Phylogeographic congruence between mtDNA and rDNA its markers in brown trout

Molecular Biology and Evolution

Volumn 19, Issue 12, 2002, Pages 2161-2175

  Presa, P ^a   Pardo, B G ^b   Martínez, Paulino ^b   Bernatchez, L ^c  

^a UNIVERSITY OF VIGO   (Spain)

^b UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^c UNIVERSITÉ LAVAL   (Canada)

Author keywords

Internal transcribed spacers; MtDNA control region; Phylogeography; RRNA genes; Salmo trutta

Indexed keywords

INTERNAL TRANSCRIBED SPACER; MITOCHONDRIAL DNA; MOLECULAR MARKER; RIBOSOME DNA; PRIMER DNA;

ARTICLE; BROWN TROUT; DNA DETERMINATION; DNA HYBRIDIZATION; GENE SEQUENCE; GENETIC MARKER; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; UNINDEXED SEQUENCE; ANIMAL; CLASSIFICATION; GENETICS; GEOGRAPHY; HYBRIDIZATION; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; TROUT;

SALMO; SALMO TRUTTA; SALMONIDAE;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL; GENETIC MARKERS; GEOGRAPHY; HYBRIDIZATION, GENETIC; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, NUCLEIC ACID; TROUT;

EID: 0036898765     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004041     Document Type: Article

References (56)

