Skip to main content

The application of non-invasive genetic tagging reveals new insights into the clay lick use by macaws in the Peruvian Amazon

Abstract

Genetic tagging, the unique identification of individuals by their DNA profile, has proven to be an effective method for research on several animal species. In this study we apply non-invasive genetic tagging from feather samples to reveal the genetic structure and estimate local population size of red-and-green macaws (Ara chloropterus) without the need to capture these animals. The study was centered in the Tambopata region of the Peruvian Amazon. Here macaws frequently visit clay licks and their naturally molted feathers provide a unique source of non-invasively sampled DNA. We analyzed 249 feathers using nine microsatellite loci and identified 221 unique genotypes. The remainder revealed 21 individuals which were ‘recaptured’ one or more times. Using a capture-mark-recapture model the average number of different individuals visiting clay licks within one breeding season was estimated to fall between 84 and 316 individuals per clay lick. Analysis of population genetic structure revealed only small genetic differences among regions and clay licks, suggesting a single red-and-green macaw genetic population. Our study confirms the utility of non-invasive genetic tagging in harsh tropical environment to obtain crucial population parameters about an abundant parrot species that is very difficult to capture in the wild.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  1. 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

    CAS  Article  PubMed  Google Scholar 

  2. Baraloto C et al (2015) Effects of road infrastructure on forest value across a tri-national Amazonian frontier. Biol Conserv 191:674–681. doi:10.1016/j.biocon.2015.08.024

    Article  Google Scholar 

  3. 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

    CAS  Article  PubMed  Google Scholar 

  4. Bridge ES et al (2011) Technology on the move: recent and forthcoming innovations for tracking migratory birds. Bioscience 61:689–698. doi:10.1525/bio.2011.61.9.7

    Article  Google Scholar 

  5. Brightsmith DJ (2004) Effects of weather on parrot geophagy in Tambopata, Peru. Wilson Bull 116:134–145

    Article  Google Scholar 

  6. Brightsmith DJ (2005) Parrot nesting in Southeastern Peru: seasonal patterns and keystone trees. Wilson Bull 117:296–305

    Article  Google Scholar 

  7. Brightsmith DJ, Aramburú Muñoz-Najar R (2004) Avian Geophagy and soil characteristics in Southeastern Peru. Biotropica 36:534–543

    Google Scholar 

  8. Brightsmith DJ, Villalobos EM (2011) Parrot behavior at a Peruvian clay lick. Wilson Journal of Ornithology 123:595–602

    Article  Google Scholar 

  9. Brightsmith DJ, Taylor J, Phillips TD (2008) The roles of soil characteristics and toxin adsorption in Avian Geophagy. Biotropica 40:766–774

    Article  Google Scholar 

  10. Brouwer K, Jones ML, King CE, Schifter H (2000) Longevity records for Psittaciformes in captivity. Int Zoo Yearb 37:299–316

    Article  Google Scholar 

  11. Bulut Z, Bragin EA, DeWoody JA, Braham MA, Katzner TE, Doyle JM (2016) Use of non-invasive genetics to assess nest and space use by White-tailed Eagles. J Raptor Res 50:351–362

    Article  Google Scholar 

  12. Burger J, Gochfeld M (2003) Parrot behavior at a Rio Manu (Peru) clay lick: temporal patterns, associations and antipredator responses. Acta Ethol 6:23–34

    Google Scholar 

  13. Bush KL et al (2011) Population structure and genetic diversity of greater sage-grouse (Centrocercus urophasianus) in fragmented landscapes at the northern edge of their range. Conserv Genet 12:527–542. doi:10.1007/s10592-010-0159-8

    Article  Google Scholar 

  14. Caparroz R, Miyaki CY, Bampi MI, Wajntal A (2001) Analysis of the genetic variability in a sample of the remaining group of Spix’s Macaw (Cyanopsitta spixii, Psittaciformes: Aves) by DNA fingerprinting. Biol Conserv 99:307–311

    Article  Google Scholar 

  15. Conover T (2003) Perú’s long haul: highway to riches, or ruin? Natl Geogr 203:80–100

    Google Scholar 

  16. Dalén L, Götherström A, Meijer T, Shapiro B (2007) Recovery of DNA from Footprints in the Snow. Can Field-Nat 121:321–324

    Article  Google Scholar 

  17. Forshaw JM (2011) Parrots of the world. vol Accessed from http://nla.gov.au/nla.cat-vn4839547. CSIRO Publishing, Collingwood

