Population Graphs: The graph theoretic shape of genetic structure

Molecular Ecology

Volumn 13, Issue 7, 2004, Pages 1713-1727

  Dyer, Rodney J ^a   Nason, John D ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Genetic structure; Graph theory; Networks; Phylogeography

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CACTACEAE; COMPARATIVE STUDY; GENETIC VARIABILITY; GENETICS; POPULATION DYNAMICS; POPULATION GENETICS;

CACTACEAE; GENETICS, POPULATION; MODELS, GENETIC; POPULATION DYNAMICS; VARIATION (GENETICS);

CACTACEAE; PACHYCEREUS; PACHYCEREUS SCHOTTII;

EID: 3042821261     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2004.02177.x     Document Type: Article

References (48)

1. Albert R, Barabási AL (2002) Statistical mechanics of complex networks. Review of Modern Physics, 74, 47-97.
2. Avise JC (2000) PhyloGeographyraphy: the History and Formation of Species. Harvard University Press, Cambridge, MA.
3. Bahlo M, Griffiths RC (2000) Inference from gene trees in a subdivided population. Theoretical Population Biology, 57, 79-95.
4. Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences USA, 98, 4563-4568.
5. Bollobás B (2001) Random Graphs, 2nd edn. Cambridge University Press, Cambridge, UK.
6. Box GEP, Draper NR (1987) Empirical Model-Building and Response Surfaces. J. Wiley and Son, New York.
7. Box GEP, Hunter WG, Hunter JS (1978) Statistics for Experimenters: an Introduction to Design, Data Analysis, and Model Building. J. Wiley and Son, New York.
8. Case TJ, Cody ML, Ezcurra E (2002) A New Island Biogeography of the Sea of Cortez. Oxford University Press, New York.
9. Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics, 153, 1989-2000.
10. Cox JM, N.Wermuth (1996) Multivariate Dependencies: Models, Analysis, and Interpretation. Chapman & Hall, New York.
11. Cracraft J (1988) Deep-history biogeography: retrieving the historical pattern of evolving continental biotas. Systematic Zoology, 37, 221-236.
12. Cruzan MB, Templeton AR (2000) Paleoecology and coalescence: phylogeographic analysis of hypotheses from the fossil record. Trends in Ecology and Evolution, 15, 491-496.
13. Dempster AP (1972) Covariance selection. Biometrics, 28, 157-175.
14. Draper NR, Smith H (1981) Applied Regression Analysis. J. Wiley and Sons, New York.
15. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Molecular Ecology, 11, 2571-2581.
16. Edwards D (1995) Introduction to Graphical Modeling. Springer-Verlag, New York.
17. Edwards AL, Sharitz RR (2000) Population genetics of two rare perennials in isolated wetlands: Sagittaria isoetiformis and S. teres (Alismataceae). American Journal of Botany, 87, 1147-1158.
18. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
19. Gavrilets S (1997) Evolution and speciation on holey adaptive landscapes. Trends in Ecology and Evolution, 12, 307-312.
20. Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53, 325-338.
21. Hewitt GM (2001) Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology, 10, 537-550.
22. Johnson RA, Wichern DW (1992) Applied Multivariate Statistical Analysis. Prentice Hall, Upper Saddle River, NJ.
23. Kempthorne O (1969) An Introduction to Genetic Statistics. Iowa State University Press, Ames, IA.
24. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635.
25. Lessa EP (1990) Multidimensional analysis of geographic genetic structure. Systematic Zoology, 39, 242-252.
26. Long JC, Smouse PE, Wood JW (1987) The allelic correlation structure of Gainj- and Kalam-speaking people. II. The genetic distance between population subdivisions. Genetics, 117, 273-283.
27. Magwene PM (2001) New tools for studying integration and modularity. Evolution, 55, 1734-1745.
28. Manly BFJ (1997) Randomization, Bootstrap and Monte Carlo Methods in Biology, 2nd edn. Chapman & Hall, New York.
29. Nason JD, Hamrick JL, Fleming TH (2002) Gene migration, range expansion, and phylogeography of the columnar cactus genus Lophocereus. Evolution, 56, 2214-2226.
30. Nei M (1972) Genetic distance between populations. American Naturalist, 106, 283-292.
31. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583-590.
32. Peñalba MC, Van Devender TR (1998) Cambios de vegetacíon y clima en Baja California, México, durante los últimos 20 000 años. Geología Del Noroeste, 2, 21-23.
33. Rhodes OEJ, Chesser RK, Smith MH (1996) Population Dynamics in Ecological Space and Time. University of Chicago Press, Chicago.
34. Riddle BR (1996) The molecular phylogeographic bridge between deep and shallow history in continental biotas. Trends in Ecology and Evolution, 11, 207-211.
35. Riddle BR, Hafner DJ, Alexander LF, Jaeger JR (2000) Cryptic vicariance in the historical assembly of a Baja California peninsular desert biota. Proceedings of the National Academy of Sciences USA, 97, 14438-14443.
36. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219-1228.
37. Slatkin M (1985) Gene flow in natural populations. Annual Review of Ecology and Systematics, 16, 393-430.
38. Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution, 47, 264-279.
39. Smouse PE, Spielman RS, Park MH (1982) Multiple-locus allocation of individuals to groups as a function of the genetic variation within and differences among human populations. American Naturalist, 119, 445-463.
40. Sokal RR, Rohlf FJ (1995) Biometry. W.H. Freeman, New York.
41. Sork VL, Nason J, Campbell DR, Fernandez JF (2001) Landscape approaches to historical and contemporary gene flow in plants. Trends in Ecology and Evolution, 14, 219-224.
42. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and post-glacial colonization routes in Europe. Molecular Ecology, 7, 453-464.
43. Van Devender TR, Burgess TL, Piper JC, Turner RM (1994) Paleoclimatic implications of Holocene plant remains from the Sierra Bacha, Sonora, Mexico. Quaternary Research, 41, 99-108.
44. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
45. Westfall RD, Conkle MT (1992) Allozyme markers in breeding zone designations. New Forests, 6, 279-309.
46. Whittaker J (1990) Graphical Methods in Applied Multivariate Statistics. J. Wiley and Son, New York.
47. Wright S (1951) The genetical structure of populations. Annals of Eugenics, 15, 323-354.
48. Zhivotovsky LA, Rosenberg NA, Feldman MW (2003) Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. American Journal of Human Genetics, 72, 1171-1186.