Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms

Molecular Ecology

Volumn 22, Issue 1, 2013, Pages 41-55

  Kraus, Robert H S ^a,b   Van Hooft, Pim ^a   Megens, Hendrik Jan ^a   Tsvey, Arseny ^c   Fokin, Sergei Y ^d   Ydenberg, Ronald C ^a,e   Prins, Herbert H T ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b SENCKENBERG RESEARCH INSTITUTE   (Germany)

^c Zoological Institute   (Russian Federation)

^d Russian Ministry of Environment   (Russian Federation)

^e SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Anas platyrhynchos; ascertainment bias; coalescent analysis; conservation management; population genomics; single nucleotide polymorphisms

Indexed keywords

ALGORITHM; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; DUCK; GENETIC MARKER; GENETICS; GENOTYPING TECHNIQUE; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION GENETICS; POPULATION MIGRATION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ANIMAL MIGRATION; ANIMALS; BAYES THEOREM; DUCKS; GENETIC MARKERS; GENETICS, POPULATION; GENOTYPING TECHNIQUES; MODELS, GENETIC; PHYLOGENY; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE;

ANAS PLATYRHYNCHOS; ANATIDAE; AVES;

EID: 84872868770     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12098     Document Type: Review

References (92)

1. Als TD, Hansen MM, Maes GE, et al,. (2011) All roads lead to home: panmixia of European eel in the Sargasso Sea. Molecular Ecology, 20, 1333-1346.
2. Altshuler D, Pollara VJ, Cowles CR, et al,. (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature, 407, 513-516.
3. Anon. U.S. Fish and Wildlife Service. Available from http://www.flyways. us/flyways/info#flyways-bio.
4. Avise JC, (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489-522.
5. Avise JC, Ankney CD, Nelson WS, (1990) Mitochondrial gene trees and the evolutionary relationship of Mallard and Black Ducks. Evolution, 44, 1109-1119.
6. Beaumont MA, Nielsen R, Robert C, et al,. (2010) In defence of model-based inference in phylogeography. Molecular Ecology, 19, 436-446.
7. Beerli P, (2010) Tutorial: Comparison of gene flow models using Bayes Factors. Available from Web Tutorial http://popgen.sc.fsu.edu/Migrate/Tutorials/ Entries/2010/7/12-Day-of-longboarding.html.
8. Beerli P, Felsenstein J, (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics, 152, 763-773. (Pubitemid 29272726)
9. Beerli P, Felsenstein J, (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences of the United States of America, 98, 4563-4568. (Pubitemid 32295016)
10. Beerli P, Palczewski M, (2010) Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics, 185, 313-326.
11. Black WC IV, Baer CF, Antolin MF, DuTeau NM, (2001) Population genomics: genome-wide sampling of insect populations. Annual Review Of Entomology, 46, 441-469. (Pubitemid 32304996)
12. Bloomquist EW, Lemey P, Suchard MA, (2010) Three roads diverged? Routes to phylogeographic inference. Trends in Ecology and Evolution, 25, 626-632.
13. Bryant D, Moulton V, (2004) Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution, 21, 255-265. (Pubitemid 38314614)
14. Campbell NR, Narum SR, (2011) Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River. Molecular Ecology Resources, 11, 20-30.
15. Carstens BC, Richards CL, (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution, 61, 1439-1454. (Pubitemid 46848830)
16. Champagnon J, Guillemain M, Gauthier-Clerc M, Lebreton JD, Elmberg J, (2009) Consequences of massive bird releases for hunting purposes: mallard Anas platyrhynchos in the Camargue, southern France. Wildfow Special issue, 2, 184-191.
17. Eaton MA, Brown AF, Noble DG, et al,. (2009) Birds of conservation concern 3: the population status of birds in the United Kingdom, Channel Islands and Isle of Man. British Birds, 102, 296-341.
