Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations
ACIA (2004) Impacts of a Warming Arctic: Arctic Climate Impact Assessment. Cambridge University Press, Cambridge, UK
Google Scholar
Alsos IG, Ehrich D, Thuiller W, Eidesen PB, Tribsch A, Schonswetter P et al. (2012) Genetic consequences of climate change for northern plants. Proc R Soc B-Biol Sci 279:2042–2051
Google Scholar
Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17:81–92CAS
PubMed
PubMed Central
Google Scholar
Archer FI, Adams PE, Schneiders BB (2017) strataG: an R package for manipulating, summarizing and analysing population genetic data. Mol Ecol Resour 17:5–11CAS
PubMed
Google Scholar
Arenas M, Ray N, Currat M, Excoffier L (2011) Consequences of range contractions and range shifts on molecular diversity. Mol Biol Evol 29:207–218PubMed
Google Scholar
Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics 153:2013–2029CAS
PubMed
PubMed Central
Google Scholar
Benjamini Y, Hochberg Y (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Statistical Soc Series B 57:289–300BirdLife International (2018). Pagophila eburnea. The IUCN Red List of Threatened Species 2018: e.T22694473A132555020. https://doi.org/10.2305/IUCN.UK.2018-2.RLTS.T22694473A132555020.en. Downloaded on11 June 2020Boertmann D, Petersen IK, Nielsen HH (2020) Ivory Gull population status in Greenland 2019. Dan Orn Foren Tidsskr 114:141–150
Google Scholar
Boitard S, Rodríguez W, Jay F, Mona S, Austerlitz F (2016) Inferring population size history from large samples of genome-wide molecular data – an approximate Bayesian computation approach. PLOS Genet 12:1–36
Google Scholar
Box JE, Colgan WT, Christensen TR, Schmidt NM, Lund M, Parmentier F-JW et al. (2019) Key indicators of Arctic climate change: 1971–2017. Environ Res Lett 14:045010CAS
Google Scholar
Braune BM, Mallory ML, Gilchrist HG (2006) Elevated mercury levels in a declining population of ivory gulls in the Canadian Arctic. Mar Pollut Bull 52:978–982CAS
PubMed
Google Scholar
Broquet T, Angelone S, Jaquiéry J, Joly P, Léna JP, Lengagne T et al. (2010) Genetic bottlenecks driven by population disconnection. Conserv Biol 24:1596–1605PubMed
Google Scholar
Chen IC, Hill JK, Ohlemüller R, Roy DB, Thomas CD (2011) Rapid range shifts of species associated with high levels of climate warming. Science 333:1024–1026CAS
PubMed
Google Scholar
Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont MA (2010) The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186:983–995PubMed
PubMed Central
Google Scholar
Collevatti RG, Nabout JC, Diniz-Filho JAF (2011) Range shift and loss of genetic diversity under climate change in Caryocar brasiliense, a Neotropical tree species. Tree Genet Genomes 7:1237–1247
Google Scholar
Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014CAS
PubMed
PubMed Central
Google Scholar
Cotto O, Schmid M, Guillaume F (2020) Nemo-age: spatially explicit simulations of eco-evolutionary dynamics in stage-structured populations under changing environments. Methods Ecol Evol 11:1227–1236
Google Scholar
Cubaynes S, Doherty PF, Schreiber EA, Gimenez O (2011) To breed or not to breed: a seabird’s response to extreme climatic events. Biol Lett 7:303–306PubMed
Google Scholar
Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB (1994). Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 91: 3166–3170Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR (2014) NeEstimator V2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour 14:209–214CAS
PubMed
Google Scholar
Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445CAS
PubMed
Google Scholar
England PR, Cornuet J-M, Berthier P, Tallmon DA, Luikart G (2006) Estimating effective population size from linkage disequilibrium: severe biasin small samples. Conserv Genet 7:303
Google Scholar
Engler JO, Secondi J, Dawson DA, Elle O, Hochkirch A (2016) Range expansion and retraction along a moving contact zone has no effect on the genetic diversity of two passerine birds. Ecography 39:884–893
Google Scholar
Environment Canada (2014) Recovery Strategy for the Ivory Gull (Pagophila eburnea) in Canada. Species at Risk Act Recovery Strategy Series. Environment Canada, Ottawa. iv+ 21 ppEstoup A, Angers B (1998) Microsatellites and minisatellites for molecular ecology: theoretical and empirical considerations. In Carvalho GR (ed) Advances in molecular ecology, 55–85. IOS Press, Burke, Virginia, USAEwens WJ (1972) The sampling theory of selectively neutral alleles. Theor Popul Biol 3:87–112CAS
