SpringerLink
Log in

DNA Barcoding in Avian Species with Special Reference to Taxonomically Wide Biogeographic Studies

  • Chapter
  • First Online:
DNA Barcoding and Molecular Phylogeny

  • 917 Accesses

Abstract

The establishment of DNA Barcode project in 2003, intending to construct a strong molecular identification tool via standardised genetic sequences, marked a new era of species identification and taxonomy. DNA barcoding so far proved to be simple and one of the excellent tools for identification of not only animals and plants but also the aves. The avian fauna represents an excellent contender for testing DNA barcode validation as aves or birds are amongst the most prominent groups in which a wide variety of morphological, genetic and behavioural studies have been conducted, thereby establishing a prime line of stable taxonomy. The idea of All Bird barcode initiative (ABBI) was conceived in 2005 with the intention to collect genetic data samples for deciphering a DNA barcode for over 10,000 known avian species. Regardless of hundreds of vigilant studies carried out during the past decade, there are still numerous avian species to be discovered and identified. ABBI is new hope for speedy identification of novel avian species and will also help in hundreds of new samples to be identified, thereby opening up new avenues for avian identification and its related scientific research. Adding on, with the advancement of the mt-DNA gene cytochrome c oxidase I (COI) library via DNA barcoding projects of avian species, there will be a better understanding of different avian realms and taxonomic territories. It will also serve as an unbiased taxonomic representation of different avian groups. The advantage is that the DNA barcode sequences deposited in these databases are of high quality and are standardised and therefore have fewer ambiguities, short sequence span, bidirectional sequencing and uniform sequence alignment. It has been observed that the rate of error on BOLD is much lower than on other databases, DNA barcoding in avian species in future will undoubtedly provide more specific species identification, recognition of cryptic species and tracing the line of avian evolution through different eras, deciphering their causes of divergence.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 189.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Aliabadian M, Beentjes KK, Roselaar CS (2013) DNA barcoding of Dutch birds. In: Nagy ZT, Backeljau T, De Meyer M, Jordaens K (eds) DNA barcoding: a practical tool for fundamental and applied biodiversity research, vol 365, pp 25–48. (ZooKeys)

    Google Scholar 

  • American Ornithologists’ Union (AOU) (1998) Check-list of North American birds, 7th edn. AOU Press, Lawrence, Kansas, p 829

    Google Scholar 

  • Arctander P, Fjeldsa J (1994) Avian tissue collections for DNA analysis. Ibis 136:359360

    Article  Google Scholar 

  • Avise JC, Walker D (1998) Pleistocene phylogeographic effects on avian populations and the speciation process. Proc R Soc Lond B Bio Sci 265:457–463

    Article  CAS  Google Scholar 

  • Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T (1987) Intraspecific phylogeography: the mitochondrial bridge between population genetics and systematics. Annu Rev Ecol Syst 18:489–522

    Article  Google Scholar 

  • Baker A, Edwards S, Hanken, J, Schindel D, Stoeckle M (2005) Barcoding life takes flight: all birds barcoding initiative (ABBI), Report of Inaugural Workshop

    Google Scholar 

  • Baker AJ, Tavares ES, Elbourne RF (2009) Countering criticisms of single mitochondrial DNA gene barcoding in birds. Mol Ecol Resour 9:257268

    Article  Google Scholar 

  • Banks RC, Cicero C, Dunn JL, Kratter AW, Ouellet H (2000) Forty-second supplement to the Ornithologists’ Union checklist of north American birds. Auk 117:847–858

    Article  Google Scholar 

  • Banks RC, Cicero C, Dunn JL, Kratter AW, Rasmussen PC (2002) Forty-third supplement to the Ornithologists’ Union checklist of north American birds. Auk 119:897–906

    Article  Google Scholar 

  • Banks RC, Cicero C, Dunn JL, Kratter AW, Rasmussen PC (2003) Forty-fourth supplement to the Ornithologists’ Union checklist of north American birds. Auk 120:923–931

    Article  Google Scholar 

  • Bilgin R, Ebeoğlu N, İnak S, Kırpık MA, Horns JJ, Şekercioğlu ÇH (2016) DNA barcoding of birds at a migratory hotspot in eastern Turkey highlights continental phylogeographic relationships. PLoS One 11(6):e0154454. https://doi.org/10.1371/journal.pone.0154454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Campagna L, St Clair JJH, Lougheed SC, Woods RW, Imberti S, Tubaro PL (2012) Divergence between passerine populations from the Malvinas – Falkland Islands and their continental counterparts: a comparative phylogeographical study. Biol J Linn Soc 106:865–879