18. Elmberg J, (2009) Are dabbling ducks major players or merely noise in freshwater ecosystems? A European perspective, with references to population limitation and density dependence. Wildfow Special issue, 2, 9-23.
19. Estoup A, Jarne P, Cornuet JM, (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular Ecology, 11, 1591-1604. (Pubitemid 35022229)
20. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620. (Pubitemid 40886055)
21. Flint PL, Ozaki K, Pearce JM, et al,. (2009) Breeding-season sympatry facilitates genetic exchange among allopatric wintering populations of Northern Pintails in Japan and California. Condor, 111, 591-598.
22. Friesen VL, Burg TM, McCoy KD, (2007) Mechanisms of population differentiation in seabirds. Molecular Ecology, 16, 1765-1785.
23. Geraci J, Béchet A, Cézilly F, et al,. (2012) Greater flamingo colonies around the Mediterranean form a single interbreeding population and share a common history. Journal of Avian Biology, 43, 341-354.
24. Guillemain M, Sadoul N, Simon G, (2005) European flyway permeability and abmigration in Teal Anas crecca, an analysis based on ringing recoveries. Ibis, 147, 688-696. (Pubitemid 43906484)
25. Gunnarsson G, Latorre-Margalef N, Hobson KA, et al,. (2012) Disease dynamics and bird migration-linking mallards Anas platyrhynchos and subtype diversity of the influenza a virus in time and space. PLoS ONE, 7, e35679.
26. Han YS, Hung CL, Liao YF, Tzeng WN, (2010) Population genetic structure of the Japanese eel Anguilla japonica: panmixia at spatial and temporal scales. Marine Ecology Progress Series, 401, 221-232.
27. Humphries EM, Winker K, (2011) Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds. Molecular Ecology, 20, 573-583.
28. Huson DH, (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics, 14, 68-73. (Pubitemid 28397727)
29. Huson DH, Bryant D, (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23, 254-267. (Pubitemid 43100040)
30. ISO3166 (2007) ISO 3166 Maintenance agency. International Organization for Standardization.
31. Ito T, Okazaki K, Kawaoka Y, et al,. (1995) Perpetuation of influenza A viruses in Alaskan waterfowl reservoirs. Archives of Virology, 140, 1163-1172.
32. IUCN (2011) IUCN Red List of Threatened Species. Downloaded on 13 July 2011, Version 2011.1.
33. Jombart T, (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403-1405. (Pubitemid 351737150)
34. Jombart T, Devillard S, Balloux F, (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics, 11, 94.
35. Jonker RM, Kraus RHS, Zhang Q, et al,. (2011a) Genetic consequences of breaking migratory traditions in barnacle geese. In: Revolutionary Non-Migratory Migrants (ed., Jonker RM,), pp. 71-83 PhD Thesis. Wageningen University. Wageningen, The Netherlands.
36. Jonker RM, Zhang Q, Van Hooft P, et al,. (2012) The development of a genome wide SNP set for the Barnacle Goose Branta leucopsis. PLoS ONE, 7, e38412.
37. Jorgensen SJ, Reeb CA, Chapple TK, et al,. (2010) Philopatry and migration of Pacific white sharks. Proceedings of the Royal Society of London, Series B: Biological Sciences, 277, 679-688.
38. Kass RE, Raftery AE, (1995) Bayes Factors. Journal of the American Statistical Association, 90, 773-795.
39. Kerstens HHD, Crooijmans RPMA, Veenendaal A, et al,. (2009) Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to Turkey. BMC Genomics, 10, 479.
40. Kingman JFC, (1982a) The coalescent. Stochastic Processes and Their Applications, 13, 235-248.
41. Kingman JFC, (1982b) On the genealogy of large populations. Journal of Applied Probability, 19, 27-43.
42. Knowles LL, (2004) The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology, 17, 1-10. (Pubitemid 38162174)
43. Koenig WD, Van Vuren D, Hooge PN, (1996) Detectability, philopatry, and the distribution of dispersal distances in vertebrates. Trends in Ecology and Evolution, 11, 514-517. (Pubitemid 126403121)