PubMed
Google Scholar
Felsenstein J (1971) Inbreeding and variance effective numbers in populations with overlapping generations. Genetics 168:581–597
Google Scholar
Fort J, Moe B, Strøm H, Grémillet D, Welcker J, Schultner J et al. (2013) Multicolony tracking reveals potential threats to little auks wintering in the North Atlantic from marine pollution and shrinking sea ice cover. Diversity Distrib 19:1322–1332
Google Scholar
Fraïsse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J et al. (2021). DILS: Demographic inferences with linked selection by using ABC. Mol Ecol Resourc 21:2629–2644Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genetical Res 66:95–107
Google Scholar
Frankham R, Bradshaw CJA, Brook BW (2014) Genetics in conservation management: revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biol Conserv 170:56–63
Google Scholar
Garnier J, Lewis MA (2016) Expansion under climate change: the genetic consequences. Bull Math Biol 78:2165–2185PubMed
Google Scholar
Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318CAS
PubMed
Google Scholar
Gavrilo M, Martynova D (2017) Conservation of rare species of marine flora and fauna of the Russian Arctic National Park, included in the Red Data Book of the Russian Federation and in the IUCN Red List. Nat Conserv Res 2:10–42
Google Scholar
Gienapp P, Teplitsky C, Alho JS, Mills JA, Merila J (2008) Climate change and evolution: disentangling environmental and genetic responses. Mol Ecol 17:167–178CAS
PubMed
Google Scholar
Gilchrist HG, Mallory ML (2005) Declines in abundance and distribution of the ivory gull (Pagophila eburnea) in Arctic Canada. Biol Conserv 121:303–309
Google Scholar
Gilchrist HG, Strøm H, Gavrilo MV, Mosbech A (2008). International ivory gull conservation strategy and action plan. CAFF International Secretariat,Circumpolar Seabird Group (CBird), CAFF Technical Report No. 18Gilg O, Boertmann D, Merkel F, Aebischer A, Sabard B (2009) Status of the endangered ivory gull, Pagophila eburnea, in Greenland. Polar Biol 32:1275–1286
Google Scholar
Gilg O, Istomina L, Heygster G, Strøm H, Gavrilo M, Mallory ML et al. (2016) Living on the edge of a shrinking habitat: the ivory gull, Pagophila eburnea, an endangered sea-ice specialist. Biol Lett 12:20160277PubMed
PubMed Central
Google Scholar
Gilg O, Kovacs KM, Aars J, Fort J, Gauthier G, Gremillet D et al. (2012) Climate change and the ecology and evolution of Arctic vertebrates. Ann N Y Acad Sci 1249:166–190PubMed
Google Scholar
Goutte A, Kriloff M, Weimerskirch H, Chastel O (2011) Why do some adult birds skip breeding? A hormonal investigation in a long-lived bird. Biol Lett 7:790–792PubMed
PubMed Central
Google Scholar
Guillaume F, Rougemont J (2006) Nemo: an evolutionary and population genetics programming framework. Bioinformatics 22:2556–2557CAS
PubMed
PubMed Central
Google Scholar
Hill WG (1972) Effective size of populations with overlapping generations. Theor Popul Biol 3:278–289CAS
PubMed
Google Scholar
Hoban SM, Mezzavilla M, Gaggiotti OE, Benazzo A, van Oosterhout C, Bertorelle G (2013) High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study. BMC Bioinforma 14:309
Google Scholar
Hoffmann AA, Sgrò CM (2011) Climate change and evolutionary adaptation. Nature 470:479–485CAS
PubMed
Google Scholar
Hohenlohe PA, Funk WC, Rajora OP (2021) Population genomics for wildlife conservation and management. Mol Ecol 30:62–82PubMed
Google Scholar
Jamieson IG, Allendorf FW (2012) How does the 50/500 rule apply to MVPs? Trends Ecol Evol 27:578–584PubMed
Google Scholar
Kimura M, Ohta T (1978) Stepwise mutation model and distribution of allelic frequencies in a finite population. Proc Natl Acad Sci USA 75:2868–2872CAS
PubMed
PubMed Central
Google Scholar
Laporte V, Charlesworth B (2002) Effective population size and population subdivision in demographically structured populations. Genetics 162:501–519CAS
PubMed
PubMed Central
Google Scholar
