Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation

Molecular Ecology

Volumn 23, Issue 11, 2014, Pages 2653-2668

  Baalsrud, Helle Tessand ^a,b   Sæther, Bernt Erik ^a   Hagen, Ingerid Julie ^a   Myhre, Ane Marlene ^a   Ringsby, Thor Harald ^a   Pärn, Henrik ^a   Jensen, Henrik ^a  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

Author keywords

dispersal; effective population size; genetic drift; microsatellites; population size; sex ratio

Indexed keywords

PASSER DOMESTICUS;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; DISPERSAL; EFFECTIVE POPULATION SIZE; GENE FLOW; GENETIC DRIFT; GENETICS; INBREEDING; MICROSATELLITES; NORWAY; POPULATION DENSITY; POPULATION DYNAMICS; POPULATION GENETICS; POPULATION SIZE; SEX RATIO; SPARROW;

DISPERSAL; EFFECTIVE POPULATION SIZE; GENETIC DRIFT; MICROSATELLITES; POPULATION SIZE; SEX RATIO;

ANIMALS; GENE FLOW; GENETIC DRIFT; GENETICS, POPULATION; INBREEDING; MODELS, GENETIC; NORWAY; POPULATION DENSITY; POPULATION DYNAMICS; SEