Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data

Genetics

Volumn 169, Issue 3, 2005, Pages 1739-1752

  Wagner, Helene H ^a   Holderegger, Rolf ^a   Werth, Silke ^a   Gugerli, Felix ^a   Hoebee, Susan E ^a   Scheidegger, Christoph ^a  

^a SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; FUNGUS; GENETIC MODEL; GENETIC VARIABILITY; GENOTYPE; GEOSTATISTICAL ANALYSIS; LOBARIA PULMONARIA; NONHUMAN; PLOIDY; POPULATION; PRIORITY JOURNAL; REVIEW; SPATIAL AUTOCORRELATION ANALYSIS; TECHNIQUE; VARIOGRAM ANALYSIS;

ANALYSIS OF VARIANCE; CHROMOSOME MAPPING; GENETICS, POPULATION; GENOTYPE; MICROSATELLITE REPEATS; MODELS, GENETIC; MODELS, STATISTICAL; PULMONARIA; VARIATION (GENETICS);

EID: 17444367614     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.036038     Document Type: Review

References (60)

1. BALLOUX, F., and J. GOUDET, 2002 Statistical properties of population differentiation estimators under stepwise mutation in a finite island model. Mol. Ecol. 11: 771-783.
2. BALLOUX, F., and N. LUGON-MOULIN, 2002 The estimation of population differentiation with microsatellite markers. Mol. Ecol. 11: 155-165.
3. BALLOUX, F., L. LEHMANN and T. DE MEEUS, 2003 The population genetics of clonal and partially clonal diploids. Genetics 164: 1635-1644.
4. BARBUJANI, G., 1987 Autocorrelation of gene frequencies under isolation by distance. Genetics 117: 777-782.
5. BERTORELLE, G., and G. BARBUJANI, 1995 Analysis of DNA diversity by spatial autocorrelation. Genetics 140: 811-819.
6. BURROUGH, P. A., 1995 Spatial aspects of ecological data, pp. 213-251 in Data Analysis in Community and Landscape Ecology, edited by R. H. G. JONGMAN, C. J. F. TER BRAAK and O. F. R. VAN TONGEREN. Cambridge University Press, Cambridge, UK.
7. CAVALLI-SFORZA, L. L., 1984 Isolation by distance, pp. 229-248 in Human Population Genetics: The Pittsburgh Symposium, edited by A. CHAKRAVARTI. Van Nostrand Reinhold, New York.
8. CHUNG, M. G., and B. K. EPPERSON, 2000 Clonal and spatial genetic structure in Eurya emarginata (Theaceae). Heredity 84: 170-177.
9. CLIFF, A. D., and J. K. ORD, 1981 Spatial Processes: Models and Applications. Pion, London.
10. CRESSIE, N. A. C., 1993 Statistics for Spatial Data. John Wiley & Sons, New York.
11. CRESSIE, N., and D. M. HAWKINS, 1980 Robust estimation of the variogram. J. Int. Assoc. Math. Geol. 12: 115-125.
12. EPPERSON, B. K., 2003 Geographical Genetics. Princeton University Press, Princeton, NJ.
13. FENSTER, C. B., X. VEKEMANS and O. J. HARDY, 2003 Quantifying gene flow from spatial genetic structure data in a metapopulation of Chamaecrista fasciculata (Leguminosae). Evolution 57: 995-1007.
14. FORTIN, M.-J., M. R. T. DALE and J. VER HOEF, 2001 Spatial analysis in ecology, pp. 2051-2058 in The Encyclopedia of Environmetrics, edited by A. H. EL-SHAARAWI and W. W. PIEGORSCH. John Wiley & Sons, Chichester, UK.
15. FORTIN, M. J., B. BOOTS, F. CSILLAG and T. K. REMMEL, 2003 On the role of spatial stochastic models in understanding landscape indices in ecology. Oikos 102: 203-212.
16. GOLDSTEIN, D. B., A. R. LINARES, L. L. CAVALLI-SFORZA and M. W. FEEDMAN, 1995 An evaluation of genetic distances for use with microsatellite loci. Genetics 139: 463-471.
