BACKGROUND: Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments. The nature of divergences between co-occurring sympatric species, factors contributing to reproductive isolation and modes of genome evolution is a much debated topic in evolutionary biology addressed by various experimental tools. To the best of our knowledge, nobody approached this field using molecular cytogenetics. We examined chromosomes and genomes of one postglacial species pair, sympatric European winter-spawning Coregonus albula and the local endemic dwarf-sized spring-spawning C. fontanae, both originating in Lake Stechlin. We have employed molecular cytogenetic tools to identify the genomic differences between the two species of the sympatric pair on the sub-chromosomal level of resolution. RESULTS: Fluorescence in situ hybridization (FISH) experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) between C. albula and C. fontanae genomes. In C. fontanae, up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C. albula only 8-10 chromosomes possessed these genes. To determine mechanisms how such extensive genome alternation might have arisen, a PCR screening for retrotransposons from genomic DNA of both species was performed. The amplified retrotransposon Rex1 was used as a probe for FISH mapping onto chromosomes of both species. These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region of one or two acrocentric chromosomes in both species. CONCLUSION: We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis. We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently affecting recombination rates in both genomes, thus, leading to a rapid genome divergence. We attribute these extensive genome re-arrangements associated with speciation event to stress-induced retrotransposons (re)activation. Such causal interplay between genome differentiation, retrotransposons (re)activation and environmental conditions may become a topic to be explored in a broader genomic context in future evolutionary studies.

Laboratory of Fish Genetics Institute of Animal Physiology and Genetics Czech Academy of Sciences Rumburská 89 277 21 Liběchov Czech Republic

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Cristescu ME, Adamowicz SJ, Vaillant JJ, Haffner DG. Ancient lakes revisited: from the ecology to the genetics of speciation. Mol Ecol. 2010;19:4837–4851. doi: 10.1111/j.1365-294X.2010.04832.x. PubMed DOI

Schluter D. Ecological speciation in postglacial fishes. Philos T Roy Soc B. 1996;351:807–814. doi: 10.1098/rstb.1996.0075. DOI

Nelson JS. Fishes of the world. 4. Hoboken, NJ: John Wiley & Sons; 2006.

Bodaly RA, Vuorinen J, Ward RD, Luczynski M, Reist JD. Genetic comparison of new and old world coregonid fishes. J Fish Biol. 1991;38:37–51. doi: 10.1111/j.1095-8649.1991.tb03089.x. DOI

Hudson AG, Vonlanthen P, Seehausen O. Rapid parallel adaptive radiations from a single hybridogenetic ancestral population. P Roy Soc B-Biol. 2011;278:58–66. doi: 10.1098/rspb.2010.0925. PubMed DOI PMC

Mehner T, Pohlmann K, Elkin C, Monaghan MT, Nitz B, Freyhof J. Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (coregonus albula complex, teleostei, coregonidae) BMC Evol Biol. 2010;10:85. doi: 10.1186/1471-2148-10-85. PubMed DOI PMC

Douglas MR, Brunner PC, Bernatchez L. Do assemblages of coregonus (teleostei: salmoniformes) in the central alpine region of Europe represent species flocks? Mol Ecol. 1999;8:589–603. doi: 10.1046/j.1365-294x.1999.00581.x. DOI

Kottelat M, Jörg F. Handbook of European Freshwater Fishes. Cornol, Switzerland: Publications Kottelat; 2007.

Vonlanthen P, Roy D, Hudson AG, Largiader CR, Bittner D, Seehausen O. Divergence along a steep ecological gradient in lake whitefish (coregonus sp.) J Evolution Biol. 2009;22:498–514. doi: 10.1111/j.1420-9101.2008.01670.x. PubMed DOI

Taylor EB. Species pairs of north temperate freshwater fishes: evolution, taxonomy, and conservation. Rev Fish Biol Fisher. 1999;9:299–324. doi: 10.1023/A:1008955229420. DOI

Vuorinen J, Himberg M, Lankinen P. Genetic differentiation in coregonus albula (salmonidae) populations in Finland. Hereditas. 1981;94:113–121.

Hudson AG, Vonlanthen P, Müller R, Seehausen O. Review: the geography of speciation and adaptive radiation in coregonines. Adv Limnol. 2007;60:111–146.

