Research article Special Issues

Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes

  • Received: 22 November 2017 Accepted: 11 January 2018 Published: 17 January 2018
  • DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.

    Citation: Jeffrey M. Marcus. Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes[J]. AIMS Genetics, 2018, 5(1): 1-23. doi: 10.3934/genet.2018.1.1

    Related Papers:

  • DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.


    加载中
    [1] Hebert PDN, Cywinska A, Ball SL, et al. (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270: 313–321. doi: 10.1098/rspb.2002.2218
    [2] Folmer O, Black MB, Hoch W, et al. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Bio Biotechnol 3: 294–299.
    [3] Chen CS, Huang CT, Hseu RS (2017) Evidence for two types of nrDNA existing in Chinese medicinal fungus Ophiocordyceps sinensis. AIMS Genetics 4: 192–201. doi: 10.3934/genet.2017.3.192
    [4] Lebonah DE, Dileep A, Chandrasekhar K, et al. (2014) DNA barcoding on bacteria: A review. Adv Biol 2014: 541787.
    [5] Sperling JL, Silva-Brandao KL, Brandao MM, et al. (2017) Comparison of bacterial 16S rRNA variable regions for microbiome surveys of ticks. Ticks and Tick-borne Diseases 8.
    [6] de Vere N, Rich TC, Trinder SA, et al. (2015) DNA barcoding for plants. Methods Mol Biol 1245: 101–118. doi: 10.1007/978-1-4939-1966-6_8
    [7] Heather JM, Chain B (2016) The sequence of sequencers: The history of sequencing DNA. Genomics 107: 1–8. doi: 10.1016/j.ygeno.2015.11.003
    [8] Schwaller C (1998) 'The millennium time bomb' or year 2000 problem: what problem? whose problem. Time Soc 7: 105–118.
    [9] Hajibabaei M, Janzen DH, Burns JM, et al. (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Nat Acad Sci USA 103: 968–971. doi: 10.1073/pnas.0510466103
    [10] Manion M, Evan WM (2000) The Y2K problem and professional responsibility: a retrospective analysis. Technol Soc 22: 361–387. doi: 10.1016/S0160-791X(00)00015-4
    [11] Kulski JK (2016) Next-Generation Sequencing-An Overview of the History, Tools, and "Omic" Applications. In: Kulski JK, editor. Next Generation Sequencing-Advances, Applications and Challenges: InTech. pp. Available from: https://www.intechopen.com/books/next-generation-sequencing-advances-applications-and-challenges/next-generation-sequencing-an-overview-of-the-history-tools-and-omic-applications.
    [12] Ratnasingham S, Hebert PDN (2007) BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes 7: 355–364. doi: 10.1111/j.1471-8286.2007.01678.x
    [13] Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Resour 12: 377–388. doi: 10.1111/j.1755-0998.2012.03119.x
    [14] Moritz C, Cicero C (2004) DNA Barcoding: Promise and Pitfalls. PLoS Biol 2: e354. doi: 10.1371/journal.pbio.0020354
    [15] Duvernell DD, Aspinwall N (1995) Introgression of Luxilus cornutus Mtdna into allopatric populations of Luxilus chrysocephalus (Teleostei, Cyprinidae) in Missouri and Arkansas. Mol Ecol 4: 173–181. doi: 10.1111/j.1365-294X.1995.tb00206.x
    [16] Good JM, Hird S, Reid N, et al. (2008) Ancient hybridization and mitochondrial capture between two species of chipmunks. Mol Ecol 17: 1313–1327. doi: 10.1111/j.1365-294X.2007.03640.x
    [17] Chambers EA, Hebert PDN (2016) Assessing DNA barcodes for species identification in North American reptiles and amphibians in natural history collections. PLoS ONE 11: e0154363. doi: 10.1371/journal.pone.0154363
    [18] McCullagh BS, Marcus JM (Submitted) When barcodes go bad: Exploring the limits of DNA barcoding with complete Junonia butterfly mitochondrial genomes Submitted to Molecular Phylogenetics and Evolution: Manuscript #MPE_2017_2019.
    [19] Bennett RF (1999) Technology-The Y2K problem. Science 284: 438–439. doi: 10.1126/science.284.5413.438