  18. Frankham R, Ballou JD, Briscoe DA (2004) A primer of conservation genetics. Cambridge University Press, Cambridge

    Book  Google Scholar 

  19. 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 80:183–192

    Article  Google Scholar 

  20. Groom C, Warren K, Le Souef A, Dawson R (2015) Attachment and performance of Argos satellite tracking devices fitted to black cockatoos (Calyptorhynchus spp.). Wildlife Research 41:571–583. doi:10.1071/WR14138

    Article  Google Scholar 

  21. Hoffman JI, Trathan PN, Amos W (2006) Genetic tagging reveals extreme site fidelity in territorial male Antarctic fur seals Arctocephalus gazella. Mol Ecol 15:3841–3847. doi:10.1111/j.1365-294X.2006.03053.x

    CAS  Article  PubMed  Google Scholar 

  22. 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

    Article  Google Scholar 

  23. IUCN (2014) The IUCN Red List of Threatened Species. Version 2014.2. http://www.iucnredlist.org/.

  24. Jacob G, Debrunner R, Gugerli F, Schmid B, Bollmann K (2009) Field surveys of capercaillie (Tetrao urogallus) in the Swiss Alps underestimated local abundance of the species as revealed by genetic analyses of non-invasive samples. Conserv Genet 11:33–44. doi:10.1007/s10592-008-9794-8

    Article  Google Scholar 

  25. 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 33:1–4

    CAS  Article  Google Scholar 

  26. Limiñana R, Arroyo B, Terraube J, McGrady M, Mougeot F (2015) Using satellite telemetry and environmental niche modelling to inform conservation targets for a long-distance migratory raptor in its wintering grounds. Oryx 49:329–337. doi:10.1017/S0030605313001075

    Article  Google Scholar 

  27. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152:1753–1766

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Mantel N (1967) The Detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    CAS  PubMed  Google Scholar 

  29. Marques ARdO (2010) Caracterização da estrutura genética populacional das araras vermelhas Ara chloropterus e Ara macao (Psittaciformes, Aves). University of São Paulo, São Paulo

    Google Scholar 

  30. May DL (2001) Grey parrots of the Congo basin forest. PsittaScene 13:8–10

    Google Scholar 

  31. Meirmans PG (2006) Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evol Int J Org Evol 60:2399–2402. doi:10.1111/j.0014-3820.2006.tb01874.x

    Article  Google Scholar 

  32. Meirmans PG, Hedrick PW (2011) Assessing population structure: FST and related measures. Mol Ecol Resour 11:5–18. doi:10.1111/j.1755-0998.2010.02927.x

    Article  PubMed  Google Scholar 

  33. Miller CR, Joyce P, Waits LP (2005) A new method for estimating the size of small populations from genetic mark–recapture data. Mol Ecol 14:1991–2005. doi:10.1111/j.1365-294X.2005.02577.x

    CAS  Article  PubMed  Google Scholar 

  34. Mollet P, Kéry M, Gardner B, Pasinelli G, Royle JA (2015) Estimating population size for capercaillie (Tetrao urogallus L.) with spatial capture-recapture models based on genotypes from one field sample. PLoS ONE 10:e0129020. doi:10.1371/journal.pone.0129020

    Article  PubMed  PubMed Central  Google Scholar 

  35. Moran-Luis M et al (2014) Demographic status and genetic tagging of endangered capercaillie in NW Spain. PLoS ONE 9:e99799. doi:10.1371/journal.pone.0099799

    Article  PubMed  PubMed Central  Google Scholar 

  36. Munn CA (1992) Macaw biology and ecotourism, or “When a bird in the bush is worth two in the hand”. In: Beissinger SR, Snyder NFR, Munn CA (eds) New world parrots in crisis: solutions from conservation biology. Smithsonian Institution Press, Washington, DC, pp 47–72

    Google Scholar 

  37. Nycander E, Blanco DH, Holle KM, del Campo A, Munn CA, Moscoso JI, Ricalde DG (1995) Manu and Tambopata: nesting success and techniques for increasing reproduction in wild macaws in southeastern Peru. In: Abramson J, Spear BL, Thomsen JB (eds) The large macaws: their care, breeding and conservation. Raintree Publications, Fort Bragg, California, pp 423–443

