Low innate immune-gene diversity in the critically endangered orange-bellied parrot (Neophema chrysogaster)

References

• Alcaide, M., and Edwards, S. V. (2011). Molecular evolution of the Toll-like receptor multigene family in birds. Molecular Biology and Evolution 28, 1703–1715. doi:10.1093/molbev/msq351
   PubMed Web of Science ®Google Scholar
• Allendorf, F. W., Hohenlohe, P. A., and Luikart, G. (2010). Genomics and the future of conservation genetics. Nature Reviews Genetics 11, 697–709. doi:10.1038/nrg2844
   PubMed Web of Science ®Google Scholar
• Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., Selker, E. U., et al. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PloS One 3, e3376. doi:10.1371/journal.pone.0003376
   PubMed Web of Science ®Google Scholar
• Ballou, J. D., Lees, C. M., Faust, L. J., Long, S., Lynch, C., Bingaman-Lackey, L., and Foose, T. J. (2010). Demographic and genetic management of captive populations. In ‘Wild Mammals in Captivity.’ (Eds D. G. Kleiman, K. V. Thompson, and C. K. Baer.) pp. 291–252. (Univeristy of Chicago Press: Chicago, IL.)
   Google Scholar
• Bateson, Z. W., Hammerly, S. C., Johnson, J. A., Morrow, M. E., Whittingham, L. A., and Dunn, P. O. (2016). Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater’s prairie-chicken. Molecular Ecology 25, 4730–4744. doi:10.1111/mec.13793
   PubMed Web of Science ®Google Scholar
• Brown, P. B., and Wilson, R. I. (1980). A survey of the Orange‐bellied Parrot Neophema chrysogaster in Tasmania, Victoria and South Australia. A report to World Wildlife Fund (Australia). Parks and Wildlife Service, Hobart.
   Google Scholar
• Brownlie, R., and Allan, B. (2011). Avian toll-like receptors. Cell and Tissue Research 343, 121–130. doi:10.1007/s00441-010-1026-0
   PubMed Web of Science ®Google Scholar
• Caughley, G. (1994). Directions in conservation biology. The Journal of Animal Ecology 63, 215–244. doi:10.2307/5542
   Web of Science ®Google Scholar
• Cunningham, A. A., and Daszak, P. (1998). Extinction of a species of land snail due to infection with a microsporidian parasite. Conservation Biology 12, 1139–1141. doi:10.1046/j.1523-1739.1998.97485.x
   Web of Science ®Google Scholar
• Dalton, D. L., Vermaak, E., Smit-Robinson, H. A., and Kotze, A. (2016). Lack of diversity at innate immunity Toll-like receptor genes in the critically endangered white-winged flufftail (Sarothrura ayresi). Scientific Reports 6, 36757. doi:10.1038/srep36757
   Web of Science ®Google Scholar
• Das, S., Sarker, S., Peters, A., and Raidal, S. R. (2015). Psittacine beak and feather disease virus in wild orange-bellied parrots. Association of Avian Veterinarians Australasian Committee Ltd. Annual Conference 23, Sydney, Australia, pp. 18–27.
   Google Scholar
• De Groot, N. G., and Bontrop, R. E. (2013). The HIV-1 pandemic: Does the selective sweep in chimpanzees mirror humankind’s future? Retrovirology 10, 53. doi:10.1186/1742-4690-10-53
   PubMed Web of Science ®Google Scholar
• Department of Environment, Land, Water and Planning. (2016). ‘National Recovery Plan for the Orange-bellied Parrot Neophema Chrysogaster.’ (Australian Government: Canberra, ACT.)
   Google Scholar
• Dierickx, E. G., Shultz, A. J., Sato, F., Hiraoka, T., and Edwards, S. V. (2015). Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: Implications for conservation. Evolutionary Applications 8, 662–678. doi:10.1111/eva.12274
   Web of Science ®Google Scholar
• Dresser, C. M., Ogle, R. M., and Fitzpatrick, B. M. (2017). Genome scale assessment of a species translocation program. Conservation Genetics (Print) 18, 1191–1199. doi:10.1007/s10592-017-0970-6
   Web of Science ®Google Scholar
• Elbers, J. P., Brown, M. B., and Taylor, S. S. (2018). Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations – A next generation sequencing approach in the gopher tortoise. BMC Genomics 19, 64. doi:10.1186/s12864-018-4452-0
   Web of Science ®Google Scholar
• Everaardt, A. (2018). Annual report and recommendations for the orange-bellied parrot. Zoo and Aquarium Association Australasia.
