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.