17. GOLDSTEIN, D. B., G. W. ROEMER, D. A. SMITH, D. E. REICH, A. BERGMAN et al., 1999 The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics 151: 797-801.
18. HÄMMERLI, A., and T. B. H. REUSCH, 2003 Genetic neighbourhood of clone structures in eelgrass meadows quantified by spatial autocorrelation of microsatellite markers. Heredity 91: 448-455.
19. HARDY, O. J., 2003 Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers. Mol. Ecol. 12: 1577-1588.
20. HARDY, O. J., and X. VEKEMANS, 1999 Isolation by distance in a continuous population: reconciliation between spatial autocorrelation analysis and population genetics models. Heredity 83: 145-154.
21. HARDY, O. J., and X. VEKEMANS, 2002 SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2: 618-620.
22. HEWITT, J. E., P. LEGENDRE, B. H. MCARDLE, S. F. THRUSH, C. BELEEHUMEUR et al., 1997 Identifying relationships between adult and juvenile bivalves at different spatial scales. J. Exp. Mar. Biol. Ecol. 216: 77-98.
23. IHAKA, R., and R. GENTLEMAN, 1996 R: a language for data analysis and graphics. J. Comp. Graph. Stat. 5: 299-314.
24. ISAAKS, E. H., and R. M. SRIVASTAVA, 1989 Applied Geostatistics. Oxford University Press, New York.
25. JOURNEL, A. G., and C. J. HUIJBREGTS, 1978 Mining Geostatistics. Academic Press, New York.
26. LEGENDRE, P., and L. LEGENDRE, 1998 Numerical Ecology. Elsevier, Amsterdam.
27. LICHSTEIN, J. W., T. R. SIMONS, S. A. SHRINER and K. E. FRANZREB, 2002 Spatial autocorrelation and autoregressive models in ecology. Ecol. Monogr. 72: 445-463.
28. LOISELLE, B. A., V. L. SORK, J. NASON and C. GRAHAM, 1995 Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am. J. Bot. 82: 1420-1425.
29. MANLY, B. F. J., 1997 Randomization, Bootstrap and Monte Carlo Methods in Biology. Chapman & Hall, London.
30. MEIRMANS, P. G., E. C. VLOT, J. C. M. DEN NIJS and S. B. J. MENKEN, 2003 Spatial ecological and genetic structure of a mixed population of sexual diploid and apomictic triploid dandelions. J. Evol. Biol. 16: 343-352.
31. MONESTIEZ, P., and M. GOULARD, 1997 Analysing spatial genetic structures by multivariate geostatistics: study of wild populations of perennial ryegrass (Lolium perenne), pp. 1197-1208 in Geostatistics Wollongong '96, edited by E. Y. BAAFI and N. A. SCHOFIELD. Kluwer, Dordrecht, The Netherlands.
32. NEI, M., 1978 Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
33. PALMER, M. W., 1990 The estimation of species richness by extrapolation. Ecology 71: 1195-1198.
34. PALMER, M. W., and P. S. WHITE, 1994 Scale dependence and the species-area relationship. Am. Nat. 144: 717-740.
35. PARKS, J. C., and C. R. WERTH, 1993 A study of spatial features of clones in a population of bracken fern, Pteridium aquilinum (Dennstaedtiaceae). Am. J. Bot. 80: 537-544.
36. PEBESMA, E. J., 2004 Multivariable geostatistics in S: the gstat package. Comput. Geosci. 30: 683-691.
37. PEBESMA, E., and C. G. WESSELING, 1998 Gstat, a program for geostatistical modelling, prediction and simulation. Comput. Geosci. 24: 17-31.
38. PIAZZA, A., and P. MENOZZI, 1983 Geographic variation in human gene frequencies, pp. 444-450 in Numerical Taxonomy, edited by J. FELSENSTEIN. Springer, Berlin.
39. PYRCZ, M., and C. DEUTSCH, 2003 The whole story on the hole effect. Newsl. Geostat. Assoc. Australas. 18: 3-5.