   Google Scholar
• Fogell, D. J., Groombridge, J. J., Tollington, S., Canessa, S., Henshaw, S., Zuel, N., Jones, C. G., et al. (2019). Hygeine and biosecurity protocols reduce infection but do not improve fledging success in an endangered parrot. Scientific Reports 9, 4779. doi:10.1038/s41598-019-41323-w
   Web of Science ®Google Scholar
• Gilpin, M. E., and Soulé, M. E. (1986). Minimum viable populations: Processes of species extinction. In ‘Conservation Biology: The Science of Scarcity and Diversity.’ (Ed. M. E. Soulé.) pp. 19–34. (Sinauer Associates: Sunderland, MA.)
   Google Scholar
• Gilroy, D. L., Oosterhout, C., Komdeur, J., and Richardson, D. S. (2017). Toll-like receptor variation in the bottlenecked population of the endangered Seychelles warbler. Animal Conservation 20, 235–250. doi:10.1111/acv.2017.20.issue-3
   Web of Science ®Google Scholar
• Grueber, C. E., and Jamieson, I. G. (2013). Primers for amplification of innate immunity toll-like receptor loci in threatened birds of the Apterygiformes, Gruiformes, Psittaciformes and Passeriformes. Conservation Genetics Resources 5, 1043–1047. doi:10.1007/s12686-013-9965-x
   Web of Science ®Google Scholar
• Grueber, C. E., Knafler, G. J., King, T. M., Senior, A. M., Grosser, S., Robertson, B., Weston, K. A., et al. (2015). Toll-like receptor diversity in 10 threatened bird species: Relationship with microsatellite heterozygosity. Conservation Genetics (Print) 16, 595–611. doi:10.1007/s10592-014-0685-x
   Web of Science ®Google Scholar
• Grueber, C. E., Wallis, G. P., Jamieson, I. G., and Ellegren, H. (2014). Episodic positive selection in the evolution of avian toll-like receptor innate immunity genes. PloS One 9, e89632. doi:10.1371/journal.pone.0089632
   PubMed Web of Science ®Google Scholar
• Grueber, C. E., Wallis, G. P., King, T. M., Jamieson, I. G., and Ellegren, H. (2012). Variation at innate immunity toll-like receptor genes in a bottlenecked population of a New Zealand robin. PloS One 7, e45011. doi:10.1371/journal.pone.0045011
   PubMed Web of Science ®Google Scholar
• Hayashi, F., Smith, K. D., Ozinsky, A., Hawn, T. R., Eugene, C. Y., Goodlett, D. R., Eng, J. K., et al. (2001). The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 410, 1099. doi:10.1038/35074106
   PubMed Web of Science ®Google Scholar
• Heng, J., Su, J., Huang, T., Dong, J., and Chen, L. (2011). The polymorphism and haplotype of TLR3 gene in grass carp (Ctenopharyngodon idella) and their associations with susceptibility/resistance to grass carp reovirus. Fish & Shellfish Immunology 30, 45–50. doi:10.1016/j.fsi.2010.09.004
   Web of Science ®Google Scholar
• Hogg, C., and Everaardt, A. (2019). In Status of captive insurance population at 23 April 2019. (Ed. Department of Primary Industries, P., Water and Environment/University of Sydney.)
   Google Scholar
• Ilmonen, P., Penn, D. J., Damjanovich, K., Clarke, J., Lamborn, D., Morrison, L., Ghotbi, L., et al. (2008). Experimental infection magnifies inbreeding depression in house mice. Journal of Evolutionary Biology 21, 834–841. doi:10.1111/j.1420-9101.2008.01510.x
   Web of Science ®Google Scholar
• IUCN. (2019). The IUCN red list of threatened species. Version 2019-1. Available at http://www.iucnredlist.org. Downloaded on 3 June 2019.