    Article  Google Scholar 

  • Chaves BRN, Chaves AV, Nascimento ACA, Chevitarese J, Vasconcelos MF, Santos FR (2015) Barcoding Neotropical birds: assessing the impact of nonmonophyly in a highly diverse group. Mol Ecol Res 15(4):921–931

    Article  Google Scholar 

  • Chung IH, Yoo HS, Eah JY, Yoon HY, Jung JW, Hwang SY, Kim CB (2010) A DNA microarray for identification of selected Korean birds based on mitochondrial cytochrome C oxidase I gene sequences. Mol Cells 30(4):295–301. https://doi.org/10.1007/s10059-010-0118-8

    Article  CAS  PubMed  Google Scholar 

  • Clements JF, Schulenberg TS, Iliff MJ, Roberson D, Fredericks TA, Sullivan BL, Wood CL (2015) The eBird/Clements checklist of birds of the world. Available from http://www.birds.cornell.edu/clementschecklist/download/

  • Coghlan ML, White NE, Parkinson L, Haile J, Spencer PB, Bunce M (2012) Egg forensics: an appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs. Forensic Sci Int Genet 6(2):268–273

    Article  CAS  Google Scholar 

  • Dasmahapatra KK, Mallet J (2006) DNA barcodes: recent successes and future prospects. Heredity 97(4):254–255

    Article  CAS  Google Scholar 

  • Evans T (2007) DNA damage. NEB Exp 2(1):1–3

    Google Scholar 

  • Frézal L, Leblois R (2008) Four years of DNA barcoding: current advances and prospects. Infect Genet Evol 8(5):727–736

    Article  Google Scholar 

  • Gill FB (2007) Ornithology, 3rd edn. W.H. Freeman, New York

    Google Scholar 

  • Gill FB, Slikas B (1992) Patterns of mitochondrial DNA divergence in north American crested titmice. Condor 94:20–28

    Article  Google Scholar 

  • González AD, Lotta IA, García LF, Moncada LI, Matta NE (2015) Avian haemosporidians from neotropical highlands: evidence from morphological and molecular data. Parasitol Int 64(4):48–59. https://doi.org/10.1016/j.parint.2015.01.007

    Article  PubMed  Google Scholar 

  • Hajibabaei M, deWaard JR, Ivanova NV, Ratnasingham S, Dooh RT, Kirk SL (2005) Critical factors for assembling a high volume of DNA barcodes. Philos Trans R Soc 360:1959–1967. https://doi.org/10.1098/rstb.1727

    Article  CAS  Google Scholar 

  • Hajibabaei M, Smith AM, Janzen DH (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Mol Ecol Notes 6:959–964

    Article  CAS  Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270:313–321

    Article  CAS  Google Scholar 

  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol. https://doi.org/10.1371/journal.pbio.0020312

  • Hoss M, Jaruga P, Zastawny TH, Dizdaroglu M, Paabo S (1996) DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res 24:1304–1307

    Article  CAS  Google Scholar 

  • Johnsen A, Rindal E, Ericson PGP, Zuccon D, Kerr KCR, Stoeckle MY (2010) DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species. J Ornithol 151:565–578. https://doi.org/10.1007/s10336-009-0490-3

    Article  Google Scholar 

  • Kerr K, Birks SM, Kalyakin MV, Red’kin YA, Koblik EA, Hebert PDN (2009) Filling the gap—COI barcode resolution in eastern Palearctic birds. Front Zool 6:10

    Article  Google Scholar 

  • Kwon YS, Kim JH, Choe JC, Park YC (2012) Low resolution of mitochondrial COI barcodes for identifying species of the genus larus (Charadriiformes: Laridae). Mitochondrial DNA 23(2):157–166. https://doi.org/10.3109/19401736.2012.660921

    Article  CAS  PubMed  Google Scholar 

  • Lee DH, Lee HJ, Lee YJ, Kang HM, Jeong OM, Kim MC, Kwon JS, Kwon JH, Kim CB, Lee JB, Park SY, Choi IS, Song CS (2010a) DNA barcoding techniques for avian influenza virus surveillance in migratory bird habitats. J Wildl Dis 46(2):649–654. https://doi.org/10.7589/0090-3558-46.2.649

    Article  PubMed  Google Scholar 

  • Lee DH, Lee HJ, Lee YN, Lee YJ, Jeong OM, Kang HM, Kim MC, Kwon JS, Kwon JH, Lee JB, Park SK, Choi IS, Song CS (2010b) Application of DNA barcoding technique in avian influenza virus surveillance of wild bird habitats in Korea and Mongolia. Avian Dis 54(1 Suppl):677–681. https://doi.org/10.1637/8783-040109-ResNote.1

