Genome scans detect consistent divergent selection among subtidal vs. intertidal populations of the marine angiosperm Zostera marina

Molecular Ecology

Volumn 16, Issue 24, 2007, Pages 5156-5157

  Oetjen, Katharina ^a   Reusch, Thorsten B H ^b  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^b UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

Divergent selection; EST; Genome scan; Microsatellite; Seagrass; Zostera marina

Indexed keywords

MAGNOLIOPHYTA; ZOSTERA MARINA;

EID: 37249047441     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03577.x     Document Type: Article

References (69)

1. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Research, 12, 1805 1814.
2. Applied Biosystems (1999, 2001) genescan v.3.7 and Genotyper v.3.7. Software packages for fragment analysis. Foster City, USA.
3. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969 980.
4. Beaumont MA, Nichols RA (1996) Evaluating Loci for Use in the Genetic Analysis of Population Structure. Proceedings of the Royal Society, Series B: Biology Sciences, 263, 1619 1626.
5. Bockelmann AC, Reusch TBH, Bijlsma R, Bakker JP (2003) Habitat differentiation vs. isolation-by-distance: the genetic population structure of Elymus athericus. European salt marshes. Molecular Ecology, 12, 505 515.
6. Bohonak AJ (2002) IBD (Isolation By Distance): a program for analyses of isolation by distance. Journal of Heredity, 93, 153 154.
7. Bonin A, Taberlet P, Miaud C, Pompanon F (2006) Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Molecular Biology and Evolution, 23, 773 783.
8. Bouck A, Vision T (2007) The molecular ecologist's guide to expressed sequence tags. Molecular Ecology, 16, 907 924.
9. Campbell D, Bernatchez L (2004) Genomic scan using AFLP markers as a means to assess the role of directional selection in the divergence of sympatric whitefish ecotypes. Molecular Biology and Evolution, 21, 945 956.
10. Casa AM, Mitchell SE, Hamblin MT et al 2005) Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. Theoretical and Applied Genetics, 111, 23 30.
11. Cherdsak L, Ritland CE, El-Kassaby YA, Ritland K (2004) Single-copy, species-tranferable microsatellite markers developed from loblolly pine ESTs. Theoretical and Applied Genetics, 109, 361 369.
12. Cho YG, Ishii T, Temnykh S et al 2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics, 100, 713 722.
13. Costanza R, d'Arge R, de Groot R et al 1997) The value of the world's ecosystem services and natural capital. Nature, 387, 253 260.
14. Dieringer D, Schlötterer C (2003) microsatellite analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167 169.
15. Excoffier L, Laval G, Schneider S (2005) arlequin, (Version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
16. Harley CDG, Hughes AR, Hultgren KM et al 2006) The impacts of climate change in coastal marine systems. Ecology Letters, 9, 228 241.
17. den Hartog C (1970) The seagrasses of the world. Verhandlingen Koninglijk Nederlandse Akademie Wetenschapen Afdeling Natuurkunde, II (59 1 275.
18. Hemminga M, Duarte C (2000) Seagrass Ecology. Cambridge University Press, Cambridge.
19. Ihle S, Ravaoarimanana I, Thomas M, Tautz D (2006) An analysis of signatures of selective sweeps in natural populations of the house mouse. Molecular Biology and Evolution, 23, 790 797.
20. IPCC (2001) Climate Change 2001: the Scientific Basis - Contribution of Working Group I to the Third Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge.
21. Jacobs RPWM (1982) Reproductive strategies of two seagrass species (Zostera Marina and Z. noltii) along west European coasts. In : Studies on Aquatic Vascular Plants (eds Symoens JJ, Hooper SS, Compére P), pp. 150 155. Royal Botanical Society of Belgium, Brussels.
22. Jensen J, Bohonak AJ, Kelley SK (2005) Isolation by distance Web service. BMC Genetics, 6, 13.
23. Jump AS, Hunt JM, Martinez-Izquierdo JA, Penuelas J (2006) Natural selection and climate change: temperature-linked spatial and temporal trends in gene frequency in Fagus sylvatica. Molecular Ecology, 15, 3469 3480.
24. Kane NC, Rieseberg LH (2007) Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in common sunflower, Helianthus annuus. Genetics, 175, 1823 1834.
25. Kauer MO, Dieringer D, Schlotterer C (2003) A microsatellite variability screen for positive selection associated with the 'Out of Africa' habitat expansion of Drosophila melanogaster. Genetics, 165, 1137 1148.
26. Kayser M, Brauer S, Stoneking M (2003) A genome scan to detect candidate regions influenced by local natural selection in human populations. Molecular Biology and Evolution, 20, 893 900.
27. Larsson LC, Laikre L, Palm S et al 2007) Concordance of allozyme and microsatellite differentiation in a marine fish, but evidence of selection at a microsatellite locus. Molecular Ecology, 16, 1135 1147.
28. Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Genetics, 74, 175 195.
29. Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Molecular Biology and Evolution, 21, 991 1007.
30. 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.
31. Luu D-T, Maurel C (2005) Aquaporins in a challenging environment: molecular gears for adjusting plant water status. Plant, Cell and Environment, 28, 85 96.
32. Moran MD (2003) Arguments for rejecting the sequential Bonferroni in ecological studies. Oikos, 100, 403 405.
33. Murray MC, Hare MP (2006) A genomic scan for divergent selection in a secondary contact zone between Atlantic and Gulf of Mexico oysters, Crassostrea virginica. Molecular Ecology, 15, 4229 4242.
