Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden charr

Molecular Ecology

Volumn 15, Issue 11, 2006, Pages 3175-3189

  Koizumi, Itsuro ^a   Yamamoto, Shoichiro ^b   Maekawa, Koji ^c  

^a UNIVERSITY OF HELSINKI   (Finland)

^b FISHERIES RESEARCH AGENCY   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Equilibrium nonequilibrium; Extinction colonization; Gene flow; Isolation by distance; Landscape genetics; Microgeographic scale

Indexed keywords

DNA; MICROSATELLITE DNA;

ANIMAL; ANIMAL DISEASE; ARTICLE; CHEMISTRY; DNA SEQUENCE; GENE FLOW; GENETIC DRIFT; GENETIC VARIABILITY; GENETICS; JAPAN; METHODOLOGY; POLYMERASE CHAIN REACTION; POPULATION GENETICS; REGRESSION ANALYSIS; RIVER; TROUT;

ANIMALS; DNA; GENE FLOW; GENETIC DRIFT; GENETICS, POPULATION; JAPAN; MICROSATELLITE REPEATS; POLYMERASE CHAIN REACTION; REGRESSION ANALYSIS; RIVERS; SEQUENCE ANALYSIS, DNA; TROUT; VARIATION (GENETICS);

SALVELINUS FONTINALIS; SALVELINUS MALMA;

EID: 33748614325     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2006.03019.x     Document Type: Article

References (57)

1. Angers B, Bernatchez L, Angers A, Desgroseillers L (1995) Specific microsatellite loci for brook charr reveal strong population subdivision on a microgeographic scale. Journal of Fish Biology, 47 (Suppl. A), 177-185.
2. Baer CF (1998) Population structure in a south-eastern US freshwater fish, Heterandria formosa: II. Gene flow and biogeography within the St. Johns River drainage. Heredity, 81, 404-411.
3. Burnham KP, Anderson DR (2002) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach, 2nd edn. Springer, New York.
4. Carlsson J, Nilsson J (2000) Population genetic structure of brown trout (Salmo trutta L.) within a northern boreal forest stream. Hereditas Lund, 132, 173-181.
5. Castric V, Bernatchez L (2004) Individual assignment test reveals differential restriction to dispersal between two salmonids despite no increase of genetic differences with distance. Molecular Ecology, 13, 1299-1312.
6. Corander J, Waldmann P, Sillanpää MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics, 163, 367-374.
7. Crispo E, Hendry AP (2005) Does time since colonization influence isolation by distance? A meta-analysis. Conservation Genetics, 6, 665-682.
8. Crow JF, Aoki K (1984) Group selection for a polygenic behavioural trait: Estimating the degree of population subdivisions. Proceedings of the National Academy of Sciences, USA, 81, 6073-6077.
9. El Mousadik A, Petit RJ (1996) High level of population differentiation for allelic richness among populations of the argan tree (Argania spinosa (L.) Skeels) endemic to Morocco. Theoretical Applied Genetics, 92, 832-839.
10. Elliott JM (1986) Spatial distribution and behavioural movements of migratory trout Salmo trutta in a Lake District stream. Journal of Animal Ecology, 55, 907-922.
11. Estoup A, Rousset F, Michalakis Y, Cornuet JM, Adriamanga M, Guyomard R (1998) Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta). Molecular Ecology, 7, 339-353.
12. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
13. Garnier S, Alibert P, Audiot P, Prieur B, Rasplus JY (2004) Isolation by distance and sharp discontinuities in gene frequencies: implications for the phylogeography of an alpine insect species, Carabus solieri. Molecular Ecology, 13, 1883-1897.
14. Goudet J (1999) PCA-GEN, a Computer Package which Performs Principal Component Analysis (PCA) on Gene Frequency Data. Available from http://www2.unil.ch/izea/softwares/pcagen.html.
15. Goudet J (2001) FSTAT, a Program to Estimate and Test Gene Diversities and Fixation Indices, Version 2.9.3. Available from http://www.unil.ch/izea/ softwares/fstat.html.
16. Harrison S, Taylor AD (1997) Empirical evidence for metapopulation dynamics. In: Metapopulation Biology (eds Hanski I, Gilpin ME), pp. 27-42. Academic Press, London.
17. Hartl DL, Clark AG (1997) Principles of Population Genetics, 3rd edn. Sinauer Associates, Sunderland, Massachusetts.
18. Hellberg ME (1994) Relationships between inferred levels of gene flow and geographic distance in a philopatric coral, Balanophyllia elegans. Evolution, 48, 1829-1854.
19. Hernandez-Martich JD, Smith MH (1997) Downstream gene flow and genetic structure of Gambusia holbrooki (eastern mosquitofish) populations. Heredity, 79, 295-301.
20. Hill MF, Hastings A, Botsford LW (2002) The effects of small dispersal rates on extinction times in structured metapopulation models. American Naturalist, 160, 389-402.
21. Hutchison DW, Templeton AR (1999) Correlation of pairwise genetic and geographic distance measures: Inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution, 53, 1898-1914.
22. Ingvarsson PK, Olsson K, Ericson L (1997) Extinction-recolonization dynamics in the mycophagous beetle Phalacrus substriatus. Evolution, 51, 187-195.
23. Irwin DE, Bensch S, Irwin JH, Price TD (2005) Speciation by distance in a ring species. Science, 307, 414-416.
24. Keyghobadi N, Roland J, Strobeck C (1999) Influence of landscape on the population genetic structure of the alpine butterfly Parnassius smintheus (Papilionidae). Molecular Ecology, 8, 1481-1495.
25. Kimura M, Weiss G (1964) The stepping stone model of population structure and the decrease of genetic correlations with distance. Genetics, 49, 561-576.
26. Koenig WD, VanVuren D, Hooge PN (1996) Detectability, philopatry, and the distribution of dispersal distances in vertebrates. Trends in Ecology and Evolution, 11, 514-517.
27. Koizumi I, Maekawa K (2003) Spawning migration of streamdwelling Dolly Varden in spring-fed tributaries of the Shiisorapuchi River, Japan. Journal of Freshwater Ecology, 18, 321-331.
28. Koizumi I, Maekawa K (2004) Metapopulation structure of stream-dwelling Dolly Varden charr inferred from patterns of occurrence in the Sorachi River basin, Hokkaido, Japan. Freshwater Biology, 49, 973-981.
29. Koizumi I, Yamamoto S, Maekawa K (2006) Female-biased migration in stream-dwelling Dolly Varden in the Shiisorapuchi River, Japan. Journal of Fish Biology, 68, 1513-1529.
30. Lande R (1993) Risks of population extinction from demographic and environmental stochasticity and random catastrophes. American Naturalist, 142, 911-927.
31. Liebers D, de Knijff P, Helbig AJ (2004) The herring gull complex is not a ring species. Proceedings of the Royal Society of London. Series B, Biological Sciences, 271, 893-901.
32. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution, 18, 189-197.
33. Manier MK, Arnold SJ (2005) Population genetic analysis identifies source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis). Molecular Ecology, 14, 3965-3976.
34. Mayr E (1942) Systematics and the Origin of Species. Columbia University Press, New York.
35. Morita K, Yamamoto S (2002) Effects of habitat fragmentation by damming on the persistence of stream-dwelling charr populations. Conservation Biology, 16, 1318-1323.
36. O'Reilly PT, Hamilton LC, McConnell SK, Wright JM (1996) Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Sciences, 53, 2292-2298.
37. Ovidio M, Philippart J-C (2002) The impact of small physical obstacles on upstream movements of six species of fish. Synthesis of a five years telemetry study in the River Meuse Basin. Hydrobiologia, 483, 55-69.
38. Peterson MA, Denno RF (1998) The influence of dispersal and diet breadth on patterns of genetic isolation by distance in phytophagous insects. American Naturalist, 152, 428-446.
39. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
40. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences, USA, 94, 9197-9201.
41. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetic software for exact tests and ecumenism. Journal of Heredity, 86, 248-249.
42. Rice W (1989) Analyzing tables of statistical tests. Evolution, 43, 223-225.
43. Rieman B, Lee D, McIntyre J, Overton K, Thurow R (1993) Consideration of extinction risks for salmonids. Currents, Fish Habitat Relations Technical Bulletin No. 14.
44. Rodríguez MA (2002) Restricted movement in stream fish: the paradigm is incomplete, not lost. Ecology, 83, 1-13.
45. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219-1228.
46. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning a Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York.
47. Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN, Version 2.001: a Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
48. Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution, 47, 264-279.
49. Spear SF, Peterson CR, Matocq MD, Storfer A (2005) Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum). Molecular Ecology, 14, 2553-2564.
50. Taylor EB, Redenbach Z, Costello AB, Pollard SM, Pacas CJ (2001) Nested analysis of genetic diversity in northwestern North American char, Dolly Varden (Salvelinus malma) and bull trout (Salvelinus confluentus). Canadian Journal of Fisheries and Aquatic Sciences, 58, 406-420.
51. Taylor EB, Stamford MD, Baxter JS (2003) Population subdivision in westslope cutthroat trout (Oncorhynchus clarki lewisi) at the northern periphery of its range: evolutionary inferences and conservation implications. Molecular Ecology, 12, 2609-2622.
52. Waples RS, Gaggiotti O (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology, 15, 1419-1439.
53. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
54. Whitlock MC (1992) Nonequilibrium population structure in forked fungus beetles: extinction, colonization, and the genetic variance among populations. American Naturalist, 139, 952-970.
55. ST ≠ 1/(4Nm + 1). Heredity, 82, 117-125.
56. Wright S (1943) Isolation by distance. Genetics, 28, 114-138.
57. Yamamoto S, Morita K, Koizumi I, Maekawa K (2004) Genetic differentiation of white-spotted charr (Salvelinus leucomaenis) populations after habitat fragmentation: spatio-temporal changes of gene frequencies. Conservation Genetics, 5, 529-538.