Conservation Genetics Resources

, Volume 8, Issue 4, pp 499–509

Validation of non-invasive genetic tagging in two large macaw species (Ara macao and A. chloropterus) of the Peruvian Amazon

  • George Olah
  • Robert G. Heinsohn
  • Donald J. Brightsmith
  • Jose R. Espinoza
  • Rod Peakall
Methods and Resources Article

Abstract

Genetic tagging is the unique identification of individuals by their DNA profile. This technique is well established in mammals, but it has not yet been widely adopted for birds. Extraction methods for minute amounts of DNA even enable the use of genetic tagging from non-invasive samples, like hair, scat, or feather. In this study, we evaluate the potential for non-invasive genetic tagging by using molted feathers of two sympatric macaw species in the Peruvian Amazon. Correct species identification is critical when relying on feathers for genetic analysis, so we describe multilocus methods for species identification. We evaluate the quality of naturally shed macaw feathers in tropical environmental conditions and present new primers for molecular sexing on the feather samples. We successfully validated 11 microsatellite markers for use in genetic tagging studies on large macaws and confirmed that DNA from blood and feather samples yields equivalent population genetic patterns. The techniques described here can be implemented for other birds with higher conservation concern.

Keywords

Parrots Macaws Feather Genetic tagging Microsatellite Molecular sexing 

Supplementary material

12686_2016_573_MOESM1_ESM.pdf (661 kb)
Supplementary material 1 (PDF 661 kb)

