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Identification of hybrid green peafowl using mitochondrial and nuclear markers

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Abstract

Green peafowl (Pavo muticus), a representative of the Southeast Asia Phasianidae, is assessed as globally endangered with populations that are declining. It is highly sensitive to human disturbance and habitat change, two threats that are unlikely to be removed soon in present range countries, and that increase the need for long-term continuous effort for in situ conservation. Captive breeding for reintroduction is potentially an important measure for localized population restoration. But green peafowl can hybridize with blue peafowl (P. cristatus) and produce fertile offspring that can backcross with ancestral species. Hybrids backcrossed to green peafowl for a few generations are indistinguishable from pure green peafowl in appearance. Such hybrids must be excluded from captive breeding programs to avoid anthropogenic genetic contamination. In this study, we developed technology to identify hybrids using mitochondrial Cyt b and COI gene sequences, and 16 microsatellites. We studied maternal species assignment for excluding individuals of the blue peafowl maternal line and genetic clustering analysis to exclude individuals containing blue peafowl nuclear genes. Maternal species assignment was accomplished using K2P pairwise genetic distance computed using transition nucleotide substitution. Nuclear genetic clustering analysis was performed using STRUCTURE (assuming K = 2) and NewHybrids. The method was validated using reference pure green (n = 18) and blue (n = 21) peafowl and known hybrids (n = 12). Two criteria were set up to discriminate hybrids based on the probability that an individual is either pure green or pure blue peafowl at 95% confidence. This method was applied to identification of 59 peafowl of ambiguous genetic composition. Our study provides an example for establishing a purity test workflow for other species that can hybridize and has potential for use in reintroduction of genetically pure green peafowl.

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References

  • Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229

    CAS  PubMed  PubMed Central  Google Scholar 

  • Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    CAS  PubMed  PubMed Central  Google Scholar 

  • Awad A, Khalil SR, Abdelhakim YM et al (2015) Molecular phylogeny of some avian species using Cytochrome b gene sequence analysis. Iran J Vet Res 16:218–222

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bao WB et al (2006) Screening of peafowl microsatellite primers and analysis of genetic diversity. Hereditas 28:1242–1246

    CAS  PubMed  Google Scholar 

  • BirdLife International (2018) Pavo muticus. The IUCN Red List of Threatened Species 2018: e.T22679440A131749282. https://doi.org/10.2305/IUCN.UK.2018-2.RLTS.T22679440A131749282.en. Accessed 20 January 2020

  • Brickle NW (2002) Habitat use, predicted distribution and conservation of green peafowl (Pavo muticus) in Dak Lak Province, Vietnam. Biol Conserv 105:189–197

    Google Scholar 

  • Brickle NW, Duckworth JW et al (2008) The status and conservation of Galliformes in Cambodia, Laos and Vietnam. Biodivers Conserv 17:1393–1427

    Google Scholar 

  • Burland TG (2000) DNASTAR’s lasergene sequence analysis software. Methods Mol Biol 132:71–91

    CAS  PubMed  Google Scholar 

  • Chang H et al (2002) A study of the wild and captive green peafowl (Pavo muticus) by random-amplified polymorphic DNA. Hereditas 24:271–274

    CAS  PubMed  Google Scholar 

  • Costa FO, Jeremy R, Boutillier J, Ratnasingham S, Dooh RT, Hajibabaei M (2007) Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci 64:272–295

    CAS  Google Scholar 

  • Demandt MH, Bergek S (2009) Identification of cyprinid hybrids by using geometric morphometrics and microsatellites. J Appl Ichthyol 25:695–701

    CAS  Google Scholar 

  • Dinh TD, Ngatia JN, Cui LY, Ma Y, Dhamer TD, Xu YC (2019) Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines. Forensic Sci Int-Gen 40:85–95

    CAS  Google Scholar 

  • Feng F, Bi YT, He XB (2007) Behavior of green peacock in breeding season in captivity. Chin J Wildl 28:16–17

    Google Scholar 

  • Ghazoul J, Evans J (2004) SUSTAINABLE FOREST MANAGEMENT | Causes of deforestation and forest fragmentation. Encyclopedia For Sci. https://doi.org/10.1016/B0-12-145160-7/00018-1

    Article  Google Scholar 

  • Goes F (2009) The status and distribution of green peafowl Pavo muticus in Cambodia. Cambodian J of Nat Hist 1:7–15