   Google Scholar
• Jung, A., Grund, C., Muller, I., and Rautenschlein, S. (2009). Avian Paramyxovirus Serotype 3 Infection in Neopsephotus, Cyanoramphus, and Neophema Species. Journal of Avian Medicine and Surgery 23, 205–208. doi:10.1647/2008-022.1
   Web of Science ®Google Scholar
• Juniper, T., and Parr, M. (1998). ‘Parrots - a Guide to Parrots of the World.’ (Pica Press: Sussex, UK.)
   Google Scholar
• Knafler, G. J., Ortiz-Catedral, L., Jackson, B., Varsani, A., Grueber, C. E., Robertson, B. C., and Jamieson, I. G. (2016). Comparison of beak and feather disease virus prevalence and immunity-associated genetic diversity over time in an island population of red-crowned parakeets. Archives of Virology 161, 811–820. doi:10.1007/s00705-015-2717-3
   Web of Science ®Google Scholar
• Kosakovsky Pond, S. L., Frost, S. D., and Muse, S. V. (2005). HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21, 676–679. doi:10.1093/bioinformatics/bti079
   PubMed Web of Science ®Google Scholar
• Kosch, T. A., Bataille, A., Didinger, C., Eimes, J. A., Rodríguez-Brenes, S., Ryan, M. J., and Waldman, B. (2016). Major histocompatibility complex selection dynamics in pathogen-infected túngara frog (Physalaemus pustulosus) populations. Biology Letters 12, 20160345. doi:10.1098/rsbl.2016.0345
   Web of Science ®Google Scholar
• Librado, P., and Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452. doi:10.1093/bioinformatics/btp187
   PubMed Web of Science ®Google Scholar
• McIsaac, S. M., Stadnyk, A. W., and Lin, T. J. (2012). Toll‐like receptors in the host defense against Pseudomonas aeruginosa respiratory infection and cystic fibrosis. Journal of Leukocyte Biology 92, 977–985. doi:10.1189/jlb.0811410
   Web of Science ®Google Scholar
• Miller, A. D., Good, R. T., Coleman, R. A., Lancaster, M. L., and Weeks, A. R. (2013). Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster. Molecular Biology Reports 40, 35–42. doi:10.1007/s11033-012-1950-z
   PubMed Web of Science ®Google Scholar
• Miller, M. R., Dunham, J. P., Amores, A., Cresko, W. A., and Johnson, E. A. (2007). Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research 17, 240–248. doi:10.1101/gr.5681207
   PubMed Web of Science ®Google Scholar
• O’Brien, S. J., Roelke, M. E., Marker, L., Newman, A., Winkler, C. A., Meltzer, D., Colly, L., et al. (1985). Genetic basis for species vulnerability in the cheetah. Science 227, 1428–1434. doi:10.1126/science.2983425
   PubMed Web of Science ®Google Scholar
• O’Connor, T. (2017). ‘Heartbreaking’ bacterial infection kills 16 endangered orange-bellied parrots in breeding program. ABC News. Available at http://www.abc.net.au/news/2017-01-24/infection-kills-16-endangered-orange-bellied-parrots/8205046
   Google Scholar
• Orange-bellied Parrot Recovery Team. (2006.) ‘National Recovery Plan for the Orange-bellied Parrot (Neophema chrysogaster).’ (Department of Primary Industries and Water (DPIW: Hobart, Tasmania.)
   Google Scholar
• Peters, A., Patterson, E. I., Baker, B. G. B., Holdsworth, M., Sarker, S., Ghorashi, S. A., and Raidal, S. R. (2014). Evidence of Psittacine beak and feather disease virus spillover into wild critically endangered orange-bellied parrots (Neophema chrysogaster). Journal of Wildlife Diseases 50, 288–296. doi:10.7589/2013-05-121
   Web of Science ®Google Scholar
• Pritchard, R. (2012). ‘Update on the Orange-bellied Parrot Recovery Program.’ (Orange-bellied Parrot Recovery Team: Australia.)