References

  1. Abe H, Hayano A, Inoue-Murayama M (2012) Forensic species identification of large macaws using DNA barcodes and microsatellite profiles. Mol Biol Rep 39:693–699CrossRefPubMedGoogle Scholar
  2. Andreou D, Vacquie-Garcia J, Cucherousset J, Blanchet S, Gozlan RE, Loot G (2012) Individual genetic tagging for teleosts: an empirical validation and a guideline for ecologists. J Fish Biol 80:181–194. doi:10.1111/j.1095-8649.2011.03165.x CrossRefPubMedGoogle Scholar
  3. Arrendal J, Vilà C, Björklund M (2007) Reliability of noninvasive genetic census of otters compared to field censuses. Conserv Genet 8:1097–1107. doi:10.1007/s10592-006-9266-y CrossRefGoogle Scholar
  4. Beck NR, Peakall R, Heinsohn R (2008) Social constraint and an absence of sex-biased dispersal drive fine-scale genetic structure in white-winged choughs. Mol Ecol 17:4346–4358. doi:10.1111/j.1365-294X.2008.03906.x CrossRefPubMedGoogle Scholar
  5. Berkunsky I, Reboreda JC (2009) Nest-site fidelity and cavity reoccupation by Blue-fronted Parrots Amazona aestiva in the dry Chaco of Argentina. Ibis 151:145–150CrossRefGoogle Scholar
  6. Blackmore CJ, Peakall R, Heinsohn R (2011) The absence of sex-biased dispersal in the cooperatively breeding grey-crowned babbler. J Anim Ecol 80:69–78. doi:10.1111/j.1365-2656.2010.01761.x CrossRefPubMedGoogle Scholar
  7. Bosnjak J, Stevanov-Pavlovic M, Vucicevic M, Stevanovic J, Simeunovic P, Resanovic R, Stanimirovic Z (2013) Feasibility of non-invasive molecular method for sexing of parrots. Pak J Zool 45:715–720Google Scholar
  8. Brightsmith DJ (2004) Effects of weather on parrot geophagy in Tambopata, Peru. Wilson Bull 116:134–145CrossRefGoogle Scholar
  9. Brightsmith DJ (2005a) Competition, predation and nest niche shifts among tropical cavity nesters: ecological evidence. J Avian Biol 36:74–83CrossRefGoogle Scholar
  10. Brightsmith DJ (2005b) Parrot nesting in Southeastern Peru: seasonal patterns and keystone trees. Wilson Bull 117:296–305CrossRefGoogle Scholar
  11. Brightsmith DJ, Aramburú Muñoz-Najar R (2004) Avian geophagy and soil characteristics in southeastern Peru. Biotropica 36:534–543Google Scholar
  12. Brightsmith DJ, Villalobos EM (2011) Parrot behavior at a Peruvian clay lick. Wilson J Ornithol 123:595–602CrossRefGoogle Scholar
  13. Brightsmith DJ, McDonald D, Matsafuji D, Bailey CA (2010) Nutritional content of the diets of free-living scarlet macaw chicks in southeastern Peru. J Avian Med Surg 24:9–23CrossRefPubMedGoogle Scholar
  14. Brock MK, White BN (1992) Application of DNA fingerprinting to the recovery program of the endangered Puerto Rican parrot. Proc Natl Acad Sci 89:11121–11125CrossRefPubMedPubMedCentralGoogle Scholar
  15. Bruford MW, Wayne RK (1993) Microsatellites and their application to population genetic studies. Curr Opin Genet Dev 3:939–943. doi:10.1016/0959-437X(93)90017-J CrossRefPubMedGoogle Scholar
  16. Chan K, Glover DR, Ramage CM, Harrison DK (2008) Low genetic diversity in the Ground parrot (Pezoporus wallicus) revealed by randomly amplified DNA fingerprinting. Ann Zool Fenn 45:211–216. doi:10.5735/086.045.0306 CrossRefGoogle Scholar
  17. Cornejo J, Dierenfeld ES, Bailey CA, Brightsmith DJ (2011) Predicted metabolizable energy density and amino acid profile of the crop contents of free-living scarlet macaw chicks (Ara macao). J Anim Physiol Anim Nutr 96:947–954CrossRefGoogle Scholar
  18. Coster SS, Kovach AI, Pekins PJ, Cooper AB, Timmins A (2011) Genetic mark-recapture population estimation in black bears and issues of scale. J Wildl Manag 75:1128–1136. doi:10.1002/jwmg.143 CrossRefGoogle Scholar
  19. Ellegren H (1996) First gene on the avian W chromosome (CHD) provides a tag for universal sexing of non-ratite birds. Proc R Soc Lond B 263:1635–1641. doi:10.1098/rspb.1996.0239 CrossRefGoogle Scholar
  20. Ellegren H, Moore S, Robinson N, Byrne K, Ward W, Sheldon BC (1997) Microsatellite evolution–a reciprocal study of repeat lengths at homologous loci in cattle and sheep. Mol Biol Evol 14:854–860CrossRefPubMedGoogle Scholar