Phillips R, Ráb P. Chromosome evolution in the salmonidae (pisces): an update. Biol Rev. 2001;76:1–25. doi: 10.1017/S1464793100005613. PubMed DOI

Quimseyh MB. Evolution of number and morphology of mammalian chromosomes. J Hered. 1994;85:455–465. PubMed

Schulz M, Freyhof J. Coregonus fontanae, a new spring-spawning Cisco from lake stechlin, northern Germany (salmoniformes: coregonidae) Ichthyol Explor Fresh. 2003;14:209–216.

Ohlberger J, Mehner T, Staaks G, Hoelke F. Is ecological segregation in a pair of sympatric coregonines supported by divergent feeding efficiencies? Can J Fish Aquat Sci. 2008;65:2105–2113. doi: 10.1139/F08-120. DOI

Jankun M, Martinez P, Pardo BG, Kirtiklis L, Rab P, Rabova M, Sanchez L. Ribosomal genes in coregonid fishes (coregonus lavaretus, C. Albula and C. Peled) (salmonidae): single and multiple nucleolus organizer regions. Heredity. 2001;87:672–679. doi: 10.1046/j.1365-2540.2001.00964.x. PubMed DOI

Schulz M, Freyhof J, Saint-Laurent R, Østbye K, Mehner T, Bernatchez L. Evidence for independent origin of two spring-spawning ciscoes (Salmoniformes: Coregonidae) in Germany. J Fish Biol. 2006;68:119–135. doi: 10.1111/j.0022-1112.2006.01039.x. DOI

Swarzacher HG, Wachtler F. The nucleolus. Anat Embryol. 1993;188:515–536. PubMed

Wachtler F, Stahl A. The nucleolus: a structural and functional interpretation. Micron. 1993;24:473–505. doi: 10.1016/0968-4328(93)90026-W. DOI

Moss T, Stefanovsky VY. Promotion and regulation of ribosomal transcription in eukaryotes by RNA polymerase I. Prog Nucleic Acids Res Mol Biol. 1994;50:25–66. PubMed

Wang S, Zhao M, Li T. Complete sequence of the 10.3 kb silkworm attacus ricini rDNA repeat,determination of the transcriptional initiation site and functional analysis of the intergenic spacer. DNA Seq. 2003;14:95–101. PubMed

Hillis DM, Dixon MT. Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol. 1991;66:411–453. doi: 10.1086/417338. PubMed DOI

Volff J-N, Körting C, Schartl M. Multiple lineages of the non-LTR retrotransposon Rex1 with varying success in invading fish genomes. Mol Biol Evol. 2000;17:1673–1684. doi: 10.1093/oxfordjournals.molbev.a026266. PubMed DOI

Cioffi MB, Martins C, Bertollo LA. Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolution in fish. BMC Evol Biol. 2010;10:271. doi: 10.1186/1471-2148-10-271. PubMed DOI PMC

Wong LH, Andy Choo KH. Evolutionary dynamics of transposable elements at the centromere. Trends Genet. 2004;20:611–616. doi: 10.1016/j.tig.2004.09.011. PubMed DOI

Teixeira WG, Ferreira IA, Cabral-de-Mello DC, Mazzuchelli J, Valente GT, Pinhal D, Poletto AB, Martins C. Organization of repeated DNA elements in the genome of the cichlid fish cichla kelberi and its contribution to the knowledge of fish genomes. Cytogenet Genome Res. 2009;125:224–234. doi: 10.1159/000230006. PubMed DOI

Valente GT, Mazzuchelli J, Ferreira IA, Poletto AB, Fantinatti BEA. Cytogenetic mapping of the retroelements Rex1, Rex3 and Rex6 among cichlid fish: new insights on the chromosomal distribution of transposable elements. Cytogenet Genome Res. 2011;133:34–42. doi: 10.1159/000322888. PubMed DOI

DaSilva C, Hadji H, Ozouf-Costaz C, Nicaud S, Jaillon O, Weissenbach J, Roest Crollius H. Remarkable compartmentalization of transposable elemetns and pseudogenes in the heterochromatin of the tetraodon nigroviridis genome. Proc Natl Acad Sci U S A. 2002;99:1636–1641. PubMed PMC

Koop BF, Davidson WS. In: Fisheries for Global Welfare and Environment. Tsukamoto K, Kawamura T, Takeuchi T, Beard TD Jr, Kaiser MJ, editor. Tokyo: Terrapub; 2008. Genomics and the Genome Duplication in Salmonids; pp. 77–86.

