Transcriptome changes after genome-wide admixture in invasive sculpins (Cottus)

Molecular Ecology

Volumn 21, Issue 19, 2012, Pages 4797-4810

  Czypionka, Till ^a   Cheng, Jie ^a   Pozhitkov, Alexander ^a,b   Nolte, Arne W ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

adaptation; hybridization; invasive species; microarray calibration; transgressive segregation

Indexed keywords

TRANSCRIPTOME;

ANIMAL; ARTICLE; BELGIUM; CLASSIFICATION; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENETICS; GERMANY; HYBRIDIZATION; INTRODUCED SPECIES; MOLECULAR GENETICS; PERCIFORMES; POPULATION GENETICS;

ANIMALS; BELGIUM; EXPRESSED SEQUENCE TAGS; GENETICS, POPULATION; GERMANY; HYBRIDIZATION, GENETIC; INTRODUCED SPECIES; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PERCIFORMES; TRANSCRIPTOME;

COTTIDAE; COTTUS;

EID: 84867101772     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05645.x     Document Type: Article

References (52)

1. Abbott RJ, Hegarty MJ, Hiscock SJ, Brennan AC, (2010) Homoploid hybrid speciation in action. Taxon, 59, 1375-1386.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
3. Barton NH, (2001) The role of hybridization in evolution. Molecular Ecology, 10, 551-568. (Pubitemid 32406342)
4. Bernatchez L, Renaut S, Whiteley AR, et al. (2010) On the origin of species: insights from the ecological genomics of lake whitefish. Philosophical Transactions of the Royal Society B: Biological Sciences, 365, 1783-1800.
5. Bougas B, Granier S, Audet C, Bernatchez L, (2010) The transcriptional landscape of cross-specific hybrids and its possible link with growth in Brook Charr (Salvelinus fontinalis Mitchill). Genetics, 186, 97-107.
6. Buerkle CA, Morris RJ, Asmussen MA, Rieseberg LH, (2000) The likelihood of homoploid hybrid speciation. Heredity, 84, 441-451. (Pubitemid 30400031)
7. Charlesworth D, Willis JH, (2009) The genetics of inbreeding depression. Nature Reviews Genetics, 10, 783-796.
8. Cheviron ZA, Whitehead A, Brumfield RT, (2008) Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient. Molecular Ecology, 17, 4556-4569.
9. Conesa A, Götz S, García-Gõmez JM, Terol J, Talõn M, Robles M, (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676. (Pubitemid 41264107)
10. Domazet-Lošo T, Tautz D, (2010) A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature, 468, 815-818.
11. Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Research, 30, 207-210. (Pubitemid 34679544)
12. Eliason EJ, Clark TD, Hague MJ, et al. (2011) Differences in thermal tolerance among Sockeye Salmon populations. Science, 332, 109-112.
13. Englbrecht CC, Freyhof J, Nolte AW, Rassmann K, Schliewen U, Tautz D, (2000) Phylogeography of the bullhead Cottus gobio (Pisces: Teleostei: Cottidae) suggests a pre-pleistocene origin of the major central European populations. Molecular Ecology, 9, 709-722. (Pubitemid 30354646)
14. Fisher WE, Berger DH, (2003) Angiogenesis and antiangiogenic strategies in pancreatic cancer. International Journal of Gastrointestinal Cancer, 33, 79-88.
15. Freyhof J, Kottelat M, Nolte AW, (2005) Taxonomic diversity of European Cottus with description of eight new species (Teleostei: Cottidae). Ichthyological Exploration of Freshwaters, 16, 107-172. (Pubitemid 40864422)
16. Hegarty MJ, Barker GL, Brennan AC, Edwards KJ, Abbott RJ, Hiscock SJ, (2009) Extreme changes to gene expression associated with homoploid hybrid speciation. Molecular Ecology, 18, 877-889.
17. Jeukens J, Renaut S, St-Cyr J, Nolte AW, Bernatchez L, (2010) The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Molecular Ecology, 19, 5389-5403.
18. Knapen D, Knaepens G, Bervoets L, Taylor MI, Eens M, Verheyen E, (2003) Conservation units based on mitochondrial and nuclear DNA variation among European bullhead populations (Cottus gobio L., 1758) from Flanders, Belgium. Conservation Genetics, 4, 129-140. (Pubitemid 36639629)
19. Lai Z, Gross BL, Zou Y, Andrews J, Rieseberg LH, (2006) Microarray analysis reveals differential gene expression in hybrid sunflower species. Molecular Ecology, 15, 1213-1227.
20. Laikre L, Schwartz MK, Waples RS, Ryman N, (2010) Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals. Trends in Ecology & Evolution, 25, 520-529.
21. Landry CR, Hartl DL, Ranz JM, (2007) Genome clashes in hybrids: insights from gene expression. Heredity, 99, 483-493. (Pubitemid 350006183)
22. Larsen PF, Schulte PM, Nielsen EE, (2011) Gene expression analysis for the identification of selection and local adaptation in fishes. Journal of Fish Biology, 78, 1-22.
23. Leong HS, Kipling D, (2009) Text-based over-representation analysis of microarray gene lists with annotation bias. Nucleic Acids Research, 37, e79.