40. RENWICK, A., L. DAVISON, H. SPRATT, J. P. KING and M. KIMMEL, 2001 DNA dinucleotide evolution in humans: fitting theory to facts. Genetics 159: 737-747.
41. REUSCH, T. B. H., W. HUKRIEDE, W. T. STAM and J. L. OLSEN, 1999 Differentiating between clonal growth and limited gene flow using spatial autocorrelation of microsatellites. Heredity 83: 120-126.
42. ROSE, F., 1992 Temperate forest management: its effects on bryophyte and lichen floras and habitats, pp. 211-233 in Bryophytes and Lichens in a Changing Environment, edited by J. W. BATES and A. FARMER. Clarendon Press, Oxford.
43. ROUSSET, F., 1997 Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219-1228.
44. ROUSSET, F., 2000 Genetic differentiation between individuals. J. Evol. Biol. 13: 58-62.
45. ROUSSET, F., 2002 Inbreeding and relatedness coefficients: What do they measure? Heredity 88: 371-380.
46. SCHEIDEGGER, C., P. CLERC, M. DIETRICH, M. FREI, U. GRONER et al., 2002 Rote Liste der gefährdeten Arten der Schweiz: Baum-und Erdbewohnende Flechten. BUWAL, Bern, Switzerland.
47. SCHNEIDER, S., D. ROESSLI and L. EXCOFFIER, 2000 ARLEQUIN Version 2.000: A Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva.
48. SLATKIN, M., 1995 A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462.
49. SMOUSE, P. E., and R. PEAKALL, 1999 Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 82: 561-573.
50. SOKAL, R. R., and D. E. WARTENBERG, 1983 A test of spatial autocorrelation analysis using an isolation-by-distance model. Genetics 105: 219-237.
51. STREIFF, R., T. LABBE, R. BACILIERI, H. STEINKELLNER, J. GLÖSSL et al., 1998 Within-population genetic structure in Quercus robur L. and Quercus petraea (Matt.) Liebl. assessed with isozymes and microsatellites. Mol. Ecol. 7: 317-328.
52. VAN DER HULST, R. G. M., T. H. M. MES, M. FALQUE, P. STAM, J. C. M. DEN NIJS et al., 2003 Genetic structure of a population sample of apomictic dandelions. Heredity 90: 326-335.
53. VEKEMANS, X., and O. J. HARDY, 2004 New insights from fine-scale spatial genetic structure analyses in plant populations. Mol. Ecol. 13: 921-935.
54. VITTOZ, P., 1998 Flore et végétation du Parc jurassien vaudois: typologie, écologie et dynamiqu des milieux. Ph.D. Thesis, Université de Lausanne, Lausanne, Switzerland.
55. WAGNER, H. H., 2003 Spatial covariance in plant communities: integrating ordination, geostatistics, and variance testing. Ecology 84: 1045-1057.
56. WAGNER, H. H., 2004 Direct multiscale ordination with canonical correspondence analysis. Ecology 85: 342-351.
57. WALSER, J. C., C. SPERISEN, M. SOLIVA and C. SCHEIDEGGER, 2003 Fungus-specific microsatellite primers of lichens: application for the assessment of genetic variation on different spatial scales in Lobaria pulmonaria. Fungal Genet. Biol. 40: 72-82.
58. WALSER, J. C., F. GUGERLI, R. HOLDEREGGER, D. KUONEN and C. SCHEIDEGCER, 2004 Recombination and clonal propagation in different populations of the lichen Lobaria pulmonaria. Heredity 93: 322-329.
59. WIRTH, V., H. SCHÖLLER, P. SCHOLZ, G. ERNST, T. FEUERER et al., 1996 Rote Liste der Flechten (Lichenes) der Bundesrepublik Deutschland. Schriftenreihe für Vegetationskunde 28: 307-368.
60. YOSHIMURA, I., 1971 The genus Lobaria of Eastern Asia. J. Hattori Bot. Lab. 34: 231-364.