References
Ahrens, D. (2006). The phylogeny of Sericini and their position within
the Scarabaeidae based on morphological characters (Coleoptera.
Scarabaeidae). Systematic Entomology , 31 (1), 113–144. DOI:
10.1111/j.1365-3113.2005.00307.x.
Ahrens, D., Monaghan, M. T., & Vogler, A. P. (2007). DNA-based taxonomy
for associating adults and larvae in multi-species assemblages of
chafers (Coleoptera. Scarabaeidae). Molecular Phylogenetics and
Evolution , 44 (1), 436–449. DOI: 10.1016/j.ympev.2007.02.024.
Ahrens, D., & Lago, P. K. (2008). Directional asymmetry reversal of
male copulatory organs in chafer beetles (Coleoptera: Scarabaeidae):
implications on left–right polarity determination in insect terminalia.Journal of Zoological Systematics and Evolutionary Research, 46
(2), 110–117. DOI: 10.1111/j.1439-0469.2007.00449.x.
Ahrens, D., Fabrizi, S., Sipek, P., & Lago, P. (2013) Integrative
analysis of DNA phylogeography and morphology of the European rose
chafer (Cetonia aurata) to infer species taxonomy and patterns of
postglacial colonisation in Europe. Molecular Phylogenetics and
Evolution , 69: 83–94.
Ahrens, D., Schwarzer, J., & Vogler, A. P. (2014). The evolution of
scarab beetles tracks the sequential rise of angiosperms and mammals.Proceedings of the Royal Society B 281 (1791), p. 20141470. DOI:
10.1098/rspb.2014.1470.
Ahrens, D., Fujisawa, T., Krammer, H.-J., Eberle, J., Fabrizi, S., &
Vogler, A. P. (2016). Rarity and Incomplete Sampling in DNA-Based
Species Delimitation. Systematic Biology , 65 (3), 478–494. DOI:
10.1093/sysbio/syw002.
Astrin, J. J., & Stüben, P. E. (2008). Phylogeny in cryptic weevils:
molecules, morphology and new genera of western Palaearctic
Cryptorhynchinae (Coleoptera: Curculionidae). Invertebrate
Systematics , 22 (5), 503-522. DOI: 10.1071/IS07057.
Avise, J. C. (2001). Phylogeography. The history and formation of
species. 3. print. Cambridge, Mass.: Harvard Univ. Press.
Ballard, J.W.O. & Whitlock, M.C. (2004) The incomplete natural history
of mitochondria. Molecular Ecology , 13, 729–744
Barnard, A. A., Fincke, O. M., McPeek, M. A., & Masly, J. P. (2017).
Mechanical and tactile incompatibilities cause reproductive isolation
between two young damselfly species. Evolution , 71 (10),
2410–2427. DOI: 10.1111/evo.13315.
Beentjes, K.K., Speksnijder, A.G.C.L., Schilthuizen, M. , Hoogeveen, M.,
Pastoor, R., & Hoorn, B.B. van der (2019) Increased performance of DNA
metabarcoding of macroinvertebrates by taxonomic sorting. PLoS ONE
14(12), e0226527. https://doi.org/10.1371/journal.pone.0226527.
Bergsten, J., Bilton, D. T., Fujisawa, T., Elliott, M., Monaghan, M. T.,
Balke, M., …& Vogler, A. P. (2012). The effect of geographical
scale of sampling on DNA barcoding. Systematic Biology , 61,
851–869. https ://doi.org/10.1093/sysbi o/sys037
Bond, J. E., & Stockman, A. K. (2008). An integrative method for
delimiting cohesion species: finding the population-species interface in
a group of Californian trapdoor spiders with extreme genetic divergence
and geographic structuring. Systematic Biology , 57 (4), 628–646.
DOI: 10.1080/10635150802302443.
Bouchard, P., Smith, A.B.T., Douglas, H., Gimmel, M.L., Brunke, A.J., &
Kanda, K. (2017) Biodiversity of Coleoptera. In: Foottit, R.G., Adler,
P.H. (Eds) Insect Biodiversity: Science and Society. John Wiley & Sons
Ltd, 337–417. https://doi.org/10.1002/9781444308211.ch11
Brown, S. D. J., Collins, R. A., Boyer, S., Lefort, M.-C.,
Malumbres-Olarte, J., Vink, C. J., & Cruickshank, R. H. (2012). SPIDER:
an R package for the analysis of species identity and evolution, with
particular reference to DNA barcoding. Molecular Ecology
Resources , 12, 562-565.
Cancian de Araujo, B., Schmidt, S., Schmidt, O., von Rintelen, T., von
Rintelen, K., Floren, A., Ubaidillah, R., Peggie, D., Balke, M. (2019)
DNA barcoding data release for Coleoptera from the Gunung Halimun canopy
fogging workpackage of the Indonesian Biodiversity Information System
(IndoBioSys) project. Biodiversity Data Journal , 7, e31432.
https://doi.org/10.3897/BDJ.7.e31432
Carstens, B. C., Pelletier, T. A., Reid, N. M., Satler, J. D. (2013).
How to fail at species delimitation. Molecular Ecology , 22 (17),
4369–4383. DOI: 10.1111/mec.12413.
Coissac, E., Riaz, T., Puillandre, N. (2012) Bioinformatic challenges
for DNA metabarcoding of plants and animals. Molecular Ecology ,
21, 1834e1847.
Dalstein, V., Eberle, J., Fabrizi, S., Etzbauer, C., Ahrens, D. (2019).
COI-based species delimitation in Indochinese Tetraserica chafers reveal
hybridisation despite strong divergence in male copulation organs.Organisms Diversity and Evolution , 19 (2), 277–286. DOI:
10.1007/s13127-019-00398-z.
Dasmahapatra, K.K. & Mallet, J. (2006) Taxonomy: DNA barcodes: recent
successes and future prospects. Heredity , 97, 254–255
Deiner, K., Bik, H.M., Mächler, E., Seymour, M., Lacoursière-Roussel,
A., Altermatt, F., Creer, S., Bista, I., Lodge, D.M., de Vere, N.,
Pfrender, M.E., Bernatchez, L. (2017). Environmental DNA metabarcoding:
Transforming how we survey animal and plant communities. Molecular
Ecology , 26, 5872-5895.
Dowton, M., Meiklejohn, K., Cameron, S.L., Wallman, J. (2014) A
preliminary framework for DNA barcoding, incorporating the multispecies
coalescent. Systematic Biology , 63, 639–644
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
Eberhard, W. G. (1985). Sexual Selection and Animal Genitalia.
Cambridge, MA and London, England: Harvard University Press.
Eberle, J., Warnock, R. C. M., Ahrens, D. (2016). Bayesian species
delimitation in Pleophylla chafers (Coleoptera) - the importance of
prior choice and morphology. BMC Evolutionary Biology, 16, p. 94.
DOI: 10.1186/s12862-016-0659-3.
Eberle, J., Fabrizi, S., Lago, P., Ahrens, D. (2017). A historical
biogeography of megadiverse Sericini-another story “out of Africa”?Cladistics , 33 (2), 183–197. DOI: 10.1111/cla.12162.
Eberle, J., Fabrizi, S., Bazzato, E., Rossi, Stella Columba, M., Cillo,
D., Uliana M., Sparacio, I., Sabatinelli, G., Warnock, R.C.M.,
Carpaneto, G.M., Ahrens, D. (2019). Sex-Biased dispersal obscures
species boundaries in integrative species delimitation approaches.Systematic Biology , 68, 441–459; published online (2018): doi:
10.1093/sysbio/syy072.
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
accuracy and high throughput. Nucleic Acids Research , 32(5),
1792-97.
Elbrecht, V., Vamos, E. E., Meissner, K., Aroviita, J., & Leese, F.
(2017). Assessing strengths and weaknesses of DNA metabarcoding-based
macroinvertebrate identification for routine stream monitoring.Methods in Ecology and Evolution , 8, 1265–1275.
doi:10.1111/2041-210x.12789
Elias, M., Hill, R. I., Willmott, K. R., Dasmahapatra, Kanchon K.,
Brower, A. V. Z., Mallet, J., & Jiggins, C. D. (2007). Limited
performance of DNA barcoding in a diverse community of tropical
butterflies. Proceedings of the Royal Society B , 274 (1627),
2881–2889. DOI: 10.1098/rspb.2007.1035.
Floyd R., Abebe E., Papert A., Blaxter M. (2002). Molecular barcodes for
soil nematode identification. Molecular Ecology , 11 (4),
839–850. DOI: 10.1046/j.1365-294X.2002.01485.x.
Fontaneto, D., Flot, J.-F., Tang, C. Q. (2015). Guidelines for DNA
taxonomy, with a focus on the meiofauna. Marine Biodiversity , 45
(3), 433–451. DOI: 10.1007/s12526-015-0319-7.
Funk, D.J. & Omland, K.E. (2003) Species-level paraphyly and polyphyly:
frequency, causes, and consequences, with insights from animal
mitochondrial DNA. Annual Review of Ecology and Evolutionary
Systematics , 34, 397–423
Gaytán, Á, Bergsten, J, Canelo, T, Pérez‐Izquierdo, C, Santoro, M,
Bonal, R. (2020) DNA Barcoding and geographical scale effect: The
problems of undersampling genetic diversity hotspots. Ecology and
Evolution , 10, 10754–10772. https://doi.org/10.1002/ece3.6733
Geiger, M. F., Moriniere, J., Hausmann, A., Haszprunar, G., Wägele, W.,
Hebert, P. D. N., Rulik, B. (2016). Testing the Global Malaise Trap
Program - How well does the current barcode reference library identify
flying insects in Germany? Biodiversity Data Journal , 4, e10671.
DOI: 10.3897/BDJ.4.e10671.
Gwiazdowski, R.A., Foottit, R.G., Maw, H.E.L., Hebert, P.D.N., Imondi,
R., & La Rocca, G. (2015) The Hemiptera (Insecta) of Canada:
Constructing a reference library of DNA barcodes. PLoS One , 10,
e0125635. https://doi.org/10.1371/journal.pone.0125635
Hawlitschek, O., Morinière, J., Lehmann, G.U.C., Lehmann, A.W., Kropf,
M., Dunz, A., Glaw, F., Detcharoen, M., Schmidt, S., Hausmann, A.,
Szucsich, N.U., Caetano‐Wyler, S.A., & Haszprunar, G. (2017). DNA
barcoding of crickets, katydids and grasshoppers (Orthoptera) from
Central Europe with focus on Austria, Germany and Switzerland.Molecular Ecology Resources , 17, 1037-1053.
doi:10.1111/1755-0998.12638
Hebert, P. D. N., Cywinska, A., Ball, Shelley L., & deWaard, J. R.
(2003a). Biological identifications through DNA barcodes.Proceedings of the Royal Society B , 270 (1512), 313–321. DOI:
10.1098/rspb.2002.2218.
Hebert, P. D. N., Ratnasingham, S., & deWaard, J. R. (2003b). Barcoding
animal life: cytochrome c oxidase subunit 1 divergences among closely
related species. In Proceedings. Biological Letters , Suppl 270,
S96-9. DOI: 10.1098/rsbl.2003.0025.
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M.
(2004). Identification of Birds through DNA Barcodes. PLoS
Biology , 2 (10), e312. DOI: 10.1371/journal.pbio.0020312.
Hebert, P. D. N., & Gregory, T. R. (2005). The promise of DNA barcoding
for taxonomy. Systematic Biology , 54 (5), 852–859. DOI:
10.1080/10635150500354886.
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 of London B , 371,
e1001127. https://doi.org/10.1098/rstb.2015.0333
Hewitt, G.M. (1996) Some genetic consequences of ice ages, and their
role in divergence and speciation. Biological Journal of the
Linnean Society , 58,247–276.
