Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species

Molecular Ecology

Volumn 13, Issue 4, 2004, Pages 909-919

  Hey, Jody ^a   Won, Yong Jin ^a   Sivasundar, Arjun ^a   Nielsen, Rasmus ^b   Markert, Jeffrey A ^c  

^a RUTGERS UNIVERSITY   (United States)

^b Department of Population Medicine and Diagnostic Sciences   (United States)

^c UNIVERSITY OF CINCINNATI   (United States)

Author keywords

Cichlid; Gene flow; Markov chain Monte Carlo; Microsatellites; Phylogeography; Speciation; Sympatric speciation

Indexed keywords

FRESH WATER; MICROSATELLITE DNA; PRIMER DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CICHLID; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; MALAWI; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; POPULATION DYNAMICS; POPULATION GENETICS; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; CICHLIDS; DNA PRIMERS; FRESH WATER; GENETICS, POPULATION; HAPLOTYPES; LIKELIHOOD FUNCTIONS; MALAWI; MICROSATELLITE REPEATS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

ANIMALIA; CICHLIDAE; PISCES;

EID: 1642326524     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-294X.2003.02031.x     Document Type: Article

References (65)

1. Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Molecular Ecology, 11, 155-165.
2. Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 2013-2029.
3. Blankenship SM, May B, Hedgecock D (2002) Evolution of a perfect simple sequence repeat locus in the context of its flanking sequence. Molecular Biology and Evolution, 19, 1943-1951.
4. Booton GC, Kaufman L, Chandler M, Fuerst PA (1996) Use of DNA microsatellite loci to identify populations and species of Lake Victoria haplochromine cichlids. In: Symposium Proceedings, International Congress on the Biology of Fishes (eds Donaldson EM, MacKinlay DD), pp. 105-113. American Fisheries Society, Physiology Section, Vancouver, CA.
5. Brohede J, Ellegren H (1999) Microsatellite evolution: polarity of substitutions within repeats and neutrality of flanking sequences. Proceedings of the Royal Society, London, Series B, 266, 825-833.
6. Broughton RE, Harrison RG (2003) Nuclear gene genealogies reveal historical, demographic and selective factors associated with speciation in field crickets. Genetics, 163, 1389-1401.
7. Bulgin NL, Gibbs HL, Vickery P, Baker AJ (2003) Ancestral polymorphisms in genetic markers obscure detection of evolutionary distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus). Molecular Ecology, 12, 831-844.
8. Colson I, Goldstein DB (1999) Evidence for complex mutations at microsatellite loci in Drosophila. Genetics, 152, 617-627.
9. Danley PD, Kocher TD (2001) Speciation in rapidly diverging systems: lessons from Lake Malawi. Molecular Ecology, 10, 1075-1086.
10. Di Rienzo A, Donnelly P, Toomajian C et al. (1998) Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories. Genetics, 148, 1269-1284.
11. Dieckmann U, Doebeli M (1999) On the origin of species by sympatric speciation. Nature, 400, 354-357.
12. Dobzhansky T (1936) Studies of hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics, 21, 113-135.
13. Estoup A, Cornuet JM, Rousset F, Guyomard R (1999) Juxtaposed microsatellite systems as diagnostic markers for admixture: theoretical aspects. Molecular Biology and Evolution, 16, 898-908.
14. Estoup A, Jarne P, Cornuet JM (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular Ecology, 11, 1591-1604.
15. Estoup A, Largiader CR, Cornuet JM et al. (2000) Juxtaposed microsatellite systems as diagnostic markers for admixture: an empirical evaluation with brown trout (Salmo trutta) as model organism. Molecular Ecology, 9, 1873-1886.
16. Estoup A, Tailliez C, Cornuet JM, Solignac M (1995) Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Molecular Biology and Evolution, 12, 1074-1084.