  21. Evett IW, Weir BS (1998) Interpreting DNA evidence: statistical genetics for forensic scientists. Sinauer, MassachusettsGoogle Scholar
  22. Fridolfsson A-K, Ellegren H (1999) A simple and universal method for molecular sexing of non-ratite birds. J Avian Biol 30:116–121. doi:10.2307/3677252 CrossRefGoogle Scholar
  23. Gebhardt KJ, Waits LP (2008a) Cross-species amplification and optimization of microsatellite markers for use in six neotropical parrots. Mol Ecol Resour 8:835–839CrossRefPubMedGoogle Scholar
  24. Gebhardt KJ, Waits LP (2008b) High error rates for avian molecular sex identification primer sets applied to molted feathers. J Field Ornithol 79:286–292CrossRefGoogle Scholar
  25. Gebhardt KJ, Brightsmith D, Powell G, Waits LP (2009) Molted feathers from clay licks in Peru provide DNA for three large macaws (Ara ararauna, A. chloropterus, and A. macao). J Field Ornithol 80:183–192CrossRefGoogle Scholar
  26. Griffiths R, Double MC, Orr K, Dawson RJG (1998) A DNA test to sex most birds. Mol Ecol 7:1071–1075. doi:10.1046/j.1365-294x.1998.00389.x CrossRefPubMedGoogle Scholar
  27. Guichoux E et al (2011) Current trends in microsatellite genotyping. Mol Ecol Resour 11:591–611. doi:10.1111/j.1755-0998.2011.03014.x CrossRefPubMedGoogle Scholar
  28. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312. doi:10.1371/journal.pbio.0020312 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Heinsohn R, Ebert D, Legge S, Peakall R (2007) Genetic evidence for cooperative polyandry in reverse dichromatic Eclectus parrots. Anim Behav 74:1047–1054. doi:10.1016/j.anbehav.2007.01.026 CrossRefGoogle Scholar
  30. Hogan FE, Cooke R, Burridge CP, Norman JA (2008) Optimizing the use of shed feathers for genetic analysis. Mol Ecol Resour 8:561–567. doi:10.1111/j.1471-8286.2007.02044.x CrossRefPubMedGoogle Scholar
  31. Horváth MB, Martínez-Cruz B, Negro JJ, Kalmár L, Godoy JA (2005) An overlooked DNA source for non-invasive genetic analysis in birds. J Avian Biol 36:84–88. doi:10.1111/j.0908-8857.2005.03370.x CrossRefGoogle Scholar
  32. IUCN (2014) The IUCN red list of threatened species. Version 2014.2. http://www.iucnredlist.org/
  33. Katzner TE, Wheeler M, Negro JJ, Kapetanakos Y, DeWoody JA, Horvath M, Lovette I (2012) To pluck or not to pluck: scientific methodologies should be carefully chosen, not ‘one size fits all’. J Avian Biol 43:15–17. doi:10.1111/j.1600-048X.2011.05592.x CrossRefGoogle Scholar
  34. Kearse M et al (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649CrossRefPubMedPubMedCentralGoogle Scholar
  35. Lee ATK, Kumar S, Brightsmith DJ, Marsden SJ (2010) Parrot claylick distribution in South America: do patterns of “where” help answer the question “why”? Ecography 33:1–4CrossRefGoogle Scholar
  36. Masello JF, Sramkova A, Quillfeldt P, Epplen JT, Lubjuhn T (2002) Genetic monogamy in burrowing parrots Cyanoliseus patagonus? J Avian Biol 33:99–103. doi:10.1034/j.1600-048X.2002.330116.x CrossRefGoogle Scholar
  37. Masello J et al (2011) The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot. Front Zool 8:16CrossRefPubMedPubMedCentralGoogle Scholar
  38. Masello JF, Montano V, Quillfeldt P, Nuhlíčková S, Wikelski M, Moodley Y (2015) The interplay of spatial and climatic landscapes in the genetic distribution of a South American parrot. J Biogeogr 42:1077–1090. doi:10.1111/jbi.12487 CrossRefGoogle Scholar
  39. Maurer G, Beck N, Double MC (2010) A ‘feather-trap’ for collecting DNA samples from birds. Mol Ecol Resour 10:129–134. doi:10.1111/j.1755-0998.2009.02711.x CrossRefPubMedGoogle Scholar
  40. McDonald PG, Griffith SC (2011) To pluck or not to pluck: the hidden ethical and scientific costs of relying on feathers as a primary source of DNA. J Avian Biol 42:197–203. doi:10.1111/j.1600-048X.2011.05365.x CrossRefGoogle Scholar
  41. McDonald PG, Griffith SC et al (2012) Feather sampling provides an unreliable source of DNA that may well have significant long-term impacts: a reply to Katzner et al. J Avian Biol 43:18–20. doi:10.1111/j.1600-048X.2011.05692.x CrossRefGoogle Scholar