Hewitt, G.M. (1999) Post-glacial re-colonization of European biota.Biological Journal of the Linnean Society , 68, 87-112.
Hoang, D.T., Chernomor, O., Haeseler, A. von, Minh, B.Q., & Vinh, L.S.
(2018) UFBoot2: Improving the ultrafast bootstrap approximation.Molecular Biology and Evolution , 35:518–522.
https://doi.org/10.1093/molbev/msx281
Huson, D. H., & Bryant, D. (2006). Application of phylogenetic networks
in evolutionary studies. Molecular Biology and Evolution , 23 (2),
254–267. DOI: 10.1093/molbev/msj030.
Janzen, D. H., Hallwachs, W., Blandin, P., et al. (2009). Integration of
DNA barcoding into an ongoing inventory of complex tropical
biodiversity. Molecular Ecology Resources , 9, Suppl s1, 1-26.
doi:10.1111/j.1755-0998.2009.02628.x
Janzen, D. H., & Hallwachs, W. (2011). Joining inventory by
parataxonomists with DNA barcoding of a large complex tropical conserved
wildland in northwestern Costa Rica. PLoS One , 6, e18123.
Janzen, D.H., Burns, J.M., Cong, Q., Hallwachs, W., Dapkey, T.,
Manjunath, R., Hajibabaei, M., Hebert, P.D.N., & Grishin, N.V. (2017)
Nuclear genomes distinguish cryptic species. Proceedings of the
National Academy of Sciences , 114 (31), 8313-8318, DOI:
10.1073/pnas.1621504114
Joly, S., McLenachan, P. A., & Lockhart, P. J. (2009). A statistical
approach for distinguishing hybridization and incomplete lineage
sorting. The American Naturalist , 174 (2), E54-70. DOI:
10.1086/600082.
Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., Haeseler, A. von, &
Jermiin, L.S. (2017) ModelFinder: Fast model selection for accurate
phylogenetic estimates. Nature Methods , 14, 587-589.
https://doi.org/10.1038/nmeth.4285
Knowles, L. L., Carstens, B. C. (2007). Delimiting species without
monophyletic gene trees. Systematic Biology , 56 (6), 887–895.
DOI: 10.1080/10635150701701091.
Liu, M., Clarke, L.J., Baker, S.C., Jordan, G.J., Burridge, C.P. (2020)
A practical guide to DNA metabarcoding for entomological ecologists.Ecological Entomology , 45, 373–385.
Lohse, K. (2009). Can mtDNA barcodes be used to delimit species? A
response to Pons et al. Systematic Biology , 58:439–442.
Macher, J.-N., Vivancos, A., Piggott, J.J., Centeno, F.C., Matthaei,
C.D., & Leese, F. (2018). Comparison of environmental DNA and
bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I
primers. Molecular Ecology Resources , 18(6), 1456–1468 DOI
10.1111/1755-0998.12940.
Maddison, W. P. (1997). Gene Trees in Species Trees. Systematic
Biology , 46 (3), 523–536. DOI: 10.1093/sysbio/46.3.523.
Meier, R., Shiyang, K., Vaidya, G., & Ng, P. K. L. (2006). DNA
barcoding and taxonomy in Diptera: a tale of high intraspecific
variability and low identification success. Systematic Biology ,
55 (5), 715–728. DOI: 10.1080/10635150600969864.
Meyer, C. P., & Paulay, G. (2005). DNA barcoding: error rates based on
comprehensive sampling. PLoS Biology , 3 (12), e422. DOI:
10.1371/journal.pbio.0030422.
Miller, S. E. (2007). DNA barcoding and the renaissance of taxonomy.Proceedings of the National Academy of Sciences of the United
States of America , 104 (12), 4775–4776. DOI: 10.1073/pnas.0700466104.
Morinière, J, Hendrich, L, Balke, M, et al. (2017). A DNA barcode
library for Germany′s mayflies, stoneflies and caddisflies
(Ephemeroptera, Plecoptera and Trichoptera). Molecular Ecology
Resources, 17, 1293– 1307.
https://doi.org/10.1111/1755-0998.12683
Moritz, C., Cicero, C. (2004). DNA barcoding. Promise and pitfalls.PLoS Biology , 2 (10), e354. DOI: 10.1371/journal.pbio.0020354.
