Recent demographic bottlenecks are not accompanied by a genetic signature in banner-tailed kangaroo rats (Dipodomys spectabilis)

Molecular Ecology

Volumn 16, Issue 12, 2007, Pages 2450-2462

  Busch, Joseph D ^a   Waser, Peter M ^b   DeWoody, J Andrew ^a  

^a PURDUE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

Demographic bottleneck; Dipodomys spectabilis; M ratio; Microsatellite; Mutation rate; Single sample methods

Indexed keywords

ANIMAL; ARTICLE; COMPARATIVE STUDY; DIPODOMYS; ENVIRONMENTAL PROTECTION; FOUNDER EFFECT; GENE FLOW; GENE FREQUENCY; GENETICS; METHODOLOGY; MUTATION; POPULATION DYNAMICS; POPULATION GENETICS; UNITED STATES;

ANIMALS; ARIZONA; CONSERVATION OF NATURAL RESOURCES; DIPODOMYS; FOUNDER EFFECT; GENE FLOW; GENE FREQUENCY; GENETICS, POPULATION; MUTATION; POPULATION DYNAMICS;

DIPODOMYS; DIPODOMYS SPECTABILIS; RATTUS;

EID: 34250198309     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03283.x     Document Type: Article

References (71)

1. Abdelkrim J, Pascal M, Samadi S (2005) Island colonization and founder effects: the invasion of the Guadeloupe Islands by ship rats (Rattus rattus). Molecular Ecology, 14, 2923 2931.
2. Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 2013 2029.
3. Beck NR, Double MC, Cockburn A (2003) Microsatellite evolution at two hypervariable loci revealed by extensive avian pedigrees. Molecular Biology and Evolution, 20, 54 61.
4. Berthier K, Charbonnel N, Galan M, Chaval Y, Cosson JF (2006) Migration and recovery of the genetic diversity during the increasing density phase in cyclic vole populations. Molecular Ecology, 15, 2665 2676.
5. Brown JH, Zeng Z (1989) Comparative population ecology of eleven species of rodents in the Chihuahuan desert. Ecology, 70, 1507 1525.
6. Burton C, Krebs CJ, Taylor EB (2002) Population genetic structure of the cyclic snowshoe hare (Lepus americanus) in southwestern Yukon, Canada. Molecular Ecology, 11, 1689 1701.
7. Cornuet JM, Luikart G (1996) Description and power analysis for two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144, 2001 2014.
8. Cutrera AP, Lacey EA, Busch C (2006) Intraspecific variation in effective population size in talar tuco-tucos (Ctenomys talarum): the role of demography. Journal of Mammalogy, 87, 108 116.
9. Davis C, Keane B, Swanson BJ et al. (2000) Characterization of microsatellite loci in banner-tailed and giant kangaroo rats, Dipodomys speciabilis and Dipodomys ingens. Molecular Ecology, 9, 642 645.
10. DeWoody JA, Fletcher DE, Wilkins SD, Nelson WS, Avise JC (1998) Molecular genetic dissection of spawning, parentage, and reproductive tactics in a population of redbreast sunfish, Lepomis auritus. Evolution, 52, 1802 1810.
11. Di Rienzo A, Peterson A, Garza JC et al. (1994) Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences, USA, 91, 3166 3170.
12. Ehrich D, Jorde PE (2005) High genetic variability despite high-amplitude population cycles in lemmings. Journal of Mammalogy, 86, 380 385.
13. Ellegren H (2000) Microsatellite mutations in the germline: implications for evolutionary inference. Trends in Genetics, 16, 551 558.
14. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5, 435 445.
15. Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Molecular Ecology, 10, 305 318.
16. Guinand B, Scribner KT (2003) Evaluation of methodology for detection of genetic bottlenecks: inferences from temporally replicated lake trout populations. Comptes Rendus Biologies, 326, S61 S67.
17. Hardy OJ, Vekemans X (2002) spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes, 2, 618 620.
18. Hartl DL, Clark AG (1989) Principles of Population Genetics, 2nd edn. Sinauer & Associates, Sunderland, Massachusetts.
19. Hedrick PW (2005) Genetics of Populations, 3rd edn. Jones and Bartlett, Sudbury, Massachusetts.