   Google Scholar
• Raidal, S., Sarker, S., and Peters, A. (2015). Review of psittacine beak and feather disease and its effect on Australian endangered species. Australian Veterinary Journal 93, 466–470. doi:10.1111/avj.12388
   PubMed Web of Science ®Google Scholar
• Ralls, K., Ballou, J. D., Dudash, M. R., Eldridge, M. D., Fenster, C. B., Lacy, R. C., Sunnucks, P., et al. (2018). Call for a paradigm shift in the genetic management of fragmented populations. Conservation Letters 11, e12412. doi:10.1111/conl.2018.11.issue-2
   Web of Science ®Google Scholar
• Raven, N., Lisovski, S., Klaassen, M., Lo, N., Madsen, T., Ho, S. Y. W., and Ujvari, B. (2017). Purifying selection and concerted evolution of RNA-sensing toll-like receptors in migratory waders. Infection, Genetics and Evolution 53, 135–145. doi:10.1016/j.meegid.2017.05.012
   Web of Science ®Google Scholar
• Roelke, M. E., Martenson, J. S., and O’Brien, S. J. (1993). The consequences of demographic reduction and genetic depletion in the endangered Florida panther. Current Biology 3, 340–350. doi:10.1016/0960-9822(93)90197-V
   PubMed Web of Science ®Google Scholar
• Ross‐Gillespie, A., O’Riain, M. J., and Keller, L. F. (2007). Viral epizootic reveals inbreeding depression in a habitually inbreeding mammal. Evolution 61, 2268–2273. doi:10.1111/j.1558-5646.2007.00177.x
   PubMed Web of Science ®Google Scholar
• Ruiz-Rodriguez, C. T., Brandt, J. R., Oliverio, R., Ishida, Y., Guedj, N., Garrett, E. F., Kahila Bar-Gal, G., et al. (2017). Polymorphisms of the Toll-like receptor 2 of goats (Capra hircus) may be associated with somatic cell count in milk. Animal Biotechnology 28, 112–119. doi:10.1080/10495398.2016.1232267
   PubMed Web of Science ®Google Scholar
• Schat, K. A., Kaspers, B., and Kaiser, P. (2014). ‘Avian Immunology.’ (Academic Press: London, UK.)
   Google Scholar
• Schloegel, L. M., Hero, J.-M., Berger, L., Speare, R., McDonald, K., and Daszak, P. (2006). The decline of the sharp-snouted day frog (Taudactylus acutirostris): The first documented case of extinction by infection in a free-ranging wildlife species? EcoHealth 3, 35–40. doi:10.1007/s10393-005-0012-6
   Web of Science ®Google Scholar
• Schwartz, M. K., Luikart, G., and Waples, R. S. (2007). Genetic monitoring as a promising tool for conservation and management. Trends in Ecology & Evolution 22, 25–33. doi:10.1016/j.tree.2006.08.009
   PubMed Web of Science ®Google Scholar
• Shivaprasad, H. L., and Phalen, D. N. (2012). A novel herpesvirus associated with respiratory disease in Bourke’s parrots (Neopsephotus bourkii). Avian Pathology 41, 531–539. doi:10.1080/03079457.2012.732692
   PubMed Web of Science ®Google Scholar
• Skevaki, C., Pararas, M., Kostelidou, K., Tsakris, A., and Routsias, J. (2015). Single nucleotide polymorphisms of Toll‐like receptors and susceptibility to infectious diseases. Clinical and Experimental Immunology 180, 165–177. doi:10.1111/cei.12578
   PubMed Web of Science ®Google Scholar
• Stojanovic, D., Alves, F., Cook, H., Crates, R., Heinsohn, R., Peters, A., Rayner, L., et al. (2018). Further knowledge and urgent action required to save orange-bellied parrots from extinction. Emu - Austral Ornithology 118, 126–134. doi:10.1080/01584197.2017.1394165
   Web of Science ®Google Scholar
• Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.