Müller, D., Suess, S., Hoffmann, A. A., Buchholz, G. (2013). The Value
of Satellite-Based Active Fire Data for Monitoring, Reporting and
Verification of REDD+ in the Lao PDR. Human Ecology , 41 (1),
7–20. DOI: 10.1007/s10745-013-9565-0.
Mutanen, M., Kivelä, S.M., Vos, R.A., et al. (2016). Species-Level Para-
and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in
European Lepidoptera. Systematic Biology , 65(6), 1024-1040.
doi:10.1093/sysbio/syw044
Nair, M. R. G. K. (1986). Insects and mites of crops in India. (Ed. 2).
Indian Council of Agricultural Research, New Delhi, 1975, 404pp.
Nguyen, L.-T., Schmidt, H.A., Haeseler, A. von, & Minh, B.Q. (2015).
IQ-TREE: A fast and effective stochastic algorithm for estimating
maximum likelihood phylogenies. Molecular Biology and Evolution ,
32, 268-274. https://doi.org/10.1093/molbev/msu300
Nicholls, J.A. et al. (2012). Mitochondrial barcodes are diagnostic of
shared refugia but not species in hybridizing oak gall wasps.Molecular Ecology , 21, 4051–4062.
Özgül-Siemund, A., & Ahrens, D. (2015). Taxonomic utility of female
copulation organs in Sericini chafers (Coleoptera, Scarabaeidae), with
special reference to asymmetry. Contributions to Zoology , 84 (2),
167–178. DOI: 10.1163/18759866-08402005.
Padial, J. M., Miralles, A., La Riva, I. de, Vences, M. (2010). The
integrative future of taxonomy. Frontiers in Zoology , 7 (1), 16.
DOI: 10.1186/1742-9994-7-16.
Pentinsaari, M., Hebert, P.D.N., & Mutanen, M. (2014). Barcoding
Beetles: A regional survey of 1872 species reveals high identification
success and unusually deep interspecific divergences. PLoS One ,
9, e108651. https://doi.org/10.1371/journal.pone.0108651
Pentinsaari, M., Anderson, R., Borowiec, L., Bouchard, P., Brunke, A.,
Douglas, H., Smith, A.B.T., Hebert, P.D.N. (2019). DNA barcodes reveal
63 overlooked species of Canadian beetles (Insecta, Coleoptera).ZooKeys , 894, 53–150.
Piper, A.M., Batovska, J., Cogan, N.O.I, Weiss, J., Cunningham, J.P.,
Rodoni, B.C., Blacket, M.J. (2019) Prospects and challenges of
implementing DNA metabarcoding for high-throughput insect surveillance.Giga Science , 8, 1–22.
Porter, T.M., Hajibabaei, M. (2018) Over 2.5 million COI sequences in
GenBank and growing. PLoS One , 13(9),e0200177.
https://doi.org/10.1371/journal.pone.0200177 PMID: 30192752
Puillandre, N., Lambert, A., Brouillet, S., Achaz, G. (2012). ABGD,
Automatic Barcode Gap Discovery for primary species delimitation.Molecular Ecology , 21 (8), 1864–1877. DOI:
10.1111/j.1365-294X.2011.05239.x.
Ratnasingham, S., & Hebert, P. D. N. (2007). BOLD: The Barcode of Life
Data System (http://www.barcodinglife.org). Molecular Ecology
Notes , 7 (3), 355–364. DOI: 10.1111/j.1471-8286.2007.01678.x.
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.
Reid, N.M., & Carstens, B.C. 2012. Phylogenetic estimation error can
decrease the accuracy of species delimitation: a Bayesian implementation
of the general mixed Yule-coalescent model. BMC Evolutionary
Biology , 12:196.