    [20] McCullagh BS, Marcus JM (2015) The complete mitochondrional genome of Lemon Pansy, Junonia lemonias (Lepidoptera: Nymphalidae: Nymphalinae). J Asia-Pacific Ent 18: 749–755. doi: 10.1016/j.aspen.2015.08.006
    [21] Hebert PDN, Penton EH, Burns JM, et al. (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Nat Acad Sci USA 101: 14812–14817. doi: 10.1073/pnas.0406166101
    [22] Janzen DH, Hallwachs W (2005) Dynamic database for an inventory of the macrocaterpillar fauna, and its food plants and parasitoids, of Area de Conservacion Guanacaste (ACG), northwestern Costa Rica http://janzen.sas.upenn.edu.
    [23] Burns JM, Janzen DH, Hajibabaei M, et al. (2007) DNA barcodes of closely related (but morphologically and ecologically distinct) species of skipper butterflies (Hesperiidae) can differ by only one to three nucleotides. J Lepid Soc 61: 138–153.
    [24] Tavares ES, Baker AJ (2008) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evol Biol 8: 81. doi: 10.1186/1471-2148-8-81
    [25] Hebert PDN, deWaard JR, Landry JF (2010) DNA barcodes for 1/1000 of the animal kingdom. Biol Lett 6: 359–362. doi: 10.1098/rsbl.2009.0848
    [26] Vamos EE, Elbrecht V, Leese F (2017) Short COI markers for freshwater macroinvertebrate metabarcoding. Metabarcoding and Metagenomics 1: e14625. doi: 10.3897/mbmg.1.14625
    [27] Stoeckle M, Bucklin A, Knowlton N, et al. (2006) Census of Marine Life DNA Barcoding Protocol. Available from: http://wwwcoreoceanorg/Dev2Goweb?id=255158.
    [28] Meusnier I, Singer GAC, Landry JF, et al. (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9: 214. doi: 10.1186/1471-2164-9-214
    [29] Gemmell AP, Marcus JM (2015) A tale of two haplotype groups: The origin and distribution of divergent New World Junonia COI haplotypes. Syst Ent 40: 532–546. doi: 10.1111/syen.12120
    [30] Redin D, Borgstrom E, He MX, et al. (2017) Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules. Nucleic Acids Res 45.
    [31] Lim J, Kim SY, Kim S, et al. (2009) BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources. BMC Genomics 10: S8.
    [32] Bezeng BS, Davies TJ, Daru BH, et al. (2017) Ten years of barcoding at the African Centre for DNA Barcoding. Genome 60: 629–638. doi: 10.1139/gen-2016-0198
    [33] Carew ME, Nichols SJ, Batovska J, et al. (2017) A DNA barcode database of Australia's freshwater macroinvertebrate fauna. Mar Freshwater Res 68: 1788–1802. doi: 10.1071/MF16304
    [34] Wheeler QD (1999) Why the phylogenetic species concept?--Elementary. J Nematol 31: 134–141.
    [35] Spooner DM (2009) DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. Am J Bot 96: 1177–1189. doi: 10.3732/ajb.0800246
    [36] DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Phil Trans R Soc B 360: 1905–1916. doi: 10.1098/rstb.2005.1722
    [37] Brower AVZ (2006) Problems with DNA barcodes for species delimitation: 'ten species' of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Syst Biodivers 4: 127–132. doi: 10.1017/S147720000500191X
    [38] Brower AVZ (2010) Alleviating the taxonomic impediment of DNA barcoding and setting a bad precedent: names for ten species of 'Astraptes fulgerator' (Lepidoptera: Hesperiidae: Eudaminae) with DNA-based diagnoses. Syst Biodivers 8: 485–491. doi: 10.1080/14772000.2010.534512
    [39] Schmidt BC, Sperling FAH (2008) Widespread decoupling of mtDNA variation and species integrity in Grammia tiger moths (Lepidoptera: Noctuidae). Syst Ent 33: 613–634. doi: 10.1111/j.1365-3113.2008.00433.x
    [40] Dupuis JR, Sperling FAH (2015) Repeated reticulate evolution in North American Papilio machaon group swallowtail butterflies. PLoS ONE 10: e0141882. doi: 10.1371/journal.pone.0141882