  42. Melo M, O’Ryan C (2007) Genetic differentiation between Príncipe Island and mainland populations of the grey parrot (Psittacus erithacus), and implications for conservation. Mol Ecol 16:1673–1685. doi:10.1111/j.1365-294X.2006.03128.x CrossRefPubMedGoogle Scholar
  43. Miyaki CY, Griffiths R, Orr K, Nahum LA, Pereira SL, Wajntal A (1998) Sex identification of parrots, toucans, and curassows by PCR: perspectives for wild and captive population studies. Zoo Biol 17:415–423. doi:10.1002/(SICI)1098-2361(1998)17:5<415:AID-ZOO6>3.0.CO;2-2 CrossRefGoogle Scholar
  44. Monge O, Schmidt K, Vaughan C, Gutiérrez-Espeleta G (2015) Genetic patterns and conservation of the Scarlet Macaw (Ara macao) in Costa Rica. Conserv Genet. doi:10.1007/s10592-015-0804-3 Google Scholar
  45. Murphy SA, Double MC, Legge SM (2007) The phylogeography of palm cockatoos, Probosciger aterrimus, in the dynamic Australo-Papuan region. J Biogeogr 34:1534–1545. doi:10.1111/j.1365-2699.2007.01706.x CrossRefGoogle Scholar
  46. Olah G, Vigo G, Heinsohn R, Brightsmith DJ (2014) Nest site selection and efficacy of artificial nests for breeding success of Scarlet Macaws Ara macao macao in lowland Peru. J Nat Conserv 22:176–185. doi:10.1016/j.jnc.2013.11.003 CrossRefGoogle Scholar
  47. Olah G, Heinsohn RG, Espinoza JR, Brightsmith DJ, Peakall R (2015) An evaluation of primers for microsatellite markers in Scarlet Macaw (Ara macao) and their performance in a Peruvian wild population. Conserv Genet Resour 7:157–159. doi:10.1007/s12686-014-0317-2 CrossRefGoogle Scholar
  48. Olah G, Butchart SHM, Symes A, Guzmán IM, Cunningham R, Brightsmith DJ, Heinsohn R (2016) Ecological and socio-economic factors affecting extinction risk in parrots. Biodivers Conserv 25:205–223. doi:10.1007/s10531-015-1036-z CrossRefGoogle Scholar
  49. Ong AHK, Vellayan S (2008) An evaluation of CHD-Specific primer sets for sex typing of birds from feathers. Zoo Biol 27:62–69. doi:10.1002/zoo.20163 CrossRefPubMedGoogle Scholar
  50. Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4:347–354. doi:10.1111/j.1365-294X.1995.tb00227.x CrossRefPubMedGoogle Scholar
  51. Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Mol Ecol 13:55–65. doi:10.1046/j.1365-294X.2004.02008.x CrossRefPubMedGoogle Scholar
  52. Palsboll PJ (1999) Genetic tagging: contemporary molecular ecology. Biol J Linn Soc 68:3–22. doi:10.1111/j.1095-8312.1999.tb01155.x CrossRefGoogle Scholar
  53. Palsboll PJ et al (1997) Genetic tagging of humpback whales. Nature 388:767–769CrossRefPubMedGoogle Scholar
  54. Payne RW (2009) GenStat. Wiley Interdiscipl Rev Comput Stat 1:255–258. doi:10.1002/wics.32 CrossRefGoogle Scholar
  55. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295. doi:10.1111/j.1471-8286.2005.01155.x CrossRefGoogle Scholar
  56. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539. doi:10.1093/bioinformatics/bts460 CrossRefPubMedPubMedCentralGoogle Scholar
  57. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275–1287CrossRefPubMedGoogle Scholar
  58. Peakall R, Ebert D, Cunningham R, Lindenmayer D (2006) Mark–recapture by genetic tagging reveals restricted movements by bush rats (Rattus fuscipes) in a fragmented landscape. J Zool 268:207–216. doi:10.1111/j.1469-7998.2005.00011.x CrossRefGoogle Scholar
  59. Phillips C et al (2014) “New turns from old STaRs”: enhancing the capabilities of forensic short tandem repeat analysis. Electrophoresis 35:3173–3187. doi:10.1002/elps.201400095 CrossRefPubMedGoogle Scholar
  60. Powell LL, Powell TU, Powell GVN, Brightsmith DJ (2009) Parrots take it with a grain of salt: available sodium content may drive collpa (clay lick) selection in southeastern Peru. Biotropica 41:279–282CrossRefGoogle Scholar
  61. Presti FT, Meyer J, Antas PTZ, Guedes NMR, Miyaki CY (2013) Non-invasive genetic sampling for molecular sexing and microsatellite genotyping of hyacinth macaw (Anodorhynchus hyacinthinus). Genet Mol Biol 36:129–133CrossRefPubMedPubMedCentralGoogle Scholar