    Google Scholar 

  • Hale ML, Petrie M, Wolff K (2010) Polymorphic microsatellite loci in peafowl (Pavo cristatus). Mol Ecol Resour 4:528–530

    Google Scholar 

  • Hebert PD, Cywinska A, Ball SL et al (2003) Biological identifications through DNA barcodes. P Roy Soc B-Biol Sci 270:313–321

    CAS  Google Scholar 

  • Hebert PD, Stoeckle MY, Zemlak TS et al (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312

    PubMed  PubMed Central  Google Scholar 

  • Hua R, Cui DY et al (2018) The status and distribution of green peafowl (Pavo muticus imperator) in China. Chin J Wildl 39:681–684

    Google Scholar 

  • Hulce D, Li X, Snyder-Leiby T et al (2011) GeneMarker® genotyping software: tools to increase the statistical power of DNA fragment analysis. J Biomol Tech 22:S35–S36

    PubMed Central  Google Scholar 

  • Jiang ZG (2016) Red list of China’s vertebrates. Biodiv Sci 24:500–951

    Google Scholar 

  • Johnsen A, Rindal E, Ericson PGP et al (2010) DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species. J Ornithol 151:565–578

    Google Scholar 

  • Johnson CN, Balmford A, Brook BW et al (2017) Biodiversity losses and conservation responses in the Anthropocene. Science 356:270–275

    CAS  PubMed  Google Scholar 

  • Jong WD (1997) Developing swidden agriculture and the threat of biodiversity loss. Agric Ecosyst Environ 62:187–197

    Google Scholar 

  • Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106

    PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581

    Article  CAS  PubMed  Google Scholar 

  • Kong DJ, Yang XJ (2017) The status and conservation of Pavo muticus in China. Biol Bull-Chin 52:9–11

    Google Scholar 

  • Kong D, Wu F, Shan P et al (2018) Status and distribution changes of the endangered Green Peafowl (Pavo muticus) in China over the past three decades (1990s–2017). Avian Res. https://doi.org/10.1186/s40657-018-0110-0

    Article  Google Scholar 

  • Linacre A, Tobe SS (2011) An overview to the investigative approach to species testing in wildlife forensic science. Investig Genet 2:2

    CAS  PubMed  PubMed Central  Google Scholar 

  • McGowan PJK et al (1998) A review of the status of the Green Peafowl Pavo muticus and recommendations for future action. Bird Conserv Int 8:331–348

    Google Scholar 

  • Miettinen J, Shi C, Liew SC (2011) Deforestation rates in insular Southeast Asia between 2000 and 2010. Global Change Biol. https://doi.org/10.1111/j.1365-2486.2011.02398.x

    Article  Google Scholar 

  • Molua EL, Lambi CM (2007) The economic impact of climate change on agriculture in Cameroon. Policy Res Working Paper 6:1–33

    Google Scholar 

  • Nuttall M, Nut M, Ung V et al (2017) Abundance estimates for the endangered green peafowl Pavo muticus in Cambodia: identification of a globally important site for conservation. Bird Conserv Int 27:127–139

    Google Scholar 

  • Ouyang YN et al (2009) Genetic divergence between Pavo muticus and Pavo cristatus by Cyt b gene. J Yunnan Agric Univ 24:220–224

    CAS  Google Scholar 

  • Parson W et al (2004) The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives. Forensic Sci Int 139:215–226

    CAS  PubMed  Google Scholar 

  • Porrashurtado L, Ruiz Y, Santos C et al (2013) An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet 4:98

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pritchard DJ, Fa JE, Oldfield S, Harrop SR (2011) Bring the captive closer to the wild: redefining the role of ex situ conservation. Oryx. https://doi.org/10.1017/S0030605310001766

    Article  Google Scholar 

  • Rédei GP (2008) PAUP (phylogenetic analysis using parsimony). Encyclopedia of genetics, genomics, proteomics and informatics. Springer, Berlin. https://doi.org/10.1007/978-1-4020-6754-9_12413

    Book  Google Scholar 

  • Randi E, Lucchini V (2002) Detecting rare introgression of domestic dog genes into wild wolf (Canis lupus) populations by Bayesian admixture analyses of microsatellite variation. Conserv Genet 3:29–43

    Google Scholar 

  • Randi E (2008) Detecting hybridization between wild species and their domesticated relatives. Mol Ecol 17:285–293

    PubMed  Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version-1.2): population genetics software for exact tests and ecumenicism. J Hered 68:248–249

    Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Straub S (2008) Infrastructure and growth in developing countries: recent advances and research challenges. Policy Res Working Paper. https://doi.org/10.1596/1813-9450-4460

    Article  Google Scholar 

  • Sukumal N, Mcgowan PJK, Savini T (2015) Change in status of green peafowl Pavo muticus (Family Phasianidae) in Southcentral Vietnam: a comparison over 15 years. Glob Ecol Conserv 3:11–19

    Google Scholar 

  • Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tobe SS, Kitchener AC et al (2010) Reconstructing mammalian phylogenies: a detailed comparison of the cytochrome b and cytochrome oxidase subunit I mitochondrial genes. Plos One 5:e14156

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vähä J, Primmer CR (2006) Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol Ecol 15:63–72

    PubMed  Google Scholar 

  • Vaidya G, Lohman DJ, Meier R et al (2011) SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27:171–180

    PubMed  Google Scholar 

  • Verma SK, Singh L (2010) Novel universal primers establish identity of enormous number of animal species for forensic application. Mol Ecol Notes 3:28–31

    Google Scholar 

  • Tang W, Wang X, Yan M et al (2019) China’s dams threaten green peafowl. Science 364:943–943

    PubMed  Google Scholar 

  • Wen XJ et al (1995) Investigations on the current status of the distribution of green peafowl in China. Chin Biodivers 3:46–51

    Google Scholar 

  • Wilson C, Bernatchez L (1998) The ghost of hybrids past: fixation of arctic charr (Salvelinus alpinus) mitochondrial DNA in an introgressed population of lake trout (S. namaycush). Mol Ecol 7:127–132

    Google Scholar 

  • Witzenberger KA, Hochkirch A (2011) Ex situ conservation genetics: a review of molecular studies on the genetic consequences of captive breeding programmes for endangered animal species. Biodivers Conserv 20:1843–1861

    Google Scholar 

  • Wu J (2004) Investigation and analysis of breeding and reproduction of green peafowl. Heilongjiang J Anim Reprod 12:46–47

    Google Scholar 

  • Wu F, Kong DJ, Shan PF et al (2019) Ongoing green peafowl protection in China. Zool Res 40:580–582

    PubMed  PubMed Central  Google Scholar 

  • Xin JX, Li WS, Wang WD (1989) The breeding and stage development of green peafowl. Ecol Sci 2:79–86

    Google Scholar 

  • Yeh F et al (2000) POPGENE - for the analysis of genetic variation among and within populations using co-dominant and dominant markers

  • Zhang CL (1995) Breeding and reproduction of green peafowl. Chin J Wildl 4:16–18

    Google Scholar 

Download references

Acknowledgements

Thanks to Mr. Wen Yuan Guan, Ms. Gui Ying Bo, Mr. Jacob Njaramba Ngatia, Qinhuangdao Wildlife Park, Changsha Zoo, Shenyang Forest Zoological Garden, Shanghai Zoo, Nanjing Zoo, Taiyuan Zoo, Chengdu Zoo, Zhengzhou Zoo, Beijing Zoo, Shenzhen Zoo and Kunming Zoo.

Funding

Funded by the Fundamental Research Funds for the Central universities of China (Grant No. 2572017PZ02), Wildlife Conservation and Management Project of State Forestry and Grassland Administration of China (2018) and Special Fund for Rescuing the Green Peafowl (Grant No. 2131101006).

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Authors and Affiliations

  1. College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China

    Han Yu Du, Xin Yuan Zhang, Thi Dao Dinh, Yue Ma, Cheng Zong & Yan Chun Xu

  2. Resources and Environment Faculty, Vietnam National University of Forestry Southern Campus, Dongnai, Vietnam

    Thi Dao Dinh

  3. National Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, China

    Yue Ma & Yan Chun Xu

  4. Planning and Design Institute of Forest Products Industry, National Forestry and Grassland Administration of China, Beijing, China

    Guang Long Li

  5. Ecosystems Ltd, Hong Kong, China

    Thomas D. Dahmer

  6. National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization of China, Harbin, China

    Yan Chun Xu

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  1. Han Yu Du
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Correspondence to Yan Chun Xu.

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Du, H.Y., Zhang, X.Y., Dinh, T.D. et al. Identification of hybrid green peafowl using mitochondrial and nuclear markers. Conservation Genet Resour 12, 669–683 (2020). https://doi.org/10.1007/s12686-020-01159-3

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