilum Kieffer (Diptera: Chironomidae) from mountains of the Atlantic Forest, Brazil. Zootaxa , 4612(4), 518–532.
Silva, F. L., & Ekrem, T. (2016). Phylogenetic relationships of non-biting midges in the subfamily Tanypodinae (Diptera: Chironomidae) inferred from morphology. Systematic Entomology , 41, 73–92.
Silva, F. L., & Farrell, B. (2017). Non-biting midges (Diptera: Chironomidae) research in South America: subsidizing biogeographic hypotheses. Annales de Limnologie - International Journal of Limnology, 53, 111–128.
Silva, F. L., Wiedenbrug, S., & Farrell, B. (2015). A preliminary survey of the non-biting midges(Diptera: Chironomidae) of the Dominican Republic. CHIRONOMUS Journal of Chironomidae Research , 28, 12–19.
Song, C., Wang, Q., Zhang, R., Sun, B., & Wang, X. (2016). Exploring the utility of DNA barcoding in species delimitation ofPolypedilum (Tripodura ) non-biting midges (Diptera: Chironomidae). Zootaxa , 4079, 534–550.
Song, C., Lin, X., Wang, Q., & Wang, X. (2018). DNA barcodes successfully delimit morphospecies in a superdiverse insect genus.Zoologica Scripta , 47(3), 311–324.
Spies, M., & Reiss, F. (1996). Catalog and bibliography of Neotropical and Mexican Chironomidae (Insecta, Diptera). Spixiana Supplement , 22, 61–119.
Stork, N. E. (2018). How many species of insects and other terrestrial arthropods are there on earth? Annual Review of Entomology , 63, 31–45.
Sæther, O. A. (1969). Some Nearctic Podonominae, Diamesinae, and Orthocladiinae (Diptera: Chironomidae), Department of Fisheries and Oceans, Ottawa, 154 pp.
Sæther, O. A, Andersen, T., Pinho, L. C., & Mendes, H. F. (2010). The problems with Polypedilum Kieffer (Diptera: Chironomidae), with the description of Probolum subgen. n. Zootaxa , 2497, 1–36.
Sæther, O. A., & Oyewo, E. A. (2008). Keys, phylogenies and biogeography of Polypedilum subgen. Uresipedilum Oyewo et Sæther (Diptera: Chironomidae). Zootaxa , 1806, 1–34.
Sæther O.A., & Sundal, A. (1999). Cerobregma , a new subgenus ofPolypedilum Kieffer, with a tentative phylogeny of subgenera and species groups within Polypedilum (Diptera: Chironomidae).Journal of the Kansas Entomological Society , 71, 315–382.
Talavera, G., Dinca, V., & Vila, R. (2013). Factors affecting species delimitations with the GMYC model: insights from a butterfly survey.Methods in Ecology & Evolution , 4, 1101–1110.
Tamura, K., Stecher, G., & Kumar S. (2021). MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution , 38(7), 3022–3027.
Tang, C. Q., Humphreys, A. M., Fontaneto, D., & Barraclough, T. G. (2014). Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data. Methods in Ecology & Evolution , 5, 1086–1094.
Townes, H. K. Jr. (1945). The Nearctic species of Tendipedini [Diptera, Tendipedidae (= Chironomidae)]. American Midland Naturalist , 34, 1–206.
Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A., Minh, B. Q. (2016). W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research , 44, W232–W235.
Vårdal, H., Bjørlo, A., & Sæther, O. A. (2002). AfrotropicalPolypedilum subgenus Tripodura , with a review of the subgenus (Diptera: Chironomidae). Zoologica Scripta , 31, 331–402.
Velasco-Castrillón, A., Page, T. J., Gibson, J. A., & Stevens, M. I. (2014). Surprisingly high levels of biodiversity and endemism amongst Antarctic rotifers uncovered with mitochondrial DNA.Biodiversity , 15(2–3), 130–142.
Wallace, A. R. (1876). The Geographical Distribution of Animals . London, UK: Macmillans.
Webb, C. O. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. The American Naturalist , 156, 145–155.
Wiemers, M., & Fiedler, K. (2007). Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae).Frontiers in Zoology , (4), 8.
Yang, Z. H., & Rannala, B. (2017). Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses. Molecular Ecology , 26(11), 3028–3036.
Zhang, J., Kapli, P., Pavlidis, P., & Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics , 29, 2869–2876.
Zhang, F., Jantarit, S., Nilsai, A., Stevens, M. I., Ding, Y., & Satasook, C. (2018). Species delimitation in the morphologically conserved Coecobrya (Collembola: Entomobryidae): a case study integrating morphology and molecular traits to advance current taxonomy.Zoologica Scripta , 47(3), 342–356.
Zhou, X., Jacobus. L. M., DeWalt, R. E., Adamowicz, S. J., & Hebert, P. D. N. (2010). Ephemeroptera, Plecoptera, and Trichoptera fauna of Churchill (Manitoba, Canada): insights into biodiversity patterns from DNA barcoding. Journal of the North American Benthological Society , 29(3), 814–837.