20. Jones WT (1984) Natal philopatry in banner-tailed kangaroo rats. Behavioral and Ecological Sociobiology, 15, 151 155.
21. Jones WT (1986) Survivorship in philopatric and dispersing kangaroo rats (Dipodomys spectabilis). Ecology, 67, 202 207.
22. Jones WT (1987) Dispersal patterns in kangaroo rats (Dipodomys spectabilis). In : Mammalian Dispersal Patterns: The Effects of Social Structure on Population Genetics (eds Chepko-Sade BD, Halpin ZT), pp. 119 127. University of Chicago Press, Chicago.
23. Jones WT, Waser PM, Elliott LF, Link NE, Bush BB (1988) Philopatry, dispersal, and habitat saturation in the banner-tailed kangaroo rat, Dipodomys spectabilis. Ecology, 69, 1466 1473.
24. Karlin S (1968) Rates of approach to homozygosity for finite stochastic models with variable population size. American Naturalist, 102, 443 455.
25. Keller LF, Jeffery KJ, Arcese P et al. (2001) Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers. Proceedings of the Royal Society of London. Series B, Biological Sciences, 268, 1387 1394.
26. Kimura M, Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics, 49, 725 738.
27. 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.
28. Kuo CH, Janzen FJ (2003) bottlesim: a bottleneck simulation program for long-lived species with overlapping generations. Molecular Ecology Notes, 3, 669 673.
29. Kuo CH, Janzen FJ (2004) Genetic effects of a persistent bottleneck on a natural population of ornate box turtles (Terrapene ornata). Conservation Genetics, 5, 425 437.
30. Lacey EA (2001) Microsatellite variation in solitary and social tuco-tucos: molecular properties and population dynamics. Heredity, 86, 628 637.
31. Li W-H, Ellsworth DL, Krushkal J, Chang BHJ, Hewett-Emmett D (1996) Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Molecular Phylogenetics and Evolution, 5, 182 817.
32. Lippe CA, Dumont P, Bernatchez L (2006) High genetic diversity and no inbreeding in the endangered copper redhorse, Moxostoma hubbsi (Catostomidae, Pisces): the positive sides of a long generation time. Molecular Ecology, 15, 1769 1780.
33. Luikart G, Cornuet JM (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology, 12, 228 237.
34. Luikart G, Allendorf FW, Cornuet JM, Sherwin WB (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity, 89, 238 247.
35. Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7, 639 655.
36. Martin AP, Palumbi SR (1993) Body size, metabolic rate, generation time, and the molecular clock. Proceedings of the National Academy of Sciences, USA, 90, 4087 4091.
37. Maruyama T, Fuerst PA (1984) Population bottlenecks and nonequilibrium models in population genetics. 2. Number of alleles in a small population that was formed by a recent bottleneck. Genetics, 108, 745 763.
38. Maruyama T, Fuerst PA (1985) Population bottlenecks and nonequilibrium models in population genetics. 3. Genic homozygosity in populations which experience periodic bottlenecks. Genetics, 111, 691 703.
39. Munger JC, Bowers MA, Jones WTJ (1983) Desert rodent populations: factors affecting abundance, distribution and genetic structure. Great Basin Naturalist, 7, 91 116.
40. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
41. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution, 29, 1 10.
42. Neumann K, Jansman H, Kayser A, Maak S, Gattermann R (2004) Multiple bottlenecks in threatened western European populations of the common hamster Cricetus cricetus (L.). Conservation Genetics, 5, 181 193.
43. Ogden R, Shuttleworth C, McEwing R, Cesarini S (2005) Genetic management of the red squirrel, Sciurus vulgaris: a practical approach to regional conservation. Conservation Genetics, 6, 511 525.
44. Ohta T, Kimura M (1973) The model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a genetic population. Genetic Research Cambridge, 22, 201 204.