    Google Scholar 

  38. 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

    Article  Google Scholar 

  39. Olah G, Butchart SHM, Symes A, Guzmán IM, Cunningham R, Brightsmith DJ, Heinsohn R (2016a) Ecological and socio-economic factors affecting extinction risk in parrots. Biodivers Conserv 25:205–223. doi:10.1007/s10531-015-1036-z

    Article  Google Scholar 

  40. Olah G, Heinsohn RG, Brightsmith DJ, Espinoza JR, Peakall R (2016b) Validation of non-invasive genetic tagging in two large macaw species (Ara macao and A. chloropterus) of the Peruvian Amazon. Conserv Genet Resour 8:499–509. doi:10.1007/s12686-016-0573-4

    Article  Google Scholar 

  41. Owens IPF, Bennett PM (2000) Ecological basis of extinction risk in birds: Habitat loss versus human persecution and introduced predators. Proc Natl Acad Sci 97:12144–12148. doi:10.1073/pnas.200223397

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. Palsboll PJ et al (1997) Genetic tagging of humpback whales. Nature 388:767–769

    CAS  Article  PubMed  Google Scholar 

  43. 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

    Article  Google Scholar 

  44. 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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  45. 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

    Article  Google Scholar 

  46. Petit E, Valiere N (2006) Estimating population size with noninvasive capture-mark-recapture data. Conserv Biol 20:1062–1073. doi:10.1111/j.1523-1739.2006.00417.x

    Article  PubMed  Google Scholar 

  47. Pires SF (2012) The illegal parrot trade: a literature review. Glob Crime 13:176–190

    Article  Google Scholar 

  48. Pollock KH, Nichols JD, Simons TR, Farnsworth GL, Bailey LL, Sauer JR (2002) Large scale wildlife monitoring studies: statistical methods for design and analysis. Environmetrics 13:105–119 doi:10.1002/env.514

    Article  Google Scholar 

  49. 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 41:279–282

    Article  Google Scholar 

  50. Prugnolle F, de Meeus T (2002) Inferring sex-biased dispersal from population genetic tools: a review. Heredity 88:161–165

    CAS  Article  PubMed  Google Scholar 

  51. Puechmaille SJ, Petit EJ (2007) Empirical evaluation of non-invasive capture–mark–recapture estimation of population size based on a single sampling session. J Appl Ecol 44:843–852. doi:10.1111/j.1365-2664.2007.01321.x

    Article  Google Scholar 

  52. Renton K, Brightsmith DJ (2009) Cavity use and reproductive success of nesting macaws in lowland forest of southeast Peru. J Field Ornithol 80:1–8

    Article  Google Scholar 

  53. Ringler E, Mangione R, Ringler M (2015) Where have all the tadpoles gone? Individual genetic tracking of amphibian larvae until adulthood. Mol Ecol Resour 15:737–746. doi:10.1111/1755-0998.12345

    Article  PubMed  Google Scholar 

  54. Rudnick JA, Katzner TE, Bragin EA, Rhodes OE, Dewoody JA (2005) Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan. Mol Ecol 14:2959–2967. doi:10.1111/j.1365-294X.2005.02641.x

    CAS  Article  PubMed  Google Scholar 

  55. Rudnick JA, Katzner TE, Bragin EA, DeWoody (2008) A non-invasive genetic evaluation of population size, natal philopatry, and roosting behavior of non-breeding eastern imperial eagles (Aquila heliaca) in central Asia. Conserv Genet 9:667. doi:10.1007/s10592-007-9397-9

    Article  Google Scholar 

  56. Ruegg KC et al (2014) Mapping migration in a songbird using high-resolution genetic markers. Mol Ecol 23:5726–5739. doi:10.1111/mec.12977

    Article  PubMed  Google Scholar 

  57. 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). Wildlife Research 37:27–38. doi:10.1071/WR09087

    CAS  Article  Google Scholar 

  58. Schmidt KL (2013) Spatial and temporal patterns of genetic variation in scarlet macaws (Ara macao): implications for population management in La Selva Maya, Central America. Columbia University, New York

    Google Scholar 

  59. 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:e62415–e62415

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  60. 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

    CAS  Google Scholar 

  61. Sekino M, Saitoh K, Yamada T, Hara M, Yamashita Y (2005) Genetic tagging of released Japanese flounder (Paralichthys olivaceus) based on polymorphic DNA markers. Aquaculture 244:49–61. doi:10.1016/j.aquaculture.2004.11.006

