Global population genetic structure of caenorhabditis remanei reveals incipient speciation

Genetics

Volumn 191, Issue 4, 2012, Pages 1257-1269

  Dey, Alivia ^a   Jeon, Yong ^a   Wang, Guo Xiu ^a,b   Cutter, Asher D ^a,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b CENTRAL CHINA NORMAL UNIVERSITY   (China)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS REMANEI; CHINA; EUROPE; GENE FLOW; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; INTERSPECIFIC HYBRID; NEMATODE; NONHUMAN; NORTH AMERICA; POPULATION GENETICS; PRIORITY JOURNAL; REPRODUCTIVE ISOLATION; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENTIATION; X CHROMOSOME;

ANIMALS; BIOLOGICAL EVOLUTION; CAENORHABDITIS; CHINA; CROSSES, GENETIC; EUROPE; GENETIC LOCI; GENETICS, POPULATION; GENOME, HELMINTH; MOLECULAR SEQUENCE DATA; NORTH AMERICA; PHYLOGENY; POLYMORPHISM, GENETIC; POPULATION DYNAMICS; REPRODUCTION; REPRODUCTIVE ISOLATION; X CHROMOSOME;

EID: 84865078062     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.140418     Document Type: Article

References (52)

1. Arunyawat, U., W. Stephan, and T. Stadler, 2007 Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes. Mol. Biol. Evol. 24: 2310-2322.
2. Baird, S. E., 1999 Natural and experimental associations of Caeonrhabditis remanei with Trachelipus rathkii and other terrestrial isopods. Nematology 1: 471-475.
3. Baird, S. E., and W. C. Yen, 2000 Reproductive isolation in Caenorhabditis: terminal phenotypes of hybrid embryos. Evol. Dev. 2: 9-15.
4. Baird, S. E., M. E. Sutherlin, and S. W. Emmons, 1992 Reproductive isolation in Rhabditidae (Nematoda:Secernentea): mechanisms that isolate six species of three genera. Evolution 46: 585-594.
5. Baird, S. E., D. H. Fitch, and S. W. Emmons, 1994 Caenorhabditis vulgaris n. sp. (Secernentea: Rhabditidae): a necromenic associate of pill bugs and snails. Nematologica 40: 1-11.
6. Braendle, C., and M. A. Felix, 2006 Sex determination: ways to evolve a hermaphrodite. Curr. Biol. 16: R468-R471.
7. Charlesworth, D., and S. I. Wright, 2001 Breeding systems and genome evolution. Curr. Opin. Genet. Dev. 11: 685-690.
8. Cutter, A. D., 2008 Multilocus patterns of polymorphism and selection across the X chromosome of Caenorhabditis remanei. Genetics 178: 1661-1672.
9. Cutter, A. D., and B. Charlesworth, 2006 Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhabditis remanei. Curr. Biol. 16: 2053-2057.
10. Cutter, A. D., S. E. Baird, and D. Charlesworth, 2006a High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei. Genetics 174: 901-913.
11. Cutter, A. D., M. A. Felix, A. Barriere, and D. Charlesworth, 2006b Patterns of nucleotide polymorphism distinguish temperate and tropical wild isolates of Caenorhabditis briggsae. Genetics 173: 2021-2031.
12. Cutter, A. D., J. D. Wasmuth, and N. L. Washington, 2008 Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing. Genetics 178: 2093-2104.
13. Cutter, A. D., A. Dey, and R. L. Murray, 2009 Evolution of the Caenorhabditis elegans genome. Mol. Biol. Evol. 26: 1199-1234.
14. Cutter, A. D., W. Yan, N. Tsvetkov, S. Sunil, and M. A. Felix, 2010 Molecular population genetics and phenotypic sensitivity to ethanol for a globally diverse sample of the nematode Caenorhabditis briggsae. Mol. Ecol. 19: 798-809.
15. Cutter, A. D., G. X. Wang, H. Ai, and Y. Peng, 2012 Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity. Mol. Ecol. 21: 1345-1359.
16. Denver, D. R., K. A. Clark, and M. J. Raboin, 2011 Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species. Mol. Phylogenet. Evol. 61: 584-592.
17. Dolgin, E. S., B. Charlesworth, S. E. Baird, and A. D. Cutter, 2007 Inbreeding and outbreeding depression in Caenorhabditis nematodes. Evolution 61: 1339-1352.
18. Earl, D. A., and B. M. vonHoldt, 2011 STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4: 359-361.
19. Evanno, G., S. Regnaut, and J. Goudet, 2005 Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620.
20. Falush, D., M. Stephens, and J. K. Pritchard, 2003 Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
21. Fay, J. C., and C. I. Wu, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
22. Fu, Y. X., and W. H. Li, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
23. Graustein, A., J. M. Gaspar, J. R. Walters, and M. F. Palopoli, 2002 Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis. Genetics 161: 99-107.