Kurzynska-Kokorniak A, Jamburuthugoda VK, Bibillo A, Eickbush TH. DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon. J Mol Biol. 2007;374:322–333. doi: 10.1016/j.jmb.2007.09.047. PubMed DOI PMC

Jakubczak JL, Xiong Y, Eickbush TH. Type I (RI) and type II (R2) ribosomal DNA insertions of drosophila melanogaster are retrotransposable elements close11 related to those of bombyx Mori. J Mol Biol. 1990;212:37–52. doi: 10.1016/0022-2836(90)90303-4. PubMed DOI

Ohlberger J, Mehner T, Staaks G, Hölker F. Temperature-related physiological adaptations promote ecological divergence in a sympatric species pair of temperate freshwater fish. Coregonus spp. Funct Ecol. 2008;22:501–508. doi: 10.1111/j.1365-2435.2008.01391.x. DOI

Ohlberger J, Staaks G, Petzoldt T, Mehner T, Hölker F. Physiological specialization by thermal adaptation drives ecological divergence in a sympatric fish species pair. Evol Ecol Res. 2008;10:1173–1185.

Fujiwara A, Abe S, Yamaha E, Yamazaki F, Yoshida MC. Chromosomal localization and heterochromatin association of ribosomal RNA gene loci and silver-stained nucleolar organizer regions in salmonid fishes. Chromosome Res. 1998;6:463–471. doi: 10.1023/A:1009200428369. PubMed DOI

Matveev V, Okadaa N. Retroposons of salmonoid fishes (actinopterygii: salmonoidei) and their evolution. Gene. 2008;434:16–28. PubMed

De Boer JG, Yazawa R, Davidson WS, Koop BF. Burst and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. BMC Genomics. 2007;8:422. doi: 10.1186/1471-2164-8-422. PubMed DOI PMC

Krasnov A, Koskinen H, Afanasyev A, Mölsä H. Transcribed Tcl-like transposons in salmonid fish. BMC Genomics. 2005;6:107. doi: 10.1186/1471-2164-6-107. PubMed DOI PMC

Helland IP, Harrod C, Freyhof J, Mehner T. Co-existence of a pair of pelagic planktivorous coregonid fishes. Evol Ecol Res. 2008;10:373–390.

Arnault C, Dufournel I. Genome and stresses: reactions against aggressions, behaviour of transposable elements. Genetica. 1994;93:149–160. doi: 10.1007/BF01435247. PubMed DOI

Rebollo R, Horard B, Hubert B, Vieira C. Jumping genes and epigenetics: towards new species. Gene. 2010;454:1–7. doi: 10.1016/j.gene.2010.01.003. PubMed DOI

Bestor TH, Tycko B. Creation of genomic methylation patterns. Nat Genet. 1996;12:363–367. doi: 10.1038/ng0496-363. PubMed DOI

Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997;13:335–340. doi: 10.1016/S0168-9525(97)01181-5. PubMed DOI

Wichman HA, Van Den Bussche RA, Hamilton MJ, Baker RJ. Transposable elements and the evolution of genome organization in mammals. Genetica. 1992;86:287–293. doi: 10.1007/BF00133727. PubMed DOI

Biémont C. A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics. 2010;186:1085–1093. doi: 10.1534/genetics.110.124180. PubMed DOI PMC

McClintock B. The significance of responses of the genome to challenge. Science. 1984;226:792–801. doi: 10.1126/science.15739260. PubMed DOI

McClintock B. Mutable loci in maize. Carnegie Inst Wash Yrbk. 1949;48:142–154.