   PubMed Web of Science ®Google Scholar
• Teacher, A. G., Garner, T. W., and Nichols, R. A. (2009). Evidence for directional selection at a novel major histocompatibility class I marker in wild common frogs (Rana temporaria) exposed to a viral pathogen (Ranavirus). PloS One 4, e4616. doi:10.1371/journal.pone.0004616
   Web of Science ®Google Scholar
• Thorne, E. T., and Williams, E. S. (1988). Disease and endangered species: The black-footed ferret as a recent example. Conservation Biology 2, 66–74. doi:10.1111/cbi.1988.2.issue-1
   Google Scholar
• Tollington, S., Greenwood, A., Jones, C. G., Hoeck, P., Chowrimootoo, A., Smith, D., Richards, H., et al. (2015). Detailed monitoring of a small but recovering population reveals sublethal effects of disease and unexpected interactions with supplemental feeding. Journal of Animal Ecology 84, 969–977. doi:10.1111/1365-2656.12348
   PubMed Web of Science ®Google Scholar
• Troy, S., Gales, R., and Williams, H. (2016). Tasmanian Wild OBP Population Breeding Season: Autumn Report 2016. (Ed. Department of Primary Industries, Parks, Water and Environment.) (Orange-bellied Parrot Recovery Team: Hobart, Tas.)
   Google Scholar
• Uematsu, S., and Akira, S. (2008). Toll-like receptors (TLRs) and their ligands. In ‘Toll-like Receptors (TLRs) and Innate Immunity.’ (Eds S. Bauer and G. Hartmann.) pp. 1–20. (Springer: Berlin, Germany.)
   Google Scholar
• Vaz, F. F., Serafini, P. P., Locatelli-Dittrich, R., Meurer, R., Durigon, E. L., Araújo, J., Thomazelli, L. M., et al. (2017). Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil. Brazilian Journal of Microbiology 48, 747–753. doi:10.1016/j.bjm.2017.03.004
   Web of Science ®Google Scholar
• Velová, H., Gutowska-Ding, M. W., Burt, D. W., and Vinkler, M. (2018). Toll-like receptor evolution in birds: Gene duplication, pseudogenization, and diversifying selection. Molecular Biology and Evolution, 35, 2170–2184.
   Web of Science ®Google Scholar
• Voogdt, C. G., Bouwman, L. I., Kik, M. J., Wagenaar, J. A., and Van Putten, J. P. (2016). Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition. Scientific Reports 6, 19046. doi:10.1038/srep19046
   PubMed Web of Science ®Google Scholar
• VTRG, O. B. P. (April 2019). Orange-bellied Parrot Recovery Team Veterinary Technical Reference Group (OBP VTRG). Annual Report. Melbourne, VIC, Australia.
   Google Scholar
• Weaver, S., Shank, S. D., Spielman, S. J., Li, M., Muse, S. V., and Pond, S. L. K. (2018). Datamonkey 2.0: A modern web application for characterizing selective and other evolutionary processes. Molecular Biology and Evolution 35, 773–777. doi:10.1093/molbev/msx335
   PubMed Web of Science ®Google Scholar
• Whiteman, N. K., Matson, K. D., Bollmer, J. L., and Parker, P. G. (2006). Disease ecology in the Galápagos Hawk (Buteo galapagoensis): Host genetic diversity, parasite load and natural antibodies. Proceedings of the Royal Society 273, 797–804. doi:10.1098/rspb.2005.3396
   Web of Science ®Google Scholar
• Yang, N., McLelland, J., McLelland, D. J., Clarke, J., Woolford, L., Eden, P., and Phalen, D. N. (2019). Psittacid Adenovirus-2 infection in the critically endangered orange-bellied parrot (Neophema chrysogastor): A key threatening process or an example of a host-adapted virus? PloS One 14, e0208674. doi:10.1371/journal.pone.0208674
   Web of Science ®Google Scholar
• Yang, Z. (2007). PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24, 1586–1591. doi:10.1093/molbev/msm088
   PubMed Web of Science ®Google Scholar
• ZAA. (2018). ‘Orange-bellied Parrot Studbook.’ (Zoo and Aquarium Association Australasia: Hobart, Tas.)
   Google Scholar
• Zhang, G. (2015). Bird sequencing project takes off. Nature 522, 34. doi:10.1038/522034d
   PubMed Web of Science ®Google Scholar
• Zhang, Z., Louboutin, J.-P., Weiner, D. J., Goldberg, J. B., and Wilson, J. M. (2005). Human airway epithelial cells sense Pseudomonas aeruginosa infection via recognition of flagellin by Toll-like receptor 5. Infection and Immunity 73, 7151–7160. doi:10.1128/IAI.73.11.7151-7160.2005
   PubMed Web of Science ®Google Scholar