Leblois R, Pudlo P, Néron J, Bertaux F, Reddy Beeravolu C, Vitalis R et al. (2014) Maximum-Likelihood Inference of Population Size Contractions from Microsatellite Data. Mol Biol Evol 31:2805–2823CAS
PubMed
Google Scholar
Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475:493–496CAS
PubMed
PubMed Central
Google Scholar
Liu X, Fu Y-X (2015) Exploring population size changes using SNP frequency spectra. Nat Genet 47:555–559CAS
PubMed
PubMed Central
Google Scholar
Lucia M, Verboven N, Strom H, Miljeteig C, Gavrilo MV, Braune BM et al. (2015) Circumpolar contamination in eggs of the high-arctic ivory gull Pagophila eburnea. Environ Toxicol Chem 34:1552–1561CAS
PubMed
Google Scholar
Luikart G, Cornuet J-M (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv Biol 12:228–237
Google Scholar
Mallory ML, Allard KA, Braune BM, Gilchrist HG, Thomas VG (2012) New longevity record for ivory gulls (Pagophila eburnea) and evidence of natal philopatry. Arctic 65:98–101
Google Scholar
Marandel F, Charrier G, Lamy J-B, Le Cam S, Lorance P, Trenkel VM (2020) Estimating effective population size using RADseq: Effects of SNP selection and sample size. Ecol Evol 10:1929–1937PubMed
PubMed Central
Google Scholar
McInerny GJ, Turner JRG, Wong HY, Travis JMJ, Benton TG (2009) How range shifts induced by climate change affect neutral evolution. Proc R Soc B: Biol Sci 276:1527–1534CAS
Google Scholar
McRae L, Deinet S, Gill M, Collen B (2012) Arctic species trend index: tracking trends in Arctic marine populations. CAFF Assessment Series No. 7. Conservation of Arctic Flora and Fauna, Iceland
Google Scholar
Meredith M, Sommerkorn M, Cassotta S, Derksen C, Ekaykin A, Hollowed A et al. (2020) Polar Regions. In: Pörtner HO, Roberts DC, Masson-Delmotte V, Zhai P, Tignor M, Poloczanska E, Mintenbeck K, Alegría A, Nicolai M, Okem A, Petzold J, Rama B, Weyer NM (eds.) IPCC Special Report on the Ocean and Cryosphere in a Changing Climate. Intergovernmental Panel on Climate Change (IPCC)) Geneva, pp 203–320Miljeteig C, Strom H, Gavrilo MV, Volkov A, Jenssen BM, Gabrielsen GW (2009) High levels of contaminants in ivory gull Pagophila eburnea eggs from the Russian and Norwegian Arctic. Environ Sci Technol 43:5521–5528CAS
PubMed
Google Scholar
Miller MP, Haig SM, Mullins TD, Popper KJ, Green M (2012) Evidence for population bottlenecks and subtle genetic structure in the yellow rail. Condor 114:100–112
Google Scholar
Nadachowska-Brzyska K, Li C, Smeds L, Zhang G, Ellegren H (2015) Temporal dynamics of avian populations during Pleistocene revealed by whole-genome sequences. Curr Biol 25:1375–1380CAS
PubMed
PubMed Central
Google Scholar
Nunney L (1993) The influence of mating system and overlapping generations on effective population size. Evolution 47:1329–1341PubMed
Google Scholar
Nunney L, Elam DR (1994) Estimating the Effective Population Size of Conserved Populations. Conserv Biol 8:175–184
Google Scholar
Nunziata SO, Weisrock DW (2018) Estimation of contemporary effective population size and population declines using RAD sequence data. Heredity 120:196–207CAS
PubMed
Google Scholar
Nyström V, Angerbjörn A, Dalén L (2006) Genetic consequences of a demographic bottleneck in the Scandinavian arctic fox. Oikos 114:84–94
Google Scholar
Orive ME (1993) Effective population size in organisms with complex life-histories. Theor Popul Biol 44:316–340CAS
PubMed
Google Scholar
Parmesan C (2006) Ecological and evolutionary responses to recent climate change. Annu Rev Ecol Evol Syst 37:637–669
Google Scholar
Parreira BR, Chikhi L (2015) On some genetic consequences of social structure, mating systems, dispersal, and sampling. Proc Natl Acad Sci USA 112:E3318CAS
PubMed
PubMed Central
Google Scholar
Parreira B, Quéméré E, Vanpé C, Carvalho I, Chikhi L (2020) Genetic consequences of social structure in the golden-crowned sifaka. Heredity 125:328–339PubMed
PubMed Central
Google Scholar
Peart CR, Tusso S, Pophaly SD, Botero-Castro F, Wu C-C, Aurioles-Gamboa D et al. (2020) Determinants of genetic variation across eco-evolutionary scales in pinnipeds. Nat Ecol Evol 4:1095–1104PubMed
Google Scholar
Peery MZ, Kirby R, Reid BN, Stoelting R, Doucet-Bëer E, Robinson S et al. (2012) Reliability of genetic bottleneck tests for detecting recent population declines. Mol Ecol 21:3403–3418PubMed
Google Scholar