  62. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  63. Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  64. Rudnick JA, Katzner TE, Bragin EA, DeWoody JA (2007) Species identification of birds through genetic analysis of naturally shed feathers. Mol Ecol Notes 7:757–762. doi:10.1111/j.1471-8286.2007.01796.x CrossRefGoogle Scholar
  65. Ruibal M, Peakall R, Claridge A, Firestone K (2009) Field-based evaluation of scat DNA methods to estimate population abundance of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial. Wildl Res 36:721–736. doi:10.1071/WR09086 CrossRefGoogle Scholar
  66. Ruibal M, Peakall R, Claridge A, Murray A, Firestone K (2010) Advancement to hair-sampling surveys of a medium-sized mammal: DNA-based individual identification and population estimation of a rare Australian marsupial, the spotted-tailed quoll (Dasyurus maculatus). Wildl Res 37:27–38. doi:10.1071/WR09087 CrossRefGoogle Scholar
  67. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotech 18:233–234CrossRefGoogle Scholar
  68. Seabury CM et al (2013) A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao). PLoS One 8:e62415CrossRefPubMedPubMedCentralGoogle Scholar
  69. Sefc KM, Payne RB, Sorenson MD (2003) Microsatellite amplification from museum feather samples: effects of fragment size and template concentration on genotyping errors. Auk 120:982–989. doi:10.2307/4090269 CrossRefGoogle Scholar
  70. Segelbacher G (2002) Noninvasive genetic analysis in birds: testing reliability of feather samples. Mol Ecol Notes 2:367–369. doi:10.1046/j.1471-8286.2002.00180.x-i2 Google Scholar
  71. Smouse PE, Whitehead MR, Peakall R (2015) An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation. Mol Ecol Resour 15:1375–1384. doi:10.1111/1755-0998.12422 CrossRefPubMedGoogle Scholar
  72. Suh A, Kriegs JO, Brosius J, Schmitz J (2011) Retroposon insertions and the chronology of avian sex chromosome evolution. Mol Biol Evol 28:2993–2997. doi:10.1093/molbev/msr147 CrossRefPubMedGoogle Scholar
  73. Taberlet P, Luikart G (1999) Non-invasive genetic sampling and individual identification. Biol J Linn Soc 68:41–55. doi:10.1111/j.1095-8312.1999.tb01157.x CrossRefGoogle Scholar
  74. Tavares E, Baker A (2008) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evol Biol 8:81CrossRefPubMedPubMedCentralGoogle Scholar
  75. Tosi J (1960) Zonas de vida natural en el Perú. Instituto Interamericano de Ciencias Agrícolas de la OEA Zona Andina. Boletín Técnico 5:271Google Scholar
  76. Vili N, Nemesházi E, Kovács S, Horváth M, Kalmár L, Szabó K (2013) Factors affecting DNA quality in feathers used for non-invasive sampling. J Ornithol 154:587–595. doi:10.1007/s10336-013-0932-9 CrossRefGoogle Scholar
  77. Waits LP, Luikart G, Taberlet P (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 10:249–256. doi:10.1046/j.1365-294X.2001.01185.x CrossRefPubMedGoogle Scholar
  78. Wenner T, Russello M, Wright T (2012) Cryptic species in a Neotropical parrot: genetic variation within the Amazona farinosa species complex and its conservation implications. Conserv Genet 13:1427–1432. doi:10.1007/s10592-012-0364-8 CrossRefGoogle Scholar
  79. Wright TF, Wilkinson GS (2001) Population genetic structure and vocal dialects in an amazon parrot. Proc R Soc B 268:609–616CrossRefPubMedPubMedCentralGoogle Scholar
  80. Wright TF, Rodriguez AM, Fleischer RC (2005) Vocal dialects, sex-biased dispersal, and microsatellite population structure in the parrot Amazona auropalliata. Mol Ecol 14:1197–1205. doi:10.1111/j.1365-294X.2005.02466.x CrossRefPubMedGoogle Scholar
  81. Yankson KK, Steck TR (2009) Strategy for extracting DNA from clay soil and detecting a specific target sequence via selective enrichment and real-time (quantitative) PCR amplification. Appl Environ Microbiol 75:6017–6021. doi:10.1128/aem.00211-09 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralia
  2. 2.Research School of BiologyThe Australian National UniversityCanberraAustralia
  3. 3.Department of Veterinary PathobiologySchubot Exotic Bird Health Center at Texas A&M UniversityCollege StationUSA
  4. 4.Unidad de Biotecnología Molecular, Laboratorios de Investigación y Desarrollo (LID)Universidad Peruana Cayetano HerediaLimaPeru

Personalised recommendations