44. Kovach AI, Breton TS, Berlinsky DL, Maceda L, Wirgin I, (2010) Fine-scale spatial and temporal genetic structure of Atlantic cod off the Atlantic coast of the USA. Marine Ecology Progress Series, 410, 177-195.
45. Kraus RHS, Kerstens HHD, van Hooft P, et al,. (2011a) Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). BMC Genomics, 12, 150.
46. Kraus RHS, Zeddeman A, Sartakov D, Soloviev SA, Ydenberg RC, Prins HHT, (2011b) Evolution and connectivity in the world-wide migration system of the mallard: inferences from mitochondrial DNA. BMC Genetics, 12, 99.
47. Kraus RHS, Kerstens HHD, van Hooft P, et al,. (2012) Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks. BMC Evolutionary Biology, 12, 45.
48. Kuhner MK, (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22, 768-770.
49. Kulikova IV, Drovetski SV, Gibson DD, et al,. (2005) Phylogeography of the Mallard (Anas platyrhynchos): hybridization, dispersal, and lineage sorting contribute to complex geographic structure. Auk, 122, 949-965. (Pubitemid 41060668)
50. Laikre L, Palmé A, Josefsson M, Utter F, Ryman N, (2006) Release of alien populations in Sweden. Ambio, 35, 255-261. (Pubitemid 44433413)
51. Lamb HH, (1975) Our understanding of global wind circulation and climatic variations. Bird Study, 22, 121-141.
52. Lebarbenchon C, Yang M, Keeler SP, et al,. (2011) Viral replication, persistence in water and genetic characterization of two influenza a viruses isolated from surface lake water. PLoS ONE, 6, e26566.
53. Li MH, Merilä J, (2010) Genetic evidence for male-biased dispersal in the Siberian jay (Perisoreus infaustus) based on autosomal and Z-chromosomal markers. Molecular Ecology, 19, 5281-5295.
54. Liechti F, (2006) Birds: Blowin' by the wind? Journal of Ornithology, 147, 202-211.
55. Liu Y, Keller I, Heckel G, (2011) Range-wide genetic population structure of common pochard (Aythya ferina): a potentially important vector of highly pathogenic avian influenza viruses. Ecology and Evolution, 1, 529-545.
56. Liu Y, Keller I, Heckel G, (2012) Breeding site fidelity and winter admixture in a long-distance migrant, the tufted duck (Aythya fuligula). Heredity, 109, 108-116.
57. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P, (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981-994. (Pubitemid 37474645)
58. Mesnick SL, Taylor BL, Archer FI, et al,. (2011) Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA. Molecular Ecology Resources, 11, 278-298.
59. Milligan BG, (2003) Maximum-likelihood estimation of relatedness. Genetics, 163, 1153-1167. (Pubitemid 36417955)
60. Miyabayashi Y, Mundkur T, (1999) Atlas of Key Sites for Anatidae in the East Asian Flyway. Wetlands International-Japan, Tokyo, and Wetlands International-Asia Pacific, Kuala Lumpur.
61. Morin PA, Luikart G, Wayne RK, (2004) SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution, 19, 208-216. (Pubitemid 38355800)
62. Nielsen R, Beaumont MA, (2009) Statistical inferences in phylogeography. Molecular Ecology, 18, 1034-1047.
63. Olsen B, Munster VJ, Wallensten A, Waldenström J, Osterhaus ADME, Fouchier RAM, (2006) Global patterns of influenza A virus in wild birds. Science, 312, 384-388.
64. Pardini AT, Jones CS, Noble LR, et al,. (2001) Sex-biased dispersal of great white sharks. Nature, 412, 139-140. (Pubitemid 32674698)
65. Peakall R, Smouse PE, (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295. (Pubitemid 43373825)
66. Peters JL, Zhuravlev Y, Fefelov I, Logie A, Omland KE, (2007) Nuclear loci and coalescent methods support ancient hybridization as cause of mitochondrial paraphyly between gadwall and falcated duck (Anas spp.). Evolution, 61, 1992-2006. (Pubitemid 47220929)
67. Peters JL, Zhuravlev YN, Fefelov I, Humphries EM, Omland KE, (2008) Multilocus phylogeography of a Holarctic duck: colonization of North America from Eurasia by gadwall (Anas strepera). Evolution, 62, 1469-1483. (Pubitemid 351754600)
