Evolutionary change during experimental ocean acidification

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 17, 2013, Pages 6937-6942

  Pespeni, Melissa H ^a   Sanford, Eric ^b,c   Gaylord, Brian ^b,c   Hill, Tessa M ^b,c   Hosfelt, Jessica D ^b,c   Jaris, Hannah K ^a   LaVigne, Michèle ^b,c   Lenz, Elizabeth A ^b,c   Russell, Ann D ^b   Young, Megan K ^b,c   Palumbi, Stephen R ^a  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA DAVIS   (United States)

Author keywords

Adaptation; Environmental mosaic; Experimental evolution; Population genomics; RNA sequencing

Indexed keywords

CARBON DIOXIDE;

ACIDIFICATION; ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; BIOMINERALIZATION; ECOSYSTEM; ECOSYSTEM RESILIENCE; EVOLUTION; EXPERIMENTAL MODEL; HOMEOSTASIS; LARVAL DEVELOPMENT; LIPID METABOLISM; MOLECULAR DYNAMICS; MORPHOLOGY; NONHUMAN; OCEAN ACIDIFICATION; PRIORITY JOURNAL; SEA; STRONGYLOCENTROTUS;

ADAPTATION, BIOLOGICAL; ANIMALS; CARBON DIOXIDE; CLIMATE CHANGE; EVOLUTION, MOLECULAR; GENETIC VARIATION; HYDROGEN-ION CONCENTRATION; LARVA; METAGENOMICS; SEAWATER; STRONGYLOCENTROTUS PURPURATUS;

ECHINOIDEA; STRONGYLOCENTROTUS PURPURATUS;

EID: 84876835091     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1220673110     Document Type: Article

References (50)