Ritcher, P. O. (1966). White grubs and their allies. A Study of North
American Scarabaeoid Larvae. Oregon State Monographs. Studies in
Entomology , 4. Corvallis, Oregon State University Press, 219pp.
Ross, H.A. (2014) The incidence of species-level paraphyly in animals: a
re-assessment. Molecular Phylogenetics and Evolution , 76, 10–17
Rougerie, R., Lopez-Vaamonde, C., Barnouin, T., Delnatte, J., Moulin,
N., Noblecourt, T., Nusillard, B., Parmain, G., Soldati, F., & Bouget,
C. (2015) PASSIFOR: A reference library of DNA barcodes for French
saproxylic beetles (Insecta, Coleoptera). Biodiversity Data
Journal , 3, e4078. https://doi.org/10.3897/BDJ.3.e4078
Ruppert, K.M., Kline, R.J., Rahman, M.S. (2019) Past, present, and
future perspectives of environmental DNA (eDNA) metabarcoding: A
systematic review in methods, monitoring, and applications of global
eDNA. Global Ecology and Conservation , 17, e00547.
Schmid‐Egger, C., Straka, J., Ljubomirov, T., Blagoev, G.A., Morinière,
J., Schmidt, S. (2019). DNA barcodes identify 99 percent of apoid wasp
species (Hymenoptera: Ampulicidae, Crabronidae, Sphecidae) from the
Western Palearctic. Molecular Ecology Resources , 19, 476– 484.
https://doi.org/10.1111/1755-0998.12963
Schmitt, T. (2007) Molecular biogeography of Europe: Pleistocene cycles
and postglacial trends. Frontiers in Zoology , 4, 11.
doi:10.1186/1742-9994-4-11
Smith, M.A. et al. (2012) Wolbachia and DNA barcoding insects: patterns,
potential, and problems. PLoS One 7, e36514
Steinke, D., Breton, V., Berzitis, E., Hebert, P.D.N. (2017) The School
Malaise Trap Program: Coupling educational outreach with scientific
discovery. PLoS Biology , 15, e2001829.
https://doi.org/10.1371/journal.pbio.2001829
Talavera, G., Dinca, V., & Vila, R. (2013). Factors affecting species
delimitations with the GMYC model: insights from a butterfly survey.
Methods in Ecology and Evolution, 4, 1101–1110.
Templeton, A. R., Crandall, K. A., Sing, C. F. (1992). A cladistic
analysis of phenotypic associations with haplotypes inferred from
restriction endonuclease mapping and DNA sequence data. III. Cladogram
estimation. Genetics , 132 (2), 619–633.
Thormann, B., Ahrens, D., Marín Armijos, D., Peters, M.K., Wagner, T.,
Wägele, J.W. (2016) Exploring the Leaf Beetle Fauna (Coleoptera:
Chrysomelidae) of an Ecuadorian Mountain Forest Using DNA Barcoding.PLoS One , 11(2), e0148268. doi:10.1371/journal.pone.0148268.
Trifinopoulos, J., Nguyen, L.-T., Haeseler, A. von, & Minh, B. Q.
(2016). W-IQ-TREE: a fast online phylogenetic tool for maximum
likelihood analysis. Nucleic Acids Research , 44 (W1), W232-5.
DOI: 10.1093/nar/gkw256.
Yeates, D. K., Seago, A., Nelson, L., Cameron, Stephen L., Joseph, L.
E.O., Trueman, J. W. H. (2011). Integrative taxonomy, or iterative
taxonomy? Systematic Entomology , 36 (2), 209–217. DOI:
10.1111/j.1365-3113.2010.00558.x.
Zhang, J., Kapli, P., Pavlidis, P., Stamatakis, A. (2013). A general
species delimitation method with applications to phylogenetic
placements. In Bioinformatics 29 (22), 2869–2876. DOI:
10.1093/bioinformatics/btt499.
Zhou, X. et al. (2016). The Trichoptera barcode initiative: a strategy
for generating a species-level Tree of Life. Phil. Trans. R. Soc.B, 371, 20160025. http://dx.doi.org/10.1098/rstb.2016.0025