34. Nielsen EE, Hansen MM, Meldrup D (2006) Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms. Molecular Ecology, 15, 3219 3229.
35. Oetjen K, Reusch TBH (2007) Identification and characterization of 14 polymorphic EST-derived microsatellites in eelgrass (Zostera marina). Molecular Ecology Notes, 7, 777 780.
36. Orr HA (1998) The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. Evolution, 52, 935 949.
37. Pashley CH, Ellis JR, McCauley DE, Burke JM (2006) EST databases as a source for molecular markers: lessons from Helianthus. Journal of Heredity, 97, 381 388.
38. Payseur BA, Cutter AD, Nachman MW (2002) Searching for Evidence of Positive Selection in the Human Genome Using Patterns of Microsatellite Variability. Molecular Biology and Evolution, 19, 1143 1153.
39. Perry AL, Low PJ, Ellis JR, Reynolds JD (2005) Climate change and distribution shifts in marina fishes. Science, 308, 1912 1915.
40. Reise K (1985) Tidal Flat Ecology: an Experimental Approach to Species Interactions. Springer Verlag, Berlin.
41. Reise K, Herre E, Sturm M (1989) Historical changes in the benthos of the Wadden Sea around the island of Sylt in the North Sea. Helgoländer Wissenschaftliche Meeresuntersuchungen, 43, 417 433.
42. Reise K, Jager Z, De Jong D, Van Katwijk M, Schanz A (2005) Seagrass. In. Wadden Sea Quality Status Report 2004. Wadden Sea Ecosystem no. 19 (eds Essink K, Dettmann C, Farke H, Laursen K, Lüerßen G, Marencic H, Wiersinga W pp. 201 207. Common Wadden Sea Secretariat, Wilhelmshaven.
43. Reusch TBH (2000) Five microsatellite loci in eelgrass Zostera marina and a test of cross-species amplification in Z. noltii and IX. japonica. Molecular Ecology Notes, 9, 371 373.
44. Reusch TBH (2002) Microsatellites reveal high population connectivity in eelgrass (Zostera marina) in two contrasting coastal areas. Limnology and Oceanography, 47, 78 85.
45. Reusch TBH, Boström C, Stam WT, Olsen JL (1999a) An ancient eelgrass clone in the Baltic Sea. Marine Ecology Progress Series, 183, 301 304.
46. Reusch TBH, Stam WT, Olsen JL (1999b) Microsatellite loci in eelgrass Zostera marina reveal marked polymorphism within and among populations. Molecular Ecology, 8, 317 321.
47. Reusch TBH, Wegner KM, Kalbe M (2001) Rapid genetic divergence in postglacial populations of threespine stickleback (Gasterosteus aculeatus): the role of habitat type, drainage and geographical proximity. Molecular Ecology, 10, 2435 2445.
48. Robertson A (1975) Gene frequency distributions as a test of selective neutrality. Genetics, 81, 775 785.
49. Schlötterer C (2002) A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics, 160, 753 763.
50. Schmidt PS, Rand DM (2001) Adaptive maintenance of genetic polymorphism in an intertidal barnacle: habitat- and life-stage-specific survivorship of MPI genotypes. Evolution, 55, 1336 1344.
51. Scotti-Saintagne C, Mariette S, Porth I et al 2004) Genome scanning for interspecific differentiation between two closely related oak species Quercus robur L. & Q petraea (Matt.) Liebl. Genetics, 168, 1615 1626.
52. Sheng L (2003) Protein phosphatases in plants. Annual Review of Plant Biology, 54, 63 92.
53. Short FT, Wyllie-Escheverria S (1996) Natural and human-induced disturbance of seagrasses. Environmental Conservation, 25, 17 27.
54. Smith JM, Haigh J (1974) Hitch-hiking effect of a favorable gene. Genetical Research, 23, 23 35.
55. Storz JF (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology, 14, 671 688.
56. Thornton KR, Jensen JD (2007) Controlling the false-positive rate in multilocus genome scans for selection. Genetics, 175, 737 750.
57. Van Katwijk MM (2000) Possibilities for Restoration of Zostera marina Beds in the Dutch Wadden Sea. PhD Thesis, University of Nijmegen, The Netherlands.
58. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535 538.
59. Vasemagi A, Primmer CR (2005) Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Molecular Ecology, 14, 3623 3642.
60. Vasemagi A, Nilsson J, Primmer CR (2005) Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Molecular Biology and Evolution, 22, 1067 1076.
61. Vigouroux Y, McMullen M, Hittinger CT et al 2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proceedings of the National Academy of Sciences USA, 99, 9650 9655.
62. Vitalis R, Dawson K, Boursot P (2001) Interpretation of Variation Across Marker Loci as Evidence of Selection. Genetics, 158, 1811 1823.
63. Vitalis R, Dawson K, Boursot P, Belkhir K (2003) DetSel 1.0: a computer program to detect markers responding to selection. Journal of Heredity, 94, 429 431.
64. Voight BF, Kudaravalli S, Wen XQ, Pritchard JK (2006) A map of recent positive selection in the human genome (Vol. 4, pg 154, 2006). Plos Biology, 4, 659 659.
65. Waycott M, Procaccini G, Les D, Reusch TBH (2006) Seagrass evolution, ecology and conservation: a genetic perspective. In : Seagrasses: Biology, Ecology and Conservation (eds Larkum AWD, Orth RJ, Duarte CM pp. 25 50. Springer, Dordrecht, The Netherlands.
66. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
67. Wilding CS, Butlin RK, Grahame J (2001) Differential gene exchange between parapatric morphs of Littorina saxatilis detected using AFLP markers. Journal of Evolutionary Biology, 14, 611 619.
68. Woodhead M, Russell J, Squirrell J et al 2005) Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions. Molecular Ecology, 14, 1681 1695.
69. Yatabe Y, Kane NC, Scotti-Saintagne C, Rieseberg LH (2007) Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris. Genetics, 175, 1883 1893.