    [41] Glemet H, Blier P, Bernatchez L (1998) Geographical extent of Arctic char (Salvelinus alpinus) mtDNA introgression in brook char populations (S. fontinalis) from eastern Quebec, Canada. Mol Ecol 7: 1655–1662.
    [42] Stegemann S, Keuthe M, Greiner S, et al. (2012) Horizontal transfer of chloroplast genomes between plant species. Proc Nat Acad Sci USA 109: 2434–2438. doi: 10.1073/pnas.1114076109
    [43] Wortley AH, Rudall PJ, Harris DJ, et al. (2005) How much data are needed to resolve a difficult phylogeny? Case study in Lamiales Syst Biol 54: 697–709.
    [44] Peters MJ, Marcus JM (2017) Taxonomy as a hypothesis: testing the status of the Bermuda buckeye butterfly Junonia coenia bergi (Lepidoptera: Nymphalidae). Syst Ent 42: 288–300. doi: 10.1111/syen.12214
    [45] Wiesemüller B, Rothe H (2006) Interpretation of bootstrap values in phylogenetic analysis. Anthropol Anz 64: 161–165.
    [46] Pfeiler E, Johnson S, Markow TA (2012) DNA barcodes and insights into the relationships and systematics of buckeye butterflies (Nymphalidae: Nymphalinae: Junonia) from the Americas. J Lepid Soc 66: 185–198. doi: 10.18473/lepi.v66i4.a1
    [47] Pfeiler E, Laclette MRL, Markow TA (2016) Polyphyly in Urbanus and Astraptes (Hesperiidae: Eudaminae) assessed using mitochondrial DNA barcodes, with a reinstated status proposed for Achalarus. J Lepid Soc 70: 85–95. doi: 10.18473/lepi.70i2.a2
    [48] Bock DG, Kane NC, Ebert DP, et al. (2014) Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol 201: 1021–1030. doi: 10.1111/nph.12560
    [49] Turner B, Paun O, Munzinger J, et al. (2016) Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species, little divergence. Ann Bot 117: 1175–1185. doi: 10.1093/aob/mcw060
    [50] Dodsworth S, Chase MW, Kelly LJ, et al. (2015) Genomic repeat abundances contain phylogenetic signal. Syst Biol 64: 112–126. doi: 10.1093/sysbio/syu080
    [51] Dodsworth S, Chase MW, Sarkinen T, et al. (2016) Using genomic repeats for phylogenomics: a case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae). Biol J Linn Soc 117: 96–105. doi: 10.1111/bij.12612
    [52] Gillett CPDT, Crampton-Platt A, Timmermans MJTN, et al. (2014) Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Mol Biol Evol 31: 2223–2237. doi: 10.1093/molbev/msu154
    [53] Timmermans MJTN, Dodsworth S, Culverwell CL, et al. (2010) Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res 38: e197.
    [54] Timmermans MJTN, Lees DC, Simonsen TJ (2014) Towards a mitogenomic phylogeny of Lepidoptera. Mol Phylogen Evol 79: 169–178. doi: 10.1016/j.ympev.2014.05.031
    [55] Wu LW, Lin LH, Lees D, et al. (2014) Mitogenomic sequences effectively recover relationships within brush-footed butterflies (Lepidoptera: Nymphalidae). BMC Genomics 15: 468 doi: 10.1186/1471-2164-15-468
    [56] Shi QH, Sun XY, Wang YL, et al. (2015) Morphological characters are compatible with mitogenomic data in resolving the phylogeny of Nymphalid butterflies (Lepidoptera: Papilionoidea: Nymphalidae). PLOS One 10: e0124349. doi: 10.1371/journal.pone.0124349
    [57] Wetterstrand KA (2018) DNA sequencing costs: Data from the NHGRI Genome Sequencing Program (GSP). Available from: http://www.genome.gov/sequencingcostsdata.
    [58] Borchers TE, Marcus JM (2014) Genetic population structure of buckeye butterflies (Junonia) from Argentina. Syst Ent 39: 242–255. doi: 10.1111/syen.12053
    [59] Gemmell AP, Borchers TE, Marcus JM (2014) Genetic population structure of buckeye butterflies (Junonia) from French Guiana, Martinique, and Guadeloupe. Psyche 2014: 1–21.
    [60] Abbasi R, Marcus JM (2015) Color pattern evolution in Vanessa butterflies (Nymphalidae: Nymphalini): Non-eyespot characters. Evol Dev 17: 63–81. doi: 10.1111/ede.12109