Hurst GDD, Werren JH. The role of selfish elements in eukaryotic evolution. Nat Rev Genet. 2001;2:597–606. PubMed

Hua-Van A, Le Rouzic A, Boutin TS, Filée J, Capy P. The struggle for life of the genome’s selfish architects. Biol Direct. 2011;6:19. doi: 10.1186/1745-6150-6-19. PubMed DOI PMC

Vieira C, Lepetit D, Dumont S, Biémont C. Wake up of transposable elements following drosophila simulans worldwide colonization. Mol Biol Evol. 1999;16:1251–1255. doi: 10.1093/oxfordjournals.molbev.a026215. PubMed DOI

Volff JN. Genome evolution and biodiversity in teleost fish. Heredity. 2005;94:280–294. doi: 10.1038/sj.hdy.6800635. PubMed DOI

Böhne A, Brunet F, Galiana-Arnoux D, Schultheis C, Volff J-N. Transposable elements as drivers of genomic and biological diversity in vertebrates. Chromosome Res. 2008;16:203–215. doi: 10.1007/s10577-007-1202-6. PubMed DOI

Noor MAF, Chang AS. Evolutionary genetics: jumping into a New species. Curr Biol. 2006;16:R890–R892. doi: 10.1016/j.cub.2006.09.022. PubMed DOI

Hurst GDD, Schilthuizen M. Selfish genetic elements and speciation. Heredity. 1998;80:2–8. doi: 10.1046/j.1365-2540.1998.00337.x. DOI

Kazazian HH Jr. Mobile elements: drivers of genome evolution. Science. 2004;303:1626–1632. doi: 10.1126/science.1089670. PubMed DOI

Renaut S, Nolte AW, Bernatchez L. Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (coregonus spp. Salmonidae) Mol Ecol. 2010;19(Suppl.1):115–131. PubMed

Ráb P, Roth P. In: Methods of chromosome analysis. Balicek P, Forejt J, Rubes J, editor. Brno: Cytogenet Sect Cs Biol Soc Publishers; 1988. Cold-blooded vertebrates; pp. 115–124.

Fujiwara A, Nishida-Umehara C, Sakamoto T, Okamoto N, Nakayama I, Abe S. Improved fish lymphocyte culture for chromosome preparation. Genetica. 2001;111:77–89. doi: 10.1023/A:1013788626712. PubMed DOI

Cremer M, Grasser F, Lanctôt C, Müller S, Neusser M, Zinner R, Solovei I, Cremer T. Multicolor 3D Fluorescence In Situ Hybridization for Imaging Interphase Chromosomes. The Nucleus: Volume I: Nuclei and Subnuclear Components, Methods in Molecular Biology™, Volume Chapter 15, Volume 463. Edited by Hancock R: Humana Press; 2008:205–239. Springer Protocols. PubMed

Database GenBank. http://www.ncbi.nlm.nih.gov/genbank/.

Zhang Q, Cooper RK, Tiersch TR. Chromosomal location of the 28S ribosomal RNA gene of channel catfish by in situ polymerase chain reaction. J Fish Biol. 2000;56:388–397. doi: 10.1111/j.1095-8649.2000.tb02113.x. DOI

Dayrat B, Tillier A, Lecointre G, Tillier S. New clades of euthyneuran gastropods (mollusca) from 28S rRNA sequences. Mol Phylogenet Evol. 2001;19:225–235. doi: 10.1006/mpev.2001.0926. PubMed DOI

Chombard C, Boury-Esnault N, Tillier S. Reassessment of homology of morphological characters in tetractinellid sponges based on molecular data. Syst Biol. 1998;47:351–366. doi: 10.1080/106351598260761. PubMed DOI

White TJ, Bruns T, Lee S, Taylor JW. In: PCR Protocols: A Guide to Methods and Applications. Innis MA, Gelfand DH, Sninsky JJ, White TJ, editor. New York: Academic Press Inc; 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics; pp. 315–322.

Volff JN, Körting C, Meyer A, Schartl M. Evolution and discontinuous distribution of Rex3 retrotransposons in fish. Mol Biol Evol. 2001;18:427–431. doi: 10.1093/oxfordjournals.molbev.a003819. PubMed DOI

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. PubMed

National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/blast.

Levan AK, Fredga K, Sandberg AA. Nomenclature for centromeric position on chromosomes. Hereditas. 1964;52:201–220.

Matthey R. L’evolution de la formule chromosomale chez les vertébrés. Experientia. 1945;1:50–56. doi: 10.1007/BF02153623. DOI

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