Microsatellite genotyping detects extra-pair paternity in the Chatham Island Black Robin, a highly inbred, socially monogamous passerine

References

• Almojil, D., Arias, M. C., Beasley, R. R., Chen, Y., Clark, R. W., Dong, Y., Dong, Z., et al. (2016). Microsatellite records for volume 8, issue 2. Conservation Genetics Resources 8(2), 169–196. doi:10.1007/s12686-016-0549-4
   Web of Science ®Google Scholar
• Arct, A., Drobniak, S. M., and Cichoń, M. (2015). Genetic similarity between mates predicts extrapair paternity - A meta-analysis of bird studies. Behavioral Ecology 26(4), 959–968. doi:10.1093/beheco/arv004
   Web of Science ®Google Scholar
• Ardern, S. L., and Lambert, D. M. (1997). Is the Black Robin in genetic peril? Molecular Ecology 6(1), 21–28. doi:10.1046/j.1365-294X.1997.00147.x
   Web of Science ®Google Scholar
• Ardern, S. L., Wei, M., Ewen, J. G., Armstrong, D. P., and Lambert, D. M. (1997). Social and sexual monogamy in translocated New Zealand Robin populations detected using minisatellite DNA. The Auk 114(1), 120–126. doi:10.2307/4089074
   Web of Science ®Google Scholar
• Blouin, M. S. (2003). DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology & Evolution 18(10), 503–511. doi:10.1016/S0169-5347(03)00225-8
   Web of Science ®Google Scholar
• Butler, D., and Merton, D. (1992). ‘The Black Robin: Saving the World’s Most Endangered Bird.’ (Oxford University Press: Auckland, NZ.)
   Google Scholar
• Castro, I., Mason, K. M., Armstrong, D. P., and Lambert, D. M. (2004). Effect of extra-pair paternity on effective population size in a reintroduced population of the endangered hihi, nad potential for biehavioural management. Conservation Genetics 5, 381–393. doi:10.1023/B:COGE.0000031146.51681.b0
   Web of Science ®Google Scholar
• Cubrinovska, I., Massaro, M., and Hale, M. L. (2015). Assessment of hybridisation between the endangered Chatham Island Black Robin (Petroica traversi) and the Chatham Island tomtit (Petroica macrocephala chathamensis). Conservation Genetics 17, 259–265. doi:10.1007/s10592-015-0778-1
   Web of Science ®Google Scholar
• de Villemereuil, P., Rutschmann, A., Lee, K. D., Ewen, J. G., Brekke, P., Santure, A. W. (2019). Little adaptive potential in a threatened passerine bird. Current Biology 29(5), 889–894. doi:10.1016/j.cub.2019.01.072
   Google Scholar
• Eliassen, S., and Kokko, H. (2008). Current analyses do not resolve whether extra-pair paternity is male or female driven. Behavioral Ecology and Sociobiology 62(11), 1795–1804. doi:10.1007/s00265-008-0608-2
   Web of Science ®Google Scholar
• Foerster, K., Delhey, K., Johnsen, A., Lifjeld, J. T., and Kempenaers, B. (2003). Females increase offspring heterozygosity and fitness through extra-pair matings. Nature 425(6959), 714–717. doi:10.1038/nature01969
   Web of Science ®Google Scholar
• Forsdick, N. J., Cubrinovska, I., Massaro, M., and Hale, M. L. (2017). Genetic diversity and population differentiation within and between island populations of two sympatric Petroica robins, the Chatham Island Black Robin and tomtit. Conservation Genetics 18(2), 275–285. doi:10.1007/s10592-016-0899-1
   Web of Science ®Google Scholar
• Frankham, R. (1995). Effective population size/adult population size ratios in wildlife: A review. Genetics Research 66, 95–107. doi:10.1017/S0016672300034455
   Web of Science ®Google Scholar
• Frankham, R. (2005). Genetics and extinction. Biological Conservation 126, 131–140. doi:10.1016/j.biocon.2005.05.002
   Web of Science ®Google Scholar
• Fridolfsson, A. K., and Ellegren, H. (1999). A simple and universal method for molecular sexing of non-ratite birds. Journal of Avian Biology 30, 116–121. doi:10.2307/3677252
   Web of Science ®Google Scholar
• Griffith, S. C., Owens, I. P. F., and Thuman, K. A. (2002). Extra pair paternity in birds: A review of interspecific variation and adaptive function. Molecular Ecology 11(11), 2195–2212. doi:10.1046/j.1365-294X.2002.01613.x
   PubMed Web of Science ®Google Scholar
• Griffiths, R., Double, M. C., Orr, K., and Dawson, R. J. G. (1998). A DNA test to sex most birds. Molecular Ecology 7(8), 1071–1075. doi:10.1046/j.1365-294x.1998.00389.x
   PubMed Web of Science ®Google Scholar
• Grueber, C. E., and Jamieson, I. G. (2008). Quantifying and managing the loss of genetic variation in a free-ranging population of takahe through the use of pedigrees. Conservation Genetics 9(3), 645–651. doi:10.1007/s10592-007-9390-3
   Web of Science ®Google Scholar
• Hammerly, S. C., Morrow, M. E., and Johnson, J. A. (2013). A comparison of pedigree- and DNA-based measures for identifying inbreeding depression in the critically endangered Attwater’s Prairie-chicken. Molecular Ecology 22(21), 5313–5328. doi:10.1111/mec.12482
   Web of Science ®Google Scholar
• Henkel, J. R., Jones, K. L., Hereford, S. G., Savoie, M. L., Leibo, S. P., and Howard, J. J. (2012). Integrating microsatellite and pedigree analyses to facilitate the captive management of the endangered Mississippi sandhill crane (Grus canadensis pulla). Zoo Biology 31(3), 322–335. doi:10.1002/zoo.20399
   Web of Science ®Google Scholar
• Jones, O. W., and Wang, J. (2010). COLONY: A program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources 10, 551–555. doi:10.1111/j.1755-0998.2009.02787.x
   PubMed Web of Science ®Google Scholar
• Kaiser, S. A., Taylor, S. A., Chen, N., Sillett, T. S., Bondra, E. R., and Webster, M. S. (2016). A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird. Molecular Ecology Resources 17, 183–193. doi:10.1111/1755-0998.12589
   Web of Science ®Google Scholar
• Kalinowski, S. T., Taper, M. L., and Marshall, T. C. (2007). Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16(5), 1099–1106. doi:10.1111/j.1365-294X.2007.03089.x
   PubMed Web of Science ®Google Scholar
• Keller, L. F. (1998). Inbreeding and its fitness effects in an insular population of Song Sparrows (Melospiza melodia). Evolution 52, 240–250. doi:10.1111/j.1558-5646.1998.tb05157.x
   Web of Science ®Google Scholar
• Kempenaers, B., Congdon, B., Boag, P., and Robertson, R. J. (1999). Extrapair paternity and egg hatchability in tree swallows: Evidence for the genetic compatibility hypothesis? Behavioral Ecology 10, 304–311. doi:10.1093/beheco/10.3.304
   Web of Science ®Google Scholar
• Kennedy, E. S. (2009). Extinction vulnerability in two small, chronically inbred populations of Chatham Island Black Robin Petroica traversi. Ph.D. Thesis, Lincoln University, Lincoln.
   Google Scholar
• Kennedy, E. S., Grueber, C. E., Duncan, R. P., and Jamieson, I. G. (2014). Severe inbreeding depression and no evidence of purging in an extremely inbred wild species - the Chatham Island Black Robin. Evolution 68, 987–995. doi:10.1111/evo.12315
   PubMed Web of Science ®Google Scholar
• Krokene, C., and Lifjeld, J. T. (2000). Variation in the frequency of extra-pair paternity in birds: A comparison of an island and a mainland population of blue tits. Behaviour 137, 1317–1330. doi:10.1163/156853900501944
   Web of Science ®Google Scholar
• Marshall, T. C., Slate, J., Kruuk, L. E., and Pemberton, J. M. (1998). Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7(5), 639–655. doi:10.1046/j.1365-294x.1998.00374.x
   PubMed Web of Science ®Google Scholar
• Massaro, M., Chick, A., Kennedy, E. S., and Whitsed, R. (2018). Post-reintroduction distribution and habitat preferences of a spatially limited island bird species. Animal Conservation 21(1), 54–64. doi:10.1111/acv.12364
   Web of Science ®Google Scholar
• Massaro, M., Sainudiin, R., Merton, D., Briskie, J. V., Poole, A. M., and Hale, M. L. (2013a). Human-assisted spread of a maladaptive behavior in a critically endangered bird. PLoS One 8, e79066. doi:10.1371/journal.pone.0079066
   Web of Science ®Google Scholar
• Massaro, M., Stanbury, M., and Briskie, J. V. (2013b). Nest site selection by the endangered Black Robin increases vulnerability to predation by an invasive bird. Animal Conservation 16(4), 404–411. doi:10.1111/acv.12007
   Web of Science ®Google Scholar
• Miller, H. C., and Lambert, D. M. (2006). A molecular phylogeny of New Zealand’s Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 40(3), 844–855. doi:10.1016/j.ympev.2006.04.012
   Web of Science ®Google Scholar
• Peakall, R., and Smouse, P. E. (2006). GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6(1), 288–295. doi:10.1111/j.1471-8286.2005.01155.x
   Web of Science ®Google Scholar
• Peakall, R., and Smouse, P. E. (2012). GENALEX 6.5: Genetic analysis in Excel. Population genetic software for teaching and research - an update. Bioinformatics 28(19), 2537–2539. doi:10.1093/bioinformatics/bts460
   PubMed Web of Science ®Google Scholar
• Pemberton, J. M. (2008). Wild pedigrees: The way forward. Proceedings of the Royal Society B: Biological Sciences 275(1635), 613–621. doi:10.1098/rspb.2007.1531
   Web of Science ®Google Scholar
• Petrie, M., and Lipsitch, M. (1994). Avian polygyny is most likely in populations with high variability in heritable male fitness. Proceedings of the Royal Society B: Biological Sciences 256, 275–280.
   Web of Science ®Google Scholar
• Reid, J. M., Keller, L. F., Marr, A. B., Nietlisbach, P., Sardell, R. J., and Arcese, P. (2014). Pedigree error due to extra-pair reproduction substantially biases estimates of inbreeding depression. Evolution 68(3), 802–815. doi:10.1111/evo.12305
   Web of Science ®Google Scholar
• Szulkin, M., Stopher, K. V., Pemberton, J. M., and Reid, J. M. (2013). Inbreeding avoidance, tolerance, or preference in animals? Trends in Ecology & Evolution 28(4), 205–211. doi:10.1016/j.tree.2012.10.016
   Web of Science ®Google Scholar
• Taylor, S. S., Boessenkool, S., and Jamieson, I. G. (2008). Genetic monogamy in two long-lived New Zealand passerines. Journal of Avian Biology 39(5), 579–583. doi:10.1111/j.0908-8857.2008.04331.x
   Web of Science ®Google Scholar
• Thrasher, D. J., Butcher, B. G., Campagna, L., Webster, M. S., and Lovette, I. J. (2018). Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird. Molecular Ecology Resources 18(5), 953–965. doi:10.1111/1755-0998.12771
   Web of Science ®Google Scholar
• Townsend, S. M., and Jamieson, I. G. (2013). Molecular and pedigree measures of relatedness provide similar estimates of inbreeding depression in a bottlenecked population. Journal of Evolutionary Biology 26(4), 889–899. doi:10.1111/jeb.12109
   PubMed Web of Science ®Google Scholar
• Tregenza, T., and Wedell, N. (2000). Genetic compatibility, mate choice and patterns of parentage: Invited review. Molecular Ecology 9(8), 1013–1027. doi:10.1046/j.1365-294x.2000.00964.x
   Web of Science ®Google Scholar
• Weinman, L. R., Solomon, J. W., and Rubenstein, D. R. (2014). A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird. Molecular Ecology Resources 15, 502–511. doi:10.1111/1755-0998.12330
   Web of Science ®Google Scholar
• Weiser, E. L., Grueber, C. E., Kennedy, E. S., and Jamieson, I. G. (2016). Unexpected positive and negative effects of continuing inbreeding in one of the world’s most inbred wild animals. Evolution 70, 154–166. doi:10.1111/evo.12840
   PubMed Web of Science ®Google Scholar
• Westneat, D. F., Sherman, P. W., and Morton, M. L. (1990). The ecology and evolution of extra-pair copulations in birds. Current Ornithology 7, 331–369.
   Google Scholar
• Westneat, D. F., and Stewart, I. R. K. (2003). Extra-pair paternity in birds: Causes, correlates, and conflict. Annual Review of Ecology, Evolution, and Systematics 34, 365–396. doi:10.1146/annurev.ecolsys.34.011802.132439
   Web of Science ®Google Scholar
• Winternitz, J. C., Promerova, M., Polakova, R., Vinker, M., Schnitzer, J., and Munclinger, P. (2015). Effects of heterozygosity and MHC diversity on patterns of extra-pair paternity in the socially monogamous scarlet rosefinch. Behavioral Ecology and Sociobiology 69, 459–469. doi:10.1007/s00265-014-1858-9
   Web of Science ®Google Scholar
• Wright, S. (1938). Size of population and breeding structure in relation to evolution. Science 87, 430–431.
   Google Scholar