    [61] Wallace JB (1975) Food partitioning in net-spinning trichoptera larvae: Hydropsyche venularis, Cheumatopsyche etrona, and Maconema zebratum (Hydropsychidae). Ann Entomol Soc Am 68: 463–472. doi: 10.1093/aesa/68.3.463
    [62] Kjer KM, Blahnik RJ, Holzenthal RW (2002) Phylogeny of caddisflies (Insecta, Trichoptera). Zool Scr 31: 83–91. doi: 10.1046/j.0300-3256.2001.00079.x
    [63] Ruiter DE, Boyle EE, Zhou X (2013) DNA barcoding facilitates associations and diagnoses for Trichoptera larvae of the Churchill (Manitoba, Canada) area. BMC Ecology 13: 5. doi: 10.1186/1472-6785-13-5
    [64] Kjer KM, Blahnik RJ, Holzenthal RW (2001) Phylogeny of Trichoptera (Caddisflies): Characterization of signal and noise within multiple datasets. Syst Biol 50: 781–816. doi: 10.1080/106351501753462812
    [65] Zhou X, Frandsen PB, Holzenthal RW, et al. (2016) The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life. Phil Trans R Soc B 371: 20160025. doi: 10.1098/rstb.2016.0025
    [66] Peters RS, Meusemann K, Petersen M, et al. (2014) The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evol Biol 14: 52. doi: 10.1186/1471-2148-14-52
    [67] Abbasi R, Marcus JM (2017) A new A-P compartment boundary and organizer in holometabolous insect wings. Sci Rep 7: 16337. doi: 10.1038/s41598-017-16553-5
    [68] Winter WD (2000) Basic Techniques for Observing and Studying Moths and Butterflies; Miller WE, editor. Los Angeles, CA: The Lepidopterists' Society. 444 p.
    [69] Living Prairie Mitogenomics Consortium (2017) The complete mitochondrial genome of the lesser aspen webworm moth Meroptera pravella (Insecta: Lepidoptera: Pyralidae). Mitochondrial DNA B Resour 2: 344–346. doi: 10.1080/23802359.2017.1334525
    [70] Peirson DSJ, Marcus JM (2017) The complete mitochondrial genome of the North American caddisfly Anabolia bimaculata (Insecta: Trichoptera: Limnephilidae). Mitochondrial DNA B Resour 2: 595–597. doi: 10.1080/23802359.2017.1372728
    [71] Lalonde MLM, Marcus JM (2017) The complete mitochondrial genome of the long-horned caddisfly Triaenodes tardus (Insecta: Trichoptera: Leptoceridae). Mitochondrial DNA B Resour 2: 765–767. doi: 10.1080/23802359.2017.1398619
    [72] McCullagh BS, Wissinger SA, Marcus JM (2015) Identifying PCR primers to facilitate molecular phylogenetics in Caddisflies (order Trichoptera). Zool Syst 40: 459–469.
    [73] Kearse M, Moir R, Wilson A, et al. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649. doi: 10.1093/bioinformatics/bts199
    [74] Reuter JS, Mathews DH (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11: 129. doi: 10.1186/1471-2105-11-129
    [75] Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415. doi: 10.1093/nar/gkg595
    [76] Wang Y, Liu X, Yang D (2014) The first mitochondrial genome for caddisfly (Insecta: Trichoptera) with phylogenetic implications. Int J Biol Scii 10: 53–63. doi: 10.7150/ijbs.7975
    [77] Wang SQ, Zhao MJ, Li TP (2003) Complete sequence of the 10.3 kb silkworm Attacus ricini rDNA repeat, determination of the transcriptional initiation site and functional analysis of the intergenic spacer. DNA Sequence 14: 95–101.
    [78] Linard B, Arribas P, Andujar C, et al. (2017) The mitogenome of Hydropsyche pellucidula (Hydropsychidae): First gene arrangement in the insect order Trichoptera. Mitochondrial DNA A DNA Mapp Seq Anal 28: 71–72.
    [79] Dietz L, Brand P, Eschner LM, et al. (2015) The mitochondrial genomes of the caddisflies Sericostoma personatum and Thremma gallicum (Insecta: Trichoptera). Mitochondrial DNA A DNA Mapp Seq Anal 27: 3293–3294.
    [80] Sievers F, Wilm A, Dineen D, et al. (2011) Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.