    Article  PubMed  Google Scholar 

  • Lijtmaer DA, Kerr KC, Barreira AS, Hebert PD, Tubaro PL (2011) DNA barcode libraries provide insight into continental patterns of avian diversification. PLoS One 6(7):e20744

    Article  CAS  Google Scholar 

  • Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709–715

    Article  CAS  Google Scholar 

  • Lohman DJ, Ingram KK, Prawiradilaga DM, Winker K, Sheldon FH, Moyle RG (2010) Cryptic genetic diversity in “widespread” southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated. Biol Conserv 143:1885–1890

    Article  Google Scholar 

  • Milá B, Tavares ES, Muñoz Saldaña A, Karubian J, Smith TB, Baker AJ (2012) A trans-amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity. PLoS One 7(7):e40541

    Article  Google Scholar 

  • Millar CD, Huynen L, Subramanian S, Mohandesan E, Lambert DM (2008) New developments in ancient genomics. Trends Ecol Evol 23:386–393

    Article  Google Scholar 

  • Murray BW, McGillivray WB, Barlow JC, Beech RN, Strobeck C (1994) The use of cytochrome B sequence variation in estimation of phylogeny in the Vireonidae. Condor 96:1037–1054

    Article  Google Scholar 

  • Newton I (2003) The speciation and biogeography of birds. Academic Press, London

    Google Scholar 

  • Nishiumi I, Kim CH (2015) Assessing the potential for reverse colonization among Japanese birds by mining DNA barcode data. J Ornithol 156(S1):325–331

    Article  Google Scholar 

  • Rosen GE, Smith KF (2010) Summarizing the evidence on the international trade in illegal wildlife. EcoHealth 7:24–32

    Article  Google Scholar 

  • Seutin GW, Bradley N, Boag PT (1991) Preservation of avian blood and tissue samples for DNA analyses. Can J Zool 69:82–90

    Article  CAS  Google Scholar 

  • Stoeckle M (2005) Barcoding life takes flight: All Birds Barcoding Initiative (ABBI), Needs and Resources Statement

    Google Scholar 

  • Tavares ES, Baker AJ (2008) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evol Biol 8(1):81

    Article  Google Scholar 

  • Tavares ES, Gonçalves P, Miyaki CY, Baker A (2011) DNA barcode detects high genetic structure within Neotropical bird species. PLoS One 6(12):e28543

    Article  CAS  Google Scholar 

  • Viana DS, Gangoso L, Bouten W (1822) Figuerola J (2016) Overseas seed dispersal by migratory birds. Proc Biol Sci 283:20152406. https://doi.org/10.1098/rspb.2015.2406

    Article  CAS  Google Scholar 

  • Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74:5088–5090

    Article  CAS  Google Scholar 

  • Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci U S A 97:8392–8396

    Article  CAS  Google Scholar 

  • Yoo HY, Eah J, Kim JS, Young JK, Min M, Peak WK (2006) DNA barcoding Korean birds. Mol Cells 22:323–327. 17202861

    CAS  PubMed  Google Scholar 

  • Zimmermann J, Hajibabaei M, Blackburn D (2008) DNA damage in preserved specimens and tissue samples: a molecular assessment. Front Zool 5:18

    Article  Google Scholar 

Download references

Acknowledgement

The authors would like to acknowledge the University of Tabuk, Tabuk, Saudi Arabia.

The author would also like to thank the Department of Biology, Faculty of Sciences, Saudi Digital Library and University Library for providing the facility for Literature survey and collection.

Author information

Authors and Affiliations

  1. Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Saudi Arabia

    Farhina Pasha

Authors
  1. Farhina Pasha
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Farhina Pasha .

Editor information

Editors and Affiliations

  1. Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia

    Subrata Trivedi

  2. Department of Urology, The University of Alabama at Birmingham (UAB), Birmingham, AL, USA

    Hasibur Rehman

  3. Department of Cell, Developmental and Integrative Biology (CDIB), The University of Alabama at Birmingham (UAB), Birmingham, AL, USA

    Shalini Saggu

  4. Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia

    Chellasamy Panneerselvam

  5. University of Kalyani, Kalyani, Nadia, West Bengal, India

    Sankar K. Ghosh

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Pasha, F. (2020). DNA Barcoding in Avian Species with Special Reference to Taxonomically Wide Biogeographic Studies. In: Trivedi, S., Rehman, H., Saggu, S., Panneerselvam, C., Ghosh, S. (eds) DNA Barcoding and Molecular Phylogeny. Springer, Cham. https://doi.org/10.1007/978-3-030-50075-7_12

Download citation

Publish with us

Policies and ethics

Search

Navigation