24. Mallet J, (2007) Hybrid speciation. Nature, 446, 279-283. (Pubitemid 46426165)
25. Mavárez J, Salazar CA, Bermingham E, Salcedo C, Jiggins CD, Linares M, (2006) Speciation by hybridization in Heliconius butterflies. Nature, 441, 868-871.
26. Mavárez J, Audet C, Bernatchez L, (2009) Major disruption of gene expression in hybrids between young sympatric anadromous and resident populations of brook charr (Salvelinus fontinalis Mitchill). Journal of Evolutionary Biology, 22, 1708-1720.
27. Michalak P, Noor MAF, (2003) Genome-wide patterns of expression in Drosophila pure species and hybrid males. Molecular Biology and Evolution, 20, 1070-1076. (Pubitemid 36792823)
28. Michalak P, Noor MAF, (2004) Association of misexpression with sterility in hybrids of Drosophila simulans and D. mauritiana. Journal of Molecular Evolution, 59, 277-282. (Pubitemid 39128350)
29. Moczek AP, Sultan S, Foster S, et al. (2011) The role of developmental plasticity in evolutionary innovation. Proceedings of the Royal Society B: Biological Sciences, 278, 2705-2713.
30. Nolte AW, Tautz D, (2010) Understanding the onset of hybrid speciation. Trends in Genetics, 26, 54-58.
31. Nolte AW, Freyhof J, Stemshorn KC, Tautz D, (2005) An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups. Proceedings of the Royal Society B: Biological Sciences, 272, 2379-2387. (Pubitemid 41579364)
32. Nolte AW, Freyhof J, Tautz D, (2006) When invaders meet locally adapted types: rapid moulding of hybrid zones between sculpins (Cottus, Pisces) in the Rhine system. Molecular Ecology, 15, 1983-1993. (Pubitemid 43725680)
33. Nolte AW, Renaut S, Bernatchez L, (2009) Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation. BMC Evolutionary Biology, 9, 59.
34. Normandeau E, Hutchings JA, Fraser DJ, Bernatchez L, (2009) Population-specific gene expression responses to hybridization between farm and wild Atlantic salmon. Evolutionary Applications, 2, 489-503.
35. Pickrell JK, Marioni JC, Pai AA, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464, 768-772.
36. Pörtner HO, Knust R, (2007) Climate change affects marine fishes through the oxygen limitation of thermal tolerance. Science, 315, 95-97. (Pubitemid 46196986)
37. Pozhitkov A, Noble PA, Domazet-Lošo T, et al. (2006) Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research, 34, e66.
38. R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org
39. Renaut S, Nolte AW, Bernatchez L, (2009) Gene expression divergence and hybrid misexpression between lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Biology and Evolution, 26, 925-936.
40. Rieseberg LH, Archer MA, Wayne RK, (1999) Transgressive segregation, adaptation and speciation. Heredity, 83, 363-372. (Pubitemid 29511313)
41. Rieseberg LH, Widmer A, Arntz AM, Burke B, (2003a) The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 358, 1141-1147. (Pubitemid 36774907)
42. Rieseberg LH, Raymond O, Rosenthal DM, et al. (2003b) Major ecological transitions in wild sunflowers facilitated by hybridization. Science, 301, 1211-1216. (Pubitemid 37052203)
43. Seehausen O, (2004) Hybridization and adaptive radiation. Trends in Ecology & Evolution, 19, 198-207. (Pubitemid 38355799)
44. Seehausen O, van Alphen JJM, Witte F, (1997) Cichlid fish diversity threatened by eutrophication that curbs sexual selection. Science, 277, 1808-1811. (Pubitemid 27449190)
45. Stelkens R, Seehausen O, (2009) Genetic distance between species predicts novel trait expression in their hybrids. Evolution, 63, 884-897.
46. Stelkens RB, Schmid C, Selz O, Seehausen O, (2009) Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish. BMC Evolutionary Biology, 9, 283.
47. Stemshorn KC, Reed FA, Nolte AW, Tautz D, (2011) Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.). Molecular Ecology, 20, 1475-1491.
48. Storey JD, (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society: Series B: Statistical Methodology, 64, 479-498.
49. Taylor EB, Boughman JW, Groenenboom M, Sniatynski M, Schluter D, Gow JL, (2006) Speciation in reverse: morphological and genetic evidence of the collapse of a three-spined stickleback (Gasterosteus aculeatus) species pair. Molecular Ecology, 15, 343-355.
50. Volckaert F, Hänfling B, Hellemanns B, Carvalho G, (2002) Timing of the population dynamics of bullhead Cottus gobio (Teleostei: Cottidae) during the Pleistocene. Journal of Evolutionary Biology, 15, 930-944. (Pubitemid 35326125)
51. Wu H, (2010). maanova: Tools for analyzing microarray experiments. R package version 1.20.0. Modified by Yang H, Sheppard K, with ideas from Churchill G, Kerr K and Cui X. http://CRAN.R-project.org/package=maanova
52. Xia Q, Cheng D, Duan J, et al. (2007) Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori. Genome Biology, 8, R162.