    CAS  Article  Google Scholar 

  62. Smith AL, Landguth EL, Bull CM, Banks SC, Gardner MG, Driscoll DA (2016) Dispersal responses override density effects on genetic diversity during post-disturbance succession. Proc R Soc Lond B. doi:10.1098/rspb.2015.2934

    Google Scholar 

  63. Smouse PE, Long JC (1992) Matrix correlation analysis in anthropology and genetics. Am J Phys Anthropol 35:187–213. doi:10.1002/ajpa.1330350608

    Article  Google Scholar 

  64. Smouse PE, Peakall R (1999) Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 82:561–573

    Article  PubMed  Google Scholar 

  65. Smouse PE, Long JC, Sokal RR (1986) Multiple regression and correlation extensions of the mantel test of matrix correspondence. Syst Zool 35:627–632. doi:10.2307/2413122

    Article  Google Scholar 

  66. Symes CT, Hughes JC, Mack AL, Marsden SJ (2006) Geophagy in birds of Crater Mountain Wildlife Management Area, Papua New Guinea. J Zool 268:87–96. doi:10.1111/j.1469-7998.2005.00002.x

    Article  Google Scholar 

  67. Valdéz-Peña RA, Ortiz-Maciel SG, Valdez Juarez SO, Enkerlin Hoeflich EC, Snyder NFR (2008) Use of clay licks by Maroon-fronted Parrots (Rhynchopsitta terrisi) in Northern Mexico. Wilson J Ornithol 120:176–180

    Article  Google Scholar 

  68. Webster MS, Marra PP, Haig SM, Bensch S, Holmes RT (2002) Links between worlds: unraveling migratory connectivity. Trends in Ecol Evol 17:76–83. doi:10.1016/S0169-5347(01)02380-1

    Article  Google Scholar 

  69. White GC, Burnham KP (1999) Program MARK: survival estimation from populations of marked animals. Bird Study 46:S120–S139 doi:10.1080/00063659909477239

    Article  Google Scholar 

  70. Woods JG, Paetkau D, Lewis D, McLellan BN, Proctor M, Strobeck C (1999) Genetic tagging of free-ranging black and brown bears. Wildl Soc Bull 27:616–627 doi:10.2307/3784082

    Google Scholar 

  71. 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

    CAS  Article  PubMed  Google Scholar 

  72. Wunderle JM Jr (1999) Pre- and post-hurricane fruit availability: implications for Puerto Rican Parrots in the Luquillo Mountains. Carib J Sci 35:249–264

    Google Scholar 

Download references

Acknowledgements

This research was supported by funds from the Rufford Small Grants Foundation, Loro Parque Foundation, Idea Wild, and The Australian National University. Thanks to the Peruvian crew of this project for their enormous help with sample collection and field logistics: Braulio Poje Mishaja, Andres Veras, Jerico Solis, Crissel Vargas, Lizzie Ortiz, Gabriela Vigo, Nancy Carlos, Mabe Aguirre, Gustavo Martinez, the full staff and guides of Rainforest Expeditions, and the volunteers of the Tambopata Macaw Project. Thanks to George Powell and the WWF for providing some extra feather samples from Peru. Thanks for laboratory technical support to Christine Hayes and Cintia Garai. We thank for the laboratory space provided by the Unidad de Biotecnología Molecular, Laboratorio de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia in Lima, Peru. Samples were collected under research permits from the Servicio Nacional de Areas Naturales Protegidas (SERNANP) in Peru. Genetic access to the samples was granted by the Servicio Nacional Forestal y de Fauna Silvestre (SERFOR) in Peru. CITES permits were provided by the Peruvian and Australian authorities (No 15PE000448/SP, No PWS2015-AU-001508). We thank to the anonymous reviewers whose constructive suggestions and comments improved the quality of this paper.

Author information

Affiliations

Authors

Corresponding author

Correspondence to George Olah.

Additional information

Scientific video abstract featuring authors and main results of the study can be found in the link (https://youtu.be/knjkWi-Ftww).

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (pdf 204 KB)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Olah, G., Heinsohn, R.G., Brightsmith, D.J. et al. The application of non-invasive genetic tagging reveals new insights into the clay lick use by macaws in the Peruvian Amazon. Conserv Genet 18, 1037–1046 (2017). https://doi.org/10.1007/s10592-017-0954-6

Download citation

Keywords

  • Parrot
  • Ara chloropterus
  • Clay lick
  • Feather
  • Genetic tagging
  • Microsatellite
  • CMR