68. Peters JL, McCracken KG, Pruett CL, et al,. (2012) A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato). Molecular Ecology, 21, 4563-4577.
69. Posada D, Crandall KA, (2001) Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution, 16, 37-45. (Pubitemid 32102347)
70. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959. (Pubitemid 30397141)
71. R Development Core Team (2009) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Available from http://www.R-project.org.
72. Reudink MW, Kyle CJ, Nocera JJ, Oomen RA, Green MC, Somers CM, (2011) Panmixia on a continental scale in a widely distributed colonial waterbird. Biological Journal of the Linnean Society, 102, 583-592.
73. Rhodes OE Jr, Smith LM, Chesser RK, (1995) Apportionment of genetic variance in migrating and wintering Mallards. Canadian Journal of Zoology, 73, 1182-1185.
74. Rhymer JM, (2006) Extinction by hybridization and introgression in anatine ducks. Acta Zoologica Sinica, 52 (Suppl), 583-585.
75. Rypien KL, Andras JP, Harvell CD, (2008) Globally panmictic population structure in the opportunistic fungal pathogen Aspergillus sydowii. Molecular Ecology, 17, 4068-4078.
76. Sacks BN, Moore M, Statham MJ, Wittmer HU, (2011) A restricted hybrid zone between native and introduced red fox (Vulpes vulpes) populations suggests reproductive barriers and competitive exclusion. Molecular Ecology, 20, 326-341.
77. Santure AW, Stapley J, Ball AD, Birkhead TR, Burke T, Slate J, (2010) On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs. Molecular Ecology, 19, 1439-1451.
78. Scott DA, Rose PM, (1996) Atlas of Anatidae Populations in Africa and Western Eurasia. Wetlands International Publication No. 41, Wetlands International, Wageningen, The Netherlands.
79. Selkoe KA, Toonen RJ, (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters, 9, 615-629.
80. Sherry ST, Ward MH, Kholodov M, et al,. (2001) DbSNP: the NCBI database of genetic variation. Nucleic Acids Research, 29, 308-311. (Pubitemid 32054478)
81. Si Y, Skidmore AK, Wang T, et al,. (2009) Spatio-temporal dynamics of global H5N1 outbreaks match bird migration patterns. Geospatial Health, 4, 65-78.
82. Smith LM, Burgoyne LA, (2004) Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper. BMC Ecology, 4, 4.
83. Stallknecht DE, Goekjian VH, Wilcox BR, Poulson RL, Brown JD, (2010) Avian influenza virus in aquatic habitats: what do we need to learn? Avian Diseases, 54, 461-465.
84. Templeton AR, (2010) Coalescent-based, maximum likelihood inference in phylogeography. Molecular Ecology, 19, 431-435.
85. Thompson AL, (1931) On 'abmigration' among the ducks, an anomaly shown by the results of bird-marking. Proceedings of the International Ornithological Congress, 7, 382-388.
86. Vignal A, Milan D, SanCristobal M, Eggen A, (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genetics Selection Evolution, 34, 275-305. (Pubitemid 34774107)
87. Wang J, (2011) Coancestry: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Molecular Ecology Resources, 11, 141-145.
88. Wang Y, Hey J, (2010) Estimating divergence parameters with small samples from a large number of loci. Genetics, 184, 363-379.
89. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y, (1992) Evolution and ecology of influenza A viruses. Microbiological Reviews, 56, 152-179.
90. Williams LM, Oleksiak MF, (2011) Ecologically and evolutionarily important SNPs identified in natural populations. Molecular Biology and Evolution, 28, 1817-1826.
91. Willing EM, Bentzen P, Van Oosterhout C, et al,. (2010) Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies. Molecular Ecology, 19, 968-984.
92. Zhang G, Shoham D, Gilichinsky D, Davydov S, Castello JD, Rogers SO, (2006) Evidence of influenza A virus RNA in Siberian lake ice. Journal of Virology, 80, 12229-12235. (Pubitemid 44904373)