    [81] Kim JS, Park JS, Kim MJ, et al. (2012) Complete nucleotide sequence and organization of the mitochondrial genome of eri-silkworm, Samia cynthia ricini (Lepidoptera: Saturniidae). J Asia Pac Entomol 15: 162–173. doi: 10.1016/j.aspen.2011.10.002
    [82] Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sunderland, Massachusetts, USA: Sinauer Associates.
    [83] Darriba D, Taboada GL, Doallo R, et al. (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9: 772.
    [84] Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276: 227–232. doi: 10.1126/science.276.5310.227
    [85] Ishizuka K, Matsuo M, Nonaka M (2015) Molecular phylogenetic analysis of Catocala moths based on the nuclear ITS2 and 28S rRNA gene sequences (Lepidoptera, Noctuidae). Tinea 23: 157–170.
    [86] Briscoe AG, Bray RA, Brabec J, et al. (2016) The mitochondrial genome and ribosomal operon of Brachycladium goliath (Digenea: Brachycladiidae) recovered from a stranded minke whale. Parasitol Int 65: 271–275. doi: 10.1016/j.parint.2016.02.004
    [87] Cameron SL (2014) Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny. Annu Rev Entomol 59: 95–117.
    [88] Geraci CJ, Zhou X, Morse JC, et al. (2010) Defining the genus Hydropsyche (Trichoptera:Hydropsychidae) based on DNA and morphological evidence. J N Amer Benthol Soc 29: 918–933. doi: 10.1899/09-031.1
    [89] Irwin DE (2012) Local adaptation along smooth ecological gradients causes phylogeographic breaks and phenotypic clustering. Am Nat 180: 35–49. doi: 10.1086/666002
    [90] Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylogenetic analysis. J Syst Evol 46: 239–257.
    [91] Janzen DH, Hajibabaei M, Burns JM, et al. (2005) Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Phil Trans Roy Soc B 360: 1835–1845. doi: 10.1098/rstb.2005.1715
    [92] Jaeger CM, Dombroskie JJ, Sperling FAH (2013) Delimitation of Phaneta taradana (Moschler 1874) and P. montanana (Walsingham 1884) (Tortricidae: Olethreutinae) in Western Canada using morphology and DNA. J Lepid Soc 67: 253–262.
    [93] Proshek B, Dupuis JR, Engberg A, et al. (2015) Genetic evaluation of the evolutionary distinctness of a federally endangered butterfly, Lange's Metalmark. BMC Evol Biol 15.
    [94] Wahlberg N, Weingartner E, Warren A, et al. (2009) Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini). BMC Evol Biol 9: 92. doi: 10.1186/1471-2148-9-92
    [95] Kodandaramaiah U, Simonsen TJ, Bromilow S, et al. (2013) Deceptive single-locus taxonomy and phylogeography: Wolbachia-associated divergence in mitochondrial DNA is not reflected in morphology and nuclear markers in a butterfly species. Ecol Evol 3: 5167–5176. doi: 10.1002/ece3.886
    [96] Dodsworth S (2015) Genome skimming for next-generation biodiversity analysis. Trends Plant Sci 20: 525–527. doi: 10.1016/j.tplants.2015.06.012
    [97] Lake JA (1988) Origin of the eukaryotic nucleus by rate-invariant analyisis of rRNA sequences. Nature 331: 184–186. doi: 10.1038/331184a0
    [98] Wahlberg N, Pena C, Ahola M, et al. (2016) PCR primers for 30 novel gene regions in the nuclear genomes of Lepidoptera. Zookeys: 129–141.
    [99] Maricic T, Whitten M, Pääbo S (2010) Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLOS ONE 11: e14004.
    [100] Breinholt JW, Earl C, Lemmon AR, et al. (2017) Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for anchored phylogenomics. Syst Biol: syx048.
  • Reader Comments
  • © 2018 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
通讯作者: 陈斌, bchen63@163.com
  • 1. 

    沈阳化工大学材料科学与工程学院 沈阳 110142

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索

Metrics

Article views(5273) PDF downloads(1298) Cited by(31)

Article outline

Figures and Tables

Figures(2)  /  Tables(2)

Other Articles By Authors

/

DownLoad:  Full-Size Img  PowerPoint
Return
Return

Catalog