17. Felsenstein J, Kuhner MK, Yamato J, Beerli P (1999) Likelihoods on coalescents: a Monte Carlo sampling approach to inferring parameters from population samples of molecular data. In: Statistics in Genetics and Molecular Biology (ed. Seillier-Moiseiwitsch F). Institute of Mathematical Statistics and American Mathematical Society, Hayward, CA.
18. Gelman A, Rubin DB (1992) Inference from iterative simulation using multiple sequences. Statistical Science, 7, 457-472.
19. Geyer CJ (1992) Practical Markov Chain Monte Carlo. Statistical Science, 7, 473-511.
20. Gilks WR, Richardson S, Spiegelhalter DJ (1996) Introducing Markov chain Monte Carlo. In: Markov Chain Monte Carlo in Practice (eds Gilks WR, Richardson S, Spiegelhalter DJ), pp. 1-20. Chapman & Hall, Boca Raton, FL.
21. Griffiths RC, Tavare S (1994) Simulating probability distributions in the coalescent. Theoretical Population Biology, 46, 131-159.
22. Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57, 97-109.
23. Hey J (1994) Bridging phylogenetics and population genetics with gene tree models. In: Molecular Approaches to Ecology and Evolution (eds Schierwater B, Streit B, Wagner G, DeSalle R), pp. 435-449. Birkhäuser-Verlag, Basel.
24. Higashi M, Takimoto G, Yamamura N (1999) Sympatric speciation by sexual selection. Nature, 402, 523-526.
25. Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends in Ecology and Evolution, 11, 424-429.
26. Kimura M (1969) The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics, 61, 893-903.
27. Kliman RM, Andolfatto P, Coyne JA et al. (2000) The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics, 156, 1913-1931.
28. Kornfield I (1978) Evidence for rapid speciation in African cichlid fishes. Experientia, 34, 335-336.
29. Kornfield I, Parker A (1997) Molecular systematics of a rapidly evolving species flock: the mbuna of Lake Malawi and the search for phylogenetic signal. In: Molecular Systematics of Fishes (eds Kocher TD, Stepien CA), pp. 25-37. Academic Press, New York.
30. Kornfield I, Smith PF (2000) African cichlid fishes: model systems for evolutionary biology. Annual Review of Ecology and Systematics, 31, 163-196.
31. Kuhner MK, Yamato J, Felsenstein J (1995) Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics, 140, 1421-1430.
32. Lehman T, Hawley WA, Collins FH (1996) An evaluation of evolutionary constraints on microsatellite loci using null alleles. Genetics, 144, 1155-1163.
33. Machado C, Kliman RM, Markert JM, Hey J (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and its close relatives. Molecular Biology and Evolution, 19, 472-488.
34. Machado CA, Hey J (2003) The causes of phylogenetic conflict in a classic Drosophila species group. Proceedings of the Royal Society, London, Series B, 270, 1193-1202.
35. McKaye ER, Kocher T, Reinthal P, Kornfield I (1982) A sympatric species complex of Petrotilapia trewavas from Lake Malawi analysed by enzyme electrophoresis (Pisces, Cichlidae). Zoological Journal of the Linnean Society, 76, 91-96.
36. McKaye KR, Gray WN (1984) Extrinsic barriers to gene flow in rock-dwelling cichlids of Lake Malawi: macrohabitat heterogeneity and reef colonization. In: Evolution of Fish Species Flocks (eds Echelle AA, Kornfield I). University of Maine Press, Orono.
37. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equations of state calculations by fast computing machines. Journal of Chemical Physics, 21, 1087-1091.
38. Moran P, Kornfield I (1993) Retention of an ancestral polymorphism in the Mbuna species flock (Teleostei: Cichlidae) of Lake Malawi. Molecular Biology and Evolution, 10, 1015-1029.
39. Mountain JL, Knight A, Jobin M et al. (2002) SNPSTRs: empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Research, 12, 1766-1772.
40. Muller HJ (1940) Bearings of the Drosophila work on systematics. In: The New Systematics (ed. Huxley J), pp. 185-268. Clarendon Press, Oxford.
41. Navarro A, Barton NH (2003) Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution, 57, 447-459.
42. Nielsen R (1997) A likelihood approach to population samples of microsatellite alleles. Genetics, 146, 711-716.
43. Nielsen R, Wakeley J (2001) Distinguishing migration from isolation. A Markov chain Monte Carlo approach. Genetics, 158, 885-896.
44. Noor MA, Grams KL, Bertucci LA, Reiland J (2001) Chromosomal inversions and the reproductive isolation of species. Proceedings of the National Academy of Sciences USA, 98, 12084-12088.
45. Ochman H, Gerber AS, Hartl DL (1988) Genetic applications of an inverse polymerase chain reaction. Genetics, 120, 621-623.
46. Orr HA (1996) Dobzhansky, Bateson, and the Genetics of Speciation. Genetics, 144, 1331-1335.
47. Renwick A, Davison L, Spratt H, King JP, Kimmel M (2001) DNA dinucleotide evolution in humans: fitting theory to facts. Genetics, 159, 737-747.
48. Ribbink AJ, Marsh AC, Marsh BA, Sharp BJ (1983) A preliminary survey of the cichlid fishes of the rocky habitats in Lake Malawi. South African Journal of Zoology, 18, 149-310.
49. Rieseberg LH, Whitton J, Gardner K (1999) Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics, 152, 713-727.
50. Saint-Laurent R, Legault M, Bernatchez L (2003) Divergent selection maintains adaptive differentiation despite high gene flow between sympatric rainbow smelt ecotypes (Osmerus mordax Mitchill). Molecular Ecology, 12, 315-330.
51. Schluter D (1998) Ecological cuases of speciation. In: Endless Forms: Species and Speciation (eds Howard DJ, Berlocher SH), pp. 114-129. Oxford University Press, New York.
52. Seutin G, White BN, Boag PT (1991) Preservation of avian blood and tissue samples for DNA analyses. Canadian Journal of Zoology, 69, 82-91.
53. Shaw KL (2002) Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proceedings of the National Academy of Sciences USA, 99, 16122-16127.
54. Surridge AK, Bell DJ, Ibrahim KM, Hewitt GM (1999) Population structure and genetic variation of European wild rabbits (Oryctolagus cuniculus) in East Anglia. Heredity, 82, 479-487.
55. Takahata N, Nei M (1985) Gene genealogy and variance of interpopulational nucleotide differences. Genetics, 110, 325-344.
56. Takahata N, Slatkin M (1990) Genealogy of neutral genes in two partially isolated populations. Theoretical Population Biology, 38, 331-350.
57. Van Oppen M, Rico C, Turner G, Hewitt G (2000) Extensive Homoplasy, nonstepwise mutations, and shared ancestral polymorphism at a complex microsatellite locus in Lake Malawi cichlids. Molecular Biology and Evolution, 17, 489-498.
58. Van Oppen MJH, Turner GF, Rico C et al. (1997) Unusually fine-scale genetic structuring found in rapidly speciating Malawi cichlid fishes. Proceedings of the Royal Society of London Series B-Biological Sciences, 264, 1803-1812.
59. Wakeley J, Hey J (1997) Estimating ancestral population parameters. Genetics, 145, 847-855.
60. Wakeley J, Hey J (1998) Testing speciation models with DNA sequence data. In: Molecular Approaches to Ecology and Evolution (eds DeSalle R, Schierwater B), pp. 157-175. Birkhäuser Verlag, Basel.
61. Wilson IJ, Balding DJ (1998) Genealogical inference from microsatellite data. Genetics, 150, 499-510.
62. Won Y, Young CR, Lutz RA, Vrijenhoek RC (2003) Dispersal barriers and isolation among deep-sea mussel populations (Mytilidae: Bathymodiolus) from eastern Pacific hydrothermal vents. Molecular Ecology, 12, 169-184.
63. Wright S (1931) Evolution in mendelian populations. Genetics, 16, 97-159.
64. Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563-584.
65. Zhivotovsky LA (2001) Estimating divergence time with the use of microsatellite genetic distances: impacts of population growth and gene flow. Molecular and Biological Evolution, 18, 700-709.