1. Gattuso JP, Buddemeier RW (2000) Ocean biogeochemistry. Calcification and CO2. Nature 407(6802):311-313, 313.
2. Hönisch B, et al. (2012) The geological record of ocean acidification. Science 335(6072):1058-1063.
3. Gruber N, et al. (2012) Rapid progression of ocean acidification in the California Current System. Science 337(6091):220-223.
4. Kroeker KJ, Kordas RL, Crim RN, Singh GG (2010) Meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms. Ecol Lett 13(11): 1419-1434.
5. 2-induced ocean acidification. Geology 37(12):1131-1134.
6. Dupont S, Ortega-Martínez O, Thorndyke M (2010) Impact of near-future ocean acidification on echinoderms. Ecotoxicology 19(3):449-462.
7. Gaylord B, et al. (2011) Functional impacts of ocean acidification in an ecologically critical foundation species. J Exp Biol 214(Pt 15):2586-2594.
8. Hoegh-Guldberg O, et al. (2007) Coral reefs under rapid climate change and ocean acidification. Science 318(5857):1737-1742.
9. 2 problem. Annu Rev Mar Sci 1:169-192.
10. Harley CDG, et al. (2006) The impacts of climate change in coastal marine systems. Ecol Lett 9(2):228-241.
11. Kirkpatrick M, Barton NH (1997) Evolution of a species' range. Am Nat 150(1):1-23.
12. Hermisson J, Pennings PS (2005) Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169(4):2335-2352.
13. Lande R, Shannon S (1996) The role of genetic variation in adaptation and population persistence in a changing environment. Evolution 50(1):434-437.
14. Feely RA, Sabine CL, Hernandez-Ayon JM, Ianson D, Hales B (2008) Evidence for up-welling of corrosive "acidified" water onto the continental shelf. Science 320(5882): 1490-1492.
15. Jacobs DK, Haney TA, Louie KD (2004) Genes, diversity, and geologic process on the Pacific Coast. Annu Rev Earth Planet Sci 32(1):601-652.
16. Estes JA, Steinberg PD (1988) Predation, herbivory, and kelp evolution. Paleobiology 14(1):19-36.
17. Strathmann R (1978) Length of pelagic period in echinoderms with feeding larvae from the Northeast Pacific. J Exp Mar Biol Ecol 34(1):23-28.
18. Sodergren E, et al.; Sea Urchin Genome Sequencing Consortium (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science 314(5801):941-952.
19. Slotte T, et al. (2011) Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol Evol 3:1210-1219.
20. Hancock AM, et al. (2010) Colloquium paper: Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. Proc Natl Acad Sci USA 107(Suppl 2):8924-8930.
21. 2 on marine animals: From Earth history to global change. J Geophys Res 110(C9):C09S10.
22. 2-driven seawater acidification. J Exp Biol212(Pt 16):2579-2594.
23. O'Donnell MJ, et al. (2010) Ocean acidification alters skeletogenesis and gene expression in larval sea urchins. Mar Ecol Prog Ser 398:157-171.
24. 2 induced sea-water acidification impacts sea urchin larval development I: Elevated metabolic rates decrease scope for growth and induce developmental delay. Comp Biochem Physiol A Mol Integr Physiol 160(3):331-340.
25. Pavlidis P, Jensen JD, Stephan W, Stamatakis A (2012) A critical assessment of storytelling: gene ontology categories and the importance of validating genomic scans. Mol Biol Evol 29(10):3237-3248.
26. Livingston BT, et al. (2006) A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus. Dev Biol 300(1):335-348.
27. Wilt FH (2002) Biomineralization of the spicules of sea urchin embryos. Zoolog Sci 19(3):253-261.
28. Pespeni MH, Barney BT, Palumbi SR (2013) Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin. Evolution, 10.1111/evo.12036.
29. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12(12):1805-1814.
30. Plotkin JB, Kudla G (2011) Synonymous but not the same: The causes and consequences of codon bias. Nat Rev Genet 12(1):32-42.
31. Forte M, Satow Y, Nelson D, Kung C (1981) Mutational alteration of membrane phospholipid composition and voltage-sensitive ion channel function in Paramecium. Proc Natl Acad Sci USA 78(11):7195-7199.
32. Alberts B, et al. (2002) Molecular Biology of the Cell (Garland Science, New York), 4th Ed.
33. Dupont S, Havenhand J, Thorndyke W, Peck L, Thorndyke M (2008) Near-future level of CO2-driven ocean acidification radically affects larval survival and development in the brittlestar Ophiothrix fragilis. Mar Ecol Prog Ser 373:285-294.
34. 2/pH. J Exp Mar Biol Ecol 400(1-2):288-295.
35. Strathmann MF (1987) Reproduction and Development of Marine Invertebrates of the Northern Pacific Coast: Data and Methods for the Study of Eggs, Embryos, and Larvae (Univ of Washington Press, Seattle), pp 511-534.
36. Pespeni MH, Oliver TA, Manier MK, Palumbi SR (2010) Restriction Site Tiling Analysis: Accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays. Genome Biol 11(4):R44.
37. Graze RM, et al. (2012) Allelic imbalance in Drosophila hybrid heads: Exons, isoforms, and evolution. Mol Biol Evol 29(6):1521-1532.
38. Zhang K, et al. (2009) Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods 6(8):613-618.
39. Wang HY, et al. (2008) Complex genetic interactions underlying expression differences between Drosophila races: Analysis of chromosome substitutions. Proc Natl Acad Sci USA 105(17):6362-6367.
40. Heap GA, et al. (2010) Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum Mol Genet 19(1): 122-134.
41. Stumpp M, Dupont S, Thorndyke MC, Melzner F (2011) CO2 induced seawater acidification impacts sea urchin larval development II: Gene expression patterns in pluteus larvae. Comp Biochem Physiol A Mol Integr Physiol 160(3):320-330.
42. 2-driven acidification. J Exp Biol 214(Pt 8):1357-1368.
43. Hofmann GE, et al. (2011) High-frequency dynamics of ocean pH: A multi-ecosystem comparison. PLoS ONE 6(12):e28983.
44. Sunday JM, Crim RN, Harley CDG, Hart MW (2011) Quantifying rates of evolutionary adaptation in response to ocean acidification. PLoS ONE 6(8):e22881.
45. Pistevos JCA, Calosi P, Widdicombe S, Bishop JDD (2011) Will variation among genetic individuals influence species responses to global climate change? Oikos 120(5): 675-689.
46. Foo SA, Dworjanyn SA, Poore AGB, Byrne M (2012) Adaptive capacity of the habitat modifying sea urchin Centrostephanus rodgersii to ocean warming and ocean acidification: Performance of early embryos. PLoS ONE 7(8):e42497.
47. Haldane JBS (1957) The cost of natural selection. J Genet 55(3):511-524.
48. Moss RH, et al. (2010) The next generation of scenarios for climate change research and assessment. Nature 463(7282):747-756.
49. Smith MM, Cruz Smith L, Cameron RA, Urry LA (2008) The larval stages of the sea urchin, Strongylocentrotus purpuratus. J Morphol 269(6):713-733.
50. De Wit P, et al. (2012) The Simple Fool's Guide to population genomics via RNA-Seq: An introduction to high-throughput sequencing data analysis. Molecular Ecology Resources 12:1058-1067.