A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

Molecular Ecology Resources

Volumn 13, Issue 4, 2013, Pages 706-714

  Pujolar, J M ^a   Jacobsen, M W ^a   Frydenberg, J ^a   Als, T D ^b   Larsen, P F ^c   Maes, G E ^d,e   Zane, L ^f   Jian, J B ^g   Cheng, L ^g   Hansen, M M ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c Kopenhagen Fur   (Denmark)

^d UNIVERSITY OF LEUVEN   (Belgium)

^e JAMES COOK UNIVERSITY   (Australia)

^f UNIVERSITY OF PADOVA   (Italy)

^g BGI SHENZHEN   (China)

Author keywords

Effective population size; Population genomics; RAD sequencing; SNP discovery

Indexed keywords

ANGUILLA (FISH); ANIMAL; ARTICLE; BIOLOGY; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANGUILLA; ANIMALS; COMPUTATIONAL BIOLOGY; GENOME; GENOMICS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

ANGUILLA ANGUILLA;

EID: 84879420457     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12117     Document Type: Article

References (57)

1. Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nature Reviews Genetics, 11, 697-709.
2. 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.
3. Baird NA, Etter PD, Atwood TS, et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3, e3376.
4. Ball AD, Stapley J, Dawson SA, Birkhead TR, Burke T, Slate J (2010) A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics, 11, 218.
5. Barchi L, Lanteri S, Acquadro A, Vale G, Toppino L, Rotino GL (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics, 12, 304.
6. Bonhommeau S, Chassot E, Rivot E (2008) Fluctuations in European eel (Anguilla anguilla) recruitment resulting from environmental changes in the Sargasso Sea. Fisheries Oceanography, 17, 32-44.
7. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution, 18, 249-256.
8. Bruneaux M, Johnston SE, Herczeg G et al. (2013) Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach. Molecular Ecology, 22, 565-582.
9. Castaño-Sanchez C, Smith TPL, Wiedmann RP et al. (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics, 10, 559.
10. Catchen JM, Amores A, Hohenlohe PA, Cresko WA, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1, 171-182.
11. Coppe A, Pujolar JM, Maes GE et al. (2010) Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics, 11, 635.
12. ST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species. Molecular Ecology, 22, 1763-1776.
13. Davey JW, Hohenlohe PA, Etter PD, et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
14. Di Rienzo A, Peterson AC, Garza JC et al. (1994) Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America, 91, 3166-3170.
15. Ellison CE, Hall C, Kowbel D et al. (2011) Population genomics and local adaptation in wild isolates of a model microbial organism. Proceedings of the National Academy of Sciences of the United States of America, 107, 2831-2837.
16. Elshire RJ, Glaubitz JC, Sun Q et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379.
17. Emerson KJ, Merz CR, Catchen JM et al. (2010) Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America, 107, 16196-16200.
18. Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE, 6, e18561.
19. Friedland KD, Miller MI, Knights B (2007) Oceanic changes in the Sargasso Sea and declines in recruitment of the European eel. ICES Journal of Marine Science, 64, 519-530.
20. Gagnaire PA, Normandeau E, Côté C et al. (2012) The genetic consequences of spatially varying selection in the panmictic American eel (Anguilla rostrata). Genetics, 190, 725-736.
21. Hansen MM, Olivieri I, Waller DM et al. (2012) Monitoring adaptive genetic responses to environmental change. Molecular Ecology, 21, 1311-1329.
22. Hauser L, Baird M, Hilborn R, Seeb LW, Seeb JE (2011) An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Molecular Ecology Resources, 11, 150-161.
23. Helyar SJ, Hemmer-Jansen J, Bekkevold D et al. (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources, 11, 123-136.
24. Henkel CV, Burgerhout E, Danielle L et al. (2012) Primitive duplicate hox clusters in the European eel's genome. PLoS ONE, 7, e32231.
25. Hess J, Matala AP, Narum SR (2011) Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of chinook salmon in the Columbia River Basin. Molecular Ecology Resources, 11, 137-149.
26. Hodgkinson A, Ladoukakis E, Eyre-Walker A (2009) Cryptic variation in the human mutation rate. PLoS Biology, 7, e10000027.
27. Hohenlohe PA, Basshan S, Etter PD, Stiffler N, Johnson EA, Cresko WA (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics, 6, e1000862.
28. Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westlope cutthroat trout. Molecular Ecology Resources, 11, 117-122.
29. ICES (2011) Report of the Joint EIFAAC/ICES Working Group on Eels (WGEEL), 5-9 September 2011, Lisbon, Portugal. ICES CM 2011/ACOM:18. International Council for the Exploration of the Seas, Copenhagen, Denmark.
30. Jones FC, Grabherr MG, Chan YF et al. (2012a) The genomics basis of adaptive evolution in threespine sticklebacks. Nature, 484, 55-61.
31. Jones FC, Chan YF, Schmutz M et al. (2012b) A genome-wide SNP genotyping array reveals patterns of local and repeated species-pair divergence in sticklebacks. Current Biology, 22, 83-90.
32. Knights B (2003) A review of the possible impacts of long-term oceanic and climatic changes and fishing mortality on recruitment of anguillid eels of the Northern hemisphere. Science of the Total Environment, 310, 237-244.
33. Kuhner MK (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22, 768-770.
34. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.
35. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction-site associated DNA (RAD) markers. Genome Research, 17, 240-248.
36. Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution, 19, 208-216.
37. Namroud MC, Beaulieu J, Juge N, Larouche J, Bousquet J (2008) Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Molecular Ecology, 17, 3599-3613.
38. Nielsen EE, Hansen MM (2008) Waking the dead: the value of population genetic analyses of historical samples. Fish and Fisheries, 9, 450-461.
39. Peterson BK, Weber JN, Kay EH et al. (2012) Double Digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7, e37135.
40. Pujolar JM, Maes GE, Van Houdt JK, Zane L (2008) Isolation and characterization of expressed sequence tag-linked microsatellite loci for the European eel, Anguilla anguilla. Molecular Ecology Resources, 9, 233-235.
41. Pujolar JM, Bevacqua D, Cappocioni F, Ciccotti E, De Leo GA, Zane L (2011) No apparent genetic bottleneck in the demographically declining European eel using molecular genetics and forward-time simulations. Conservation Genetics, 12, 813-825.
42. Pujolar JM, Marino IAM, Milan M et al. (2012) Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel. BMC Genomics, 13, 507.
43. Scaglione S, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus. BMC Genomics, 13, 3.
44. Seeb JE, Carvalho GR, Hauser L, Niash K, Roberts S, Seeb LW (2011) Single-nucleotide polymorphism (SNP) discovery and application of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11, 1-8.
45. Storz JF, Beaumont MA (2002) Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution, 56, 154-166.
46. Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437-460.
47. van den Thillart G, Rankin JC, Dufour S (2009) Spawning migration of the European eel: reproduction index, a useful tool for conservation management. Springer, Dordecht, The Netherlands.
48. Tomkiewicz J (2012) Reproduction of European eel in aquaculture (REEL): consolidation and new production methods. DTU Aqua Report No 249-2012. National Institute of Aquatic Resources, Technical University of Denmark, 47 p.
49. Turner TL, Han MW, Nuzhdin SV (2005) Genomic islands of speciation in Anopheles gambiae. PLoS Biology, 3, e285.
50. Turner TL, Levine MT, Eckert ML, Begun DJ (2008) Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics, 179, 455-473.
51. Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV (2010) Population resequencing reveals local adaptation in Arabidopsis lyrata to serpentine soils. Nature Genetics, 42, 260-263.
52. Van Bers NEM, Van Oers K, Kerstens HHD (2010) Genome-wide SNP detection in the great tit Parus major using high throughtput sequencing. Molecular Ecology, 19, 89-99.
53. Wagner CE, Keller I, Wittwer S et al. (2012) Genome-wide RAD sequence data provide unprecedented resolution in species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22, 787-798.
54. Waples RS (2005) Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Molecular Ecology, 14, 3335-3352.
55. Wielgoss S, Wirth T, Meyer A (2008) Isolation and characterization of 12 dinocleotide microsatellites in the European eel, Anguilla anguilla, and tests for amplification in other species of eels. Molecular Ecology Resources, 8, 1382-1385.
56. 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.
57. Wirth T, Bernatchez L (2003) Decline of North Atlantic eels: a fatal synergy? Proceedings of the National Academy of Sciences of the United States of America, 270, 681-688.