1. Aquadro, C. F., S. F. Desse, M. M. Bland, C. H. Langley, and C. Laurie-Ahlberg. 1986. Molecular population genetics of the alcohol dehydrogenase gene region of Drosophila melanogaster. Genetics 114:1165-1190.
2. Aquadro, C. F., A. L. Weaver, S. W. Schaeffer, and W. W. Anderson. 1991. Molecular evolution of inversions in Drosophila pseudoobscura: The amylase gene region. Proc. Natl. Acad. Sci. USA. 88:305-309.
3. Arnheim, N., M. Krystal, R. Schmickel, G. Wilson, O. Ryder, and E. Zimmer. 1980. Molecular evidence for genetic exchanges among ribosomal genes on non-homologous chromosomes in man and apes. Proc. Natl. Acad. Sci. USA 77:7323-7327.
4. Avise, J. C. 1998. The history and purview of phylogeography: Personal reflection. Mol. Ecol. 7:371-379.
5. -. 2000. Phylogeography. Harvard University Press, London.
6. Bermingham, E., and C. Moritz. 1998. Comparative phylogeography: Concepts and applications. Mol. Ecol. 7:367-369.
7. Bernardi, G., P. Sordino, and D. A. Powers. 1993. Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish Fundulus heteroclitus. Proc. Natl. Acad. Sci. USA. 90:9271-9274.
8. Bernatchez, L. 2001. The evolutionary history of brown trout Salmo trutta L. inferred from phylogeographic, nested clade and mismatch analyses of mitochondrial DNA variation. Evolution 55:351-379.
9. Bernatchez, L., R. Guyomard, and F. Bonhomme. 1992. DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Sahno trutta populations. Mol. Ecol. 1: 161-173.
10. Bouza, C., J. Arias, J. Castro, L. Sanchez, and P. Martinez. 1999. Genetic structure of brown trout, Salmo trutta L., at the southern limit of the distribution range of the anadromous form. Mol. Ecol. 8:1991-2001.
11. Bouza, C., J. Castro, L. Sanchez, and P. Martinez. 2001. Allozymic evidence of parapatric differentiation of brown trout (Salmo trutta L.) within an Atlantic river basin of the Iberian Peninsula. Mol. Ecol. 10:1455-1469.
12. Burton, R. S., and B. N. Lee. 1994. Nuclear and mitochondrial gene genealogies and allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus. Proc. Nat. Acad. Sci. USA. 91:5197-5201.
13. Castro, J., B. G. Pardo, L. Sanchez, and P. Martinez. 1999. rDNA RFLPs as genetic markers for resource management in brown trout. J. Fish Biol. 55:221-225.
14. Castro, J., S. Rodriquez, B. G. Pardo, L. Sanchez, and P. Martinez. 2001. Population analysis of an unusual NORsite polymorphism in brown trout (Salmo trutta, L.). Heredity 86:291-302.
15. 3-staining, and fluorescent in situ hybridization. Cytogenet. Cell Genet. 75:234-239.
16. Crandall, K. A., and A. R. Templeton. 1993. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134:959-969.
17. Degnan, S. M. 1993. The perils of single-gene trees - Mitochondrial versus single-copy nuclear-DNA variation in white-eyes (Aves, Zosteropidae). Mol. Ecol. 2:219-225.
18. Doyle, J. J. 1992. Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17:144-163.
19. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package). Version 3.5. Distributed by the author, Department of Genetics, University of Washington, Seattle.
20. Ferguson, A. 1989. Genetic differences among brown trout (Salmo trutta) stocks and their importance for the conservation and management of the species. Freshw. Biol. 21: 35-64.
21. Fritz, G. N., J. Conn, A. Cockburn, and J. Seawright. 1994. Sequence analysis of the ribosomal DNA internal transcribed spacer 2 from populations of Anopheles nuneztovari (Diptera: Culicidae). Mol. Biol. Evol. 11:406-416.
22. García-Marín, J. L., F. M. Utter, and C. Pla. 1999. Postglacial colonization of brown trout in Europe based on distribution of allozyme variants. Heredity 82:46-56.
23. Gonzalez, I. L., J. E. Sylvester, T. F. Smith, D. Stambolian, and R. D. Schmickel. 1990. Ribosomal RNA gene sequences and hominoid phylogeny. Mol. Biol. Evol. 7: 203-219.
24. Gyllensten, U., and A. C. Wilson. 1987. Mitochondrial DNA of salmonids: Inter- and intraspecific variability detected with restriction enzymes. Pp. 301-317 in F. Utter and N. Ryman, eds. Population Genetics and Fishery Management. University of Washington Press, Seattle.
25. Hamilton, K. E., A. Ferguson, J. B. Taggart, T. Tomasson, A. Walker, and E. Fahy. 1989. Post-glacial colonization of brown trout, Salmo trutta L.: Ldh-5 as a phylogeographical marker locus. J. Fish Biol. 35:651-664.
26. Hillis, D. M., and M. T. Dixon. 1991. Ribosomal DNA: Molecular evolution and phylogenetic inference. Q. Rev. Biol. 66:411-453.
27. Hillis, D. M., C. Moritz, C. A. Porter, and R. J. Baker. 1991. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science 251:308-310.
28. Jorde, P. E., and N. Ryman. 1995. Temporal allele frequency change and estimation of effective size in populations with overlapping generations. Genetics 139:1077-1090.
29. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
30. King, T. L., M. S. Eackles, B. Gjetvaj, and W. R. Hoeh. 1999. Intraspecific phylogeography of Lasmigona subviridis (Bivalvia: Unionidae): Conservation implications of range discontinuity. Mol. Ecol. 8:S65-S78.
31. Krieg, C. B., and R. Guyomard. 1985. Population genetics of French brown trout (Salmo trutta L.): Large geographical differentiation of wild populations and high similarity of domesticated stocks. Génét. Sél. Evol. 17:225-242.
32. Kuhner, M. K., J. Yamato, and J. Felsenstein. 2000. Maximum likelihood estimation of recombination rates from population data. Genetics 156:1393-1401.
33. Kumar, S., K. Tamora, and M. Nei. 1993. MEGA: Molecular Evolutionary Genetics Analysis. 1.0 Edition. Pennsylvania State University, University Park, Pa.
34. Machordom, A., J. Suarez, A. Almodovar, and J. M. Bautista. 2000. Mitochondrial haplotype variation and phylogeography of Iberian brown trout populations. Mol. Ecol. 9:1325-1339.
35. Manos, P. S., J. J. Doyle, and K. C. Nixon. 1999. Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae). Mol. Phylogenet. Evol. 12:333-349.
36. Mayer, M. S., and P. S. Soltis. 1999. Intraspecific phylogeny analysis using ITS sequences: Insights from studies of the Streptanthus glandulosus complex (Cruciferae). Syst. Bot. 24:47-61.
37. McVeigh, H. P., R. A. Hynes, and A. Ferguson. 1995. Mitochondrial DNA differentiation of sympatric populations of brown trout, Salmo trutta L, from Lough Melvin, Ireland. Can. J. Fish. Aquat. Sci. 52:1617-1622.
38. Morán, P., K. M. Reed, J. Pérez, T. H. Oakley, R. B. Phillips, E. García-Vázquez, and A. M. Pendás. 1997. Physical localization and characterization of the BglI element in the genomes of Atlantic salmon (Salmo salar L.) and brown trout (S. trutta L.). Gene 194(1):9-18.
39. Osinov, A. G., and L. Bernatchez. 1996. Atlantic and Danubian phylogenetic groupings of brown trout Salmo trutta complex: Genetic divergence, evolution, and conservation. J. Appl. Ichthyol. 36:762-786.
40. Palumbi, S. R., and C. S. Baker. 1994. Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol. Biol. Evol. 11:426-435.
41. Phillips, R. B., S. A. Manley, and T. J. Daniels. 1994. Systematics of the salmonid genus Salvelinus inferred from ribosomal DNA sequences. Can. J. Fish. Aquat. Sci. 51(Suppl. 1):198-204.
42. Phillips, R. B., S. L. Sajdak, and M. J. Domanico. 1995. Relationships among charrs based on DNA sequences. Nord. J. Freshw. Res. 71:378-391.
43. Presa, P., F. Krieg, A. Estoup, and R. Guyomard. 1994. Diversité et gestion génétique de la truite commune: Apport de l'étude du polymorphisme des locus proteiques et microsatéllites. Génét. Sél. Evol. 26:183-202.
44. Ritland, C. E., K. Ritland, and N. A. Straus. 1993. Variation in the ribosomal internal transcribed spacers (ITS1 and ITS2) among eight taxa of the Mimulus guttatus species complex. Mol. Biol. Evol. 10:1273-1288.
45. Sajdak, S. L., and R. B. Phillips. 1997. Phylogenetic relationships among Coregonus species inferred from the DNA sequence of the first internal transcribed spacer (ITS1) of ribosomal DNA. Can. J. Fish. Aquat. Sci. 54:1494-1503.
46. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning. A Laboratory Manual. 2nd Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
47. Sang, T., D. J. Crawford, and T. F. Stuessy. 1995. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution. Proc. Natl. Acad. Sci. USA 92:6813-6817.
48. Sanz, N., J. L. García-Marín, and C. Pla. 2000. Divergence of brown trout (Salmo trutta) within glacial refugia. Can. J. Fish. Aquat. Sci. 57:2201-2210.
49. Schlötterer, C., and D. Tautz. 1991. Slippages synthesis of simple sequence DNA. Nucleic Acids Res. 20:211-215.
50. Shaw, A. J. 2000. Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae). Mol. Ecol. 9:595-608.
51. Suh, Y., L. B. Thien, H. E. Reeve, and E. A. Zimmer. 1993. Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae. Am. J. Bot. 80:1042-1055.
52. Swofford, D. L. 1998. PAUP* Version 4d64. Sinauer Associates, Sunderland, Mass.
53. Templeton, A. R., K. A. Crandall, and C. F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred form restriction endonuclease mapping. III. Cladofram estimation. Genetics 132:619-633.
54. Vogler, A. P., and R. Desalle. 1994. Evolution and phylogenetic information content of the ITS-1 region in the tiger beetle Cicindela dorsalis. Mol. Biol. Evol. 11:393-405.
55. 3 and ISH. Genetica 108:113-118.
56. Zhuo, L., S. L. Sajdak, and R. B. Phillips. 1994. Minimal intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA of lake trout (Salvelinus namaycush). Genome 37:664-671.