Piry S, Luikart G, Cornuet J-M (1999) Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. J Heredity 90:502–503
Google Scholar
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Heredity 86:248–249
Google Scholar
Rousset F (1999) Genetic Differentiation in Populations with Different Classes of Individuals. Theor Popul Biol 55:297–308CAS
PubMed
Google Scholar
Rousset F (2008) Genepop’007: a complete re-implementation of the Genepop software for windows and linux. Mol Ecol Notes 8:103–1006
Google Scholar
Rousset F, Beeravolu CR, Leblois R (2018) Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations. J de la Société Française de Statistique 159:142–166
Google Scholar
Rubidge EM, Patton JL, Lim M, Burton AC, Brashares JS, Moritz C (2012) Climate-induced range contraction drives genetic erosion in an alpine mammal. Nat Clim Change 2:285–288
Google Scholar
Shafer ABA, Gattepaille LM, Stewart REA, Wolf JBW (2015) Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Mol Ecol 24:328–345PubMed
Google Scholar
Spencer NC, Gilchrist HG, Mallory ML (2014) Annual movement patterns of endangered ivory gulls: the importance of sea ice. Plos ONE 9:e115231PubMed
PubMed Central
Google Scholar
Stenhouse IJ, Robertson GJ, Gilchrist HG (2004) Recoveries and survival rates of ivory gulls (Pagophila eburnea) banded in Nunavut, Canada 1971–1999. Waterbirds 27:486–492
Google Scholar
Storz J, Ramakrishnan U, Alberts S (2002) Genetic effective size of a wild primate population: influence of current and historical demography. Evolution 56:817–29PubMed
Google Scholar
Strøm H, Bakken V, Skoglund, Descamps S, Fjeldheim VB, Steen H (2020) Population status and trend of the threatened ivory gull Pagophila eburnea in Svalbard. Endanger Species Res 43:435–445
Google Scholar
Volkov AE, de Korte J (2000) Breeding ecology of the Ivory Gull (Pagophila eburnea) in Sedov Archipelago, Severnaya Zemlya. Heritage of the Russian Arctic. Research, conservation and international cooperation. Ecopros Publishers, Moscow, p 483–500
Google Scholar
Waples RS (2016) Life-history traits and effective population size in species with overlapping generations revisited: the importance of adult mortality. Heredity 117:241–250CAS
PubMed
PubMed Central
Google Scholar
Waples RS, Antao T, Luikart G (2014) Effects of overlapping generations on linkage disequilibrium estimates of effective population size. Genetics 197:769–780PubMed
PubMed Central
Google Scholar
Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolut Appl 3:244–262
Google Scholar
Waples RS, Luikart G, Faulkner JR, Tallmon DA (2013) Simple life-history traits explain key effective population size ratios across diverse taxa. Proc R Soc B: Biol Sci 280:20131339
Google Scholar
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CAS
PubMed
PubMed Central
Google Scholar
Williamson-Natesan EG (2005) Comparison of methods for detecting bottlenecks from microsatellite loci. Conserv Genet 6:551–562
Google Scholar
Wogan GOU, Voelker G, Oatley G, Bowie RCK (2020) Biome stability predicts population structure of a southern African aridland bird species. Ecol Evol 10:4066–4081PubMed
PubMed Central
Google Scholar
Xenikoudakis G, Ersmark E, Tison J-L, Waits L, Kindberg J, Swenson JE et al. (2015) Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear. Mol Ecol 24:3441–3454CAS
PubMed
Google Scholar
Yannic G, Broquet T, Strøm H, Aebischer A, Dufresnes C, Gavrilo MV et al. (2016) Genetic and morphological sex identification methods reveal a male-biased sex ratio in the Ivory Gull Pagophila eburnea. J Ornithol 157:861–873
Google Scholar
Yannic G, Sermier R, Aebischer A, Gavrilo MV, Gilg O, Miljeteig C et al. (2011) Description of microsatellite markers and genotyping performances using feathers and buccal swabs for the ivory gull (Pagophila eburnea). Mol Ecol Resour 11:877–889PubMed
Google Scholar
Yannic G, Yearsley J, Sermier R, Dufresnes C, Gilg O, Aebischer A et al. (2016) High connectivity in a long-lived high-Arctic seabird, the ivory gull Pagophila eburnea. Polar Biol 39:221–236
Google Scholar
Yurkowski DJ, Auger-Méthé M, Mallory ML, Wong SNP, Gilchrist G, Derocher AE et al. (2019) Abundance and species diversity hotspots of tracked marine predators across the North American Arctic. Diversity Distrib 25:328–345
Google Scholar More