24. Haag, E. S., 2009 Caenorhabditis nematodes as a model for the adaptive evolution of germ cells. Curr. Top. Dev. Biol. 86: 43-66.
25. Haag, E. S., and A. D. Ackerman, 2005 Intraspecific variation in fem-3 and tra-2, two rapidly coevolving nematode sex-determining genes. Gene 349: 35-42.
26. Hey, J., and C. Pinho, 2012 Population genetics and objectivity in species diagnosis. Evolution 66: 1413-1429.
27. Hill, R. C., C. E. de Carvalho, J. Salogiannis, B. Schlager, D. Pilgrim et al., 2006 Genetic flexibility in the convergent evolution of hermaphroditism in Caenorhabditis nematodes. Dev. Cell 10: 531-538.
28. Hubisz, M. J., D. Falush, M. Stephens, and J. K. Pritchard, 2009 Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9: 1322-1332.
29. Huson, D. H., and D. Bryant, 2006 Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23: 254-267.
30. Jovelin, R., 2009 Rapid sequence evolution of transcription factors controlling neuron differentiation in Caenorhabditis. Mol. Biol. Evol. 26: 2373-2386.
31. Jovelin, R., B. C. Ajie, and P. C. Phillips, 2003 Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus Caenorhabditis. Mol. Ecol. 12: 1325-1337.
32. Jovelin, R., J. P. Dunham, F. S. Sung, and P. C. Phillips, 2009 High nucleotide divergence in developmental regulatory genes contrasts with the structural elements of olfactory pathways in Caenorhabditis. Genetics 181: 1387-1397.
33. Jukes, T. H., and C. R. Cantor, 1969 Evolution of protein molecules, pp. 21-132 in Mammalian Protein Metabolism, edited by H. N. Munro. Academic Press, New York.
34. Kiontke, K., N. P. Gavin, Y. Raynes, C. Roehrig, F. Piano et al., 2004 Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc. Natl. Acad. Sci. USA 101: 9003-9008.
35. Kiontke, K. C., M. A. Felix, M. Ailion, M. V. Rockman, C. Braendle et al., 2011 A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol. Biol. 11: 339.
36. Kozlowska, J. L., A. R. Ahmad, E. Jahesh, and A. D. Cutter, 2012 Genetic variation for postzygotic reproductive isolation between Caenorhabditis briggsae and Caenorhabditis sp. 9. Evolution 66: 1180-1195.
37. Librado, P., and J. Rozas, 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
38. McDonald, J. H., and M. Kreitman, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
39. Nei, M., and T. Gojobori, 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
40. Ness, R. W., S. I. Wright, and S. C. Barrett, 2010 Mating-system variation, demographic history and patterns of nucleotide diversity in the tristylous plant Eichhornia paniculata. Genetics 184: 381-392.
41. Pritchard, J. K., M. Stephens, and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
42. Rane, H. S., J. M. Smith, U. Bergthorsson, and V. Katju, 2010 Gene conversion and DNA sequence polymorphism in the sex-determination gene fog-2 and its paralog ftr-1 in Caenorhabditis elegans. Mol. Biol. Evol. 27: 1561-1569.
43. Ross-Ibarra, J., S. I. Wright, J. P. Foxe, A. Kawabe, L. DeRose-Wilson et al., 2008 Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS ONE 3: e2411.
44. Stenico, M., A. T. Lloyd, and P. M. Sharp, 1994 Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res. 22: 2437-2446.
45. St. Onge, K. R., T. Källman, T. Slotte, M. Lascoux, and A. E. Palmé, 2011 Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems. Mol. Ecol. 20: 3306-3320.
46. Sudhaus, W., and K. Kiontke, 1996 Phylogeny of Rhabditis subgenus Caenorhabditis (Rhabditidae, Nematoda). J. Zoolog. Syst. Evol. Res. 34: 217-233.
47. Sudhaus, W., and K. Kiontke, 2007 Comparison of the cryptic nematode species Caenorhabditis brenneri sp. n. and C. remanei (Nematoda: Rhabditidae) with the stem species pattern of the Caenorhabditis elegans group. Zootaxa 1456: 45-62.
48. Sweigart, A. L., and J. H. Willis, 2003 Patterns of nucleotide diversity in two species of Mimulus are affected by mating system and asymmetric introgression. Evolution 57: 2490-2506.
49. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
50. Wang, G. X., S. Ren, Y. Ren, H. Ai, and A. D. Cutter, 2010 Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5. Mol. Ecol. 19: 5022-5029.
51. Woodruff, G. C., O. Eke, S. E. Baird, M. A. Felix, and E. S. Haag, 2010 Insights into species divergence and the evolution of hermaphroditism from fertile interspecies hybrids of Caenorhabditis nematodes. Genetics 186: 997-1012.
52. Wright, S. I., R.W. Ness, J. P. Foxe, and S. C. H. Barrett, 2008 Genomic consequences of outcrossing and selfing in plants. Int. J. Plant Sci. 169: 105-118.