45. Peakall R, Smouse PE (2006) genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295.
46. Piry S, Luikart G, Cornuet J-M (1999) bottleneck: a computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity, 90, 502 503.
47. Pope LC, Estoup A, Moritz C (2000) Phylogeography and population structure of an ecotonal marsupial, Bettongia tropica, determined using mtDNA and microsatellites. Molecular Ecology, 9, 2041 2053.
48. Redeker S, Andersen LW, Pertoldi C et al. (2006) Genetic structure, habitat fragmentation and bottlenecks in Danish bank voles (Clethrionomys glareolus). Mammalian Biology, 71, 144 158.
49. Rogers AR, Harpending H (1992) Population-growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552 569.
50. Sambrook J, Russell DW (2001) Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York.
51. Skvarla JL, Nichols JD, Hines JE, Waser PM (2004) Modeling interpopulation dispersal by banner-tailed kangaroo rats. Ecology, 85, 2737 2746.
52. Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial-DNA sequences in stable and exponentially growing populations. Genetics, 129, 555 562.
53. Spear SF, Peterson CR, Matocq MD, Storfer A (2006) Molecular evidence for historical and recent population size reductions of tiger salamanders (Ambystoma tigrinum) in Yellowstone National Park. Conservation Genetics, 7, 605 611.
54. Spencer CC, Neigel JE, Leberg PL (2000) Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Molecular Ecology, 9, 1517 1528.
55. Swanson BJ (2001) An empirical evaluation of effective population size estimators. PhD Thesis, Purdue University, West Lafayette, Indiana.
56. Triant DA, DeWoody JA (2006) Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences. Genetica, 128, 95 108.
57. Trizio I, Crestanello B, Galbusera et al. (2005) Geographical distance and physical barriers shape the genetic structure of Eurasian red squirrels (Sciurus vulgaris) in the Italian Alps. Molecular Ecology, 14, 469 481.
58. Wang JL (2005) Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360, 1395 1409.
59. Wang YQ, Williams DA, Gaines MS (2005) Evidence for a recent genetic bottleneck in the endangered Florida Keys silver rice rat (Oryzomys argentatus) revealed by microsatellite DNA analyses. Conservation Genetics, 6, 575 585.
60. Waples RS (1989) A generalized-approach for estimating effective population-size from temporal changes in allele frequency. Genetics, 121, 379 391.
61. Waser PM, Ayers JM (2003) Microhabitat use and population decline in banner-tailed kangaroo rats. Journal of Mammalogy, 84, 1031 1043.
62. Waser PM, DeWoody JA (2006) Polyandry in a philopatric rodent: female strategy or side effect of mate competition? Behavioral Ecology, 17, 971 978.
63. Waser P, Elliott LF (1991) Dispersal and genetic structure in kangaroo rats. Evolution, 45, 935 943.
64. Waser PM, Jones WT (1991) Survival and reproductive effort in banner-tailed kangaroo rats. Ecology, 72, 771 777.
65. Waser PM, Busch JD, McCormick CR, DeWoody JA (2006) Parentage analysis detects cryptic pre-capture dispersal in a philopatric rodent. Molecular Ecology, 15, 1929 1937.
66. Weber JL, Wong C (1993) Mutation of human short tandem repeats. Human Molecular Genetics, 2, 1123 1128.
67. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
68. Williamson-Natesan EG (2005) Comparison of methods for detecting bottlenecks from microsatellite loci. Conservation Genetics, 6, 551 562.
69. Winters JB, Waser PM (2003) Gene dispersal and outbreeding in a philopatric mammal. Molecular Ecology, 12, 2251 2259.
70. Wright S (1938) Size of population and breeding structure in relation to evolution. Science, 13, 430 431.
71. Zenger KR, Richardson BJ, Vachot-Griffin AM (2003) A rapid population expansion retains genetic diversity within European rabbits in Australia. Molecular Ecology, 12, 789 794.