The Alaskan population of Emperor Geese (Chen canagica) nests on the Yukon–Kuskokwim Delta in western Alaska. Numbers of Emperor Geese in Alaska declined from the 1960s to the mid-1980s and since then, their numbers have slowly increased. Low statistical power of microsatellite loci developed in other waterfowl species and used in previous studies of Emperor Geese are unable to confidently assign individual identity. Microsatellite loci for Emperor Goose were therefore developed using shotgun amplification and next-generation sequencing technology. Forty-one microsatellite loci were screened and 14 were found to be polymorphic in Emperor Geese. Only six markers – a combination of four novel loci and two loci developed in other waterfowl species – are needed to identify an individual from among the Alaskan Emperor Goose population. Genetic markers for identifying sex in Emperor Geese were also developed. The 14 novel variable loci and 15 monomorphic loci were screened for polymorphism in four other Arctic-nesting goose species, Black Brant (Branta bernicla nigricans), Greater White-fronted (Anser albifrons), Canada (B. canadensis) and Cackling (B. hutchinsii) Goose. Emperor Goose exhibited the smallest average number of alleles (3.3) and the lowest expected heterozygosity (0.467). Greater White-fronted Geese exhibited the highest average number of alleles (4.7) and Cackling Geese the highest expected heterozygosity (0.599). Six of the monomorphic loci were variable and able to be characterised in the other goose species assayed, a predicted outcome of reverse ascertainment bias. These findings fail to support the hypothesis of ascertainment bias due to selection of microsatellite markers.
AbrahamK.F., JefferiesR.L. and AlisauskasR.T. (2005) The dynamics of landscape change and Snow Geese in midcontinent North America. Glob. Chang. Biol., 11, 841–855.
2.
AlisauskasR.T. (2002) Arctic climate, spring nutrition, and recruitment in midcontinent Lesser Snow Geese. J. Wildl. Manage., 66, 181–193.
3.
BirdLife International (2012) Anser canagicus. IUCN red list threat species v.2015.2. https://www.iucnredlist.org [accessed 26 May 2017].
4.
BuchholzW.G., PearceJ.M., PiersonB.J. and ScribnerK.T. (1998) Dinucleotide repeat polymorphisms in waterfowl (family Anatidae): characterization of a sex-linked (Z-specific) and 14 autosomal loci. Anim. Genet., 29, 323–325.
5.
CeplitisH. and EllegrenH. (2004) Adaptive molecular evolution of HINTW, a female-specific gene in birds. Mol. Biol. Evol., 21, 249–254.
6.
CornuetJ.M. and LuikartG. (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144, 2001–2014.
7.
DelportW., GrantT.J., RyanP.G. and BloomerP. (2006) Ten microsatellite loci for evolutionary research on Nesospiza buntings. Mol. Ecol. Notes, 6, 1180–1183.
8.
Di RienzoA., PetersonA.C., GarzaJ.C., ValdesA.M., SlatkinM. and FreimerN.B. (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl Acad. Sci. USA, 91, 3166–3170.
9.
Donne-GousséC., LaudetV. and HänniC. (2002) A molecular phylogeny of Anseriformes based on mitochondrial DNA analysis. Mol. Phylogenet. Evol., 23, 339–356.
10.
EisenhauerD.I. and KirkpatrickC.M. (1977) Ecology of the Emperor Goose in Alaska. Wildl. Monogr., 57, 3–62.
11.
EllegrenH., MooreS., RobinsonN., WardW. and SheldonB.C. (1997) Microsatellite evolution-a reciprocal study of repeat lengths at homologous loci in cattle and sheep. Mol. Biol. Evol., 14, 854–860.
12.
FairclothB.C. (2008) MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol. Ecol. Resour., 8, 92–94.
13.
GarzaJ.C. and WilliamsonE.G. (2001) Detection of reduction in population size using data from microsatellite loci. Mol. Ecol., 10, 305–318.
14.
GriffithsR., DoubleM.C., OrrK. and DawsonR.J.G. (1998) A DNA test to sex most birds. Mol. Ecol., 7, 1071–1075.
15.
GuzzettiB.M., TalbotS.L., TesslerD.F., GillV.A. and MurphyE.C. (2008) Secrets in the eyes of Black Oystercatchers: a new sexing technique. J. F. Ornithol., 79, 215–223.
16.
HandelC.M., PajotL.M., TalbotS.L. and SageG.K. (2006) Use of buccal swabs for sampling DNA from nestling and adult birds. Wildl. Soc. Bull., 34, 1094–1100.
17.
HoganF.E., CookeR. and NormanJ.A. (2009) Reverse ascertainment bias in microsatellite allelic diversity in owls (Aves, Strigiformes). Conserv. Genet., 10, 635–638.
18.
HoriT., AsakawaS., ItohY., ShimizuN. and MizunoS. (2000) Wpkci, encoding an altered form of PKCI, is conserved widely on the avian W chromosome and expressed in early female embryos: implication of its role in female sex determination. Mol. Biol. Cell, 11, 3645–3660.
19.
JonesA.G. and ArdrenW.R. (2003) Methods of parentage analysis in natural populations. Mol. Ecol., 12, 2511–2523.
20.
KalinowskiS.T., TaperM.L. and MarshallT.C. (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol., 16, 1099–1106.
21.
LiB. and KimmelM. (2013) Factors influencing ascertainment bias of microsatellite allele sizes: impact on estimates of mutation rates. Genetics, 195, 563–572.
22.
LuikartG., SherwinW.B., SteeleB.M. and AllendorfF.W. (1998) Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Mol. Ecol., 7, 963–974.
23.
MaakS., WimmersK., WeigendS. and NeumannK. (2003) Isolation and characterization of 18 microsatellites in the Peking Duck (Anas platyrhynchos) and their application in other waterfowl species. Mol. Ecol. Notes, 3, 224–227.
24.
MaruyamaT. and FuerstP.A. (1985) Population bottlenecks and nonequilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics, 111, 675–689.
25.
McCloskeyS.E. (2013) Variation in metabolic rates of eggs of Emperor Geese: a possible adaptation for instraspecific nest parasitism.Alaska Pacific University, Anchorage, AK.
26.
MedranoJ.F., AasenE. and SharrowL. (1990) DNA extraction from nucleated red blood cells. Biotechniques, 8, 43.
27.
Muñoz-FuentesV., GyllenstrandN., NegroJ.J., GreenA.J. and VilàC. (2005) Microsatellite markers for two stifftail ducks: the White-headed Duck, Oxyura leucocephala, and the Ruddy Duck, O. jamaicensis. Mol. Ecol. Notes, 5, 263–265.
28.
OettingW.S., LeeH.K., FlandersD.J., WiesnerG.L., SellersT.A. and KingR.A. (1995) Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics, 30, 450–458.
29.
OhtaJ. and KimuraM. (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet. Res., 22, 201–204.
30.
O'NeillM., BinderM., SmithC., AndrewsJ., ReedK., SmithM., MillarC., LambertD. and SinclairA. (2000) ASW: a gene with conserved avian W-linkage and female specific expression in chick embryonic gonad. Dev. Genes Evol., 210, 243–249.
31.
ParkS. (2000) Microsatellite toolkit for MS Excel 97 or 2000 (PC). Stephen Park, Molecular Population Genetics Lab, Smurfit Institute of Genetics, Dublin.
32.
PaulusK.B. and TiedemannR. (2003) Ten polymorphic autosomal microsatellite loci for the Eider Duck Somateria mollissima and their cross-species applicability among waterfowl species (Anatidae). Mol. Ecol. Notes, 3, 250–252.
33.
PetersenM.R. (1991) Reproductive ecology of Emperor Geese. PhD thesis, University of California, Davis.
34.
PiryS., LuikartG. and CornuetJ.-M. (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J. Hered., 90, 502–503.
35.
RaymondM. and RoussetF. (1995) Genepop (version 1.2): population-genetics software for exact tests and ecumenicism. J. Hered., 86, 248–249.
36.
RoussetF. (2008) GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol. Ecol. Resour., 8, 103–106.
37.
SchmutzJ.A. (1994) Age, habitat and tide effects on feeding activity of Emperor Geese during autumn migration. Condor, 96, 46–51.
38.
SchmutzJ.A., PetersenM.R. and RockwellR.F. (2011) Emperor Goose (Chen canagica). The Birds of North America. Cornell Laboratory of Ornithology, Ithaca. https://birdsna.org [accessed 4 July 2017].
39.
SefcK.M., PayneR.B. and SorensonM.D. (2003) Microsatellite amplification from museum feather samples: effects of fragment size and template concentration on genotyping errors. Auk, 120, 982–989.
40.
SheteS., TiwariH. and ElstonR.C. (2000) On estimating the heterozygosity and polymorphism information content value. Theor. Popul. Biol., 57, 265–271.
41.
SonsthagenS.A., SageG.K., FowlerM., HopeA.G., CookJ.A. and TalbotS.L. (2013) Development and characterization of 21 polymorphic microsatellite markers for the barren-ground shrew, Sorex ugyunak (Mammalia: Sorcidae), through next-generation sequencing, and cross-species amplification in the masked shrew, S. cinereus. Conserv. Genet. Resour., 5, 315–318.
42.
SonsthagenS.A., TalbotS.L. and WhiteC.M. (2004) Gene flow and genetic characterization of Northern Goshawks breeding in Utah. Condor, 106, 826–836.
43.
TalbotS.L. (2017) Data from: DNA microsatellite and sex identification markers for Emperor Goose (Chen canagica) and cross-species amplification of microsatellites in select goose species. Alaska 2016: U.S. Geological Survey data release. https://doi.org/10.5066/F71V5C4S.
44.
TerebaA. (1999) Tools for analysis of population statistics. Profiles in DNA, 2, 14–16.
45.
US Fish and Wildlife Service (2015) Waterfowl Population Status.US Department of the Interior, Washington D.C., USA.
46.
US Fish and Wildlife Service (2016) Waterfowl Population Status.US Department of the Interior, Washington D.C., USA.
47.
Van OosterhoutC., HutchinsonW.F., WillsD.P.M. and ShipleyP. (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes, 4, 535–538.
48.
ValièreN. (2002) GIMLET: a computer program for analysing genetic individual identification data. Mol. Ecol. Notes, 2, 377–379.
49.
VillanuevaB., VerspoorE. and VisscherP.M. (2002) Parental assignment in fish using microsatellite genetic markers with finite numbers of parents and offspring. Anim. Genet., 33, 33–41.
50.
WaitsL.P., LuikartG. and TaberletP. (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol., 10, 249–256.
51.
WaldeckP., HagenJ.I., HanssenS.A. and AnderssonM. (2011) Brood parasitism, female condition and clutch reduction in the Common Eider Somateria mollisima. J. Avian Biol., 42, 231–238.
52.
WatkinsV.S. (2006) Intraspecific nest parasitism in Emperor Geese (Chen canagica): a population genetic analysis.Alaska Pacific University, Anchorage, AK.
53.
WilliamsI., GuzzettiB.M., GustJ.R., SageG.K., GillR.E., TibbittsT.L., SonsthagenS.A. and TalbotS.L. (2012) Polymorphic microsatellite loci identified through development and cross-species amplification within shorebirds. J. Ornithol., 153, 593–601.
54.
WrightT.F., JohnsP.M., WaltersJ.R., LernerA.P., SwallowJ.G. and WilkinsonG.S. (2004) Microsatellite variation among divergent populations of stalk-eyed flies, genus Cyrtodiopsis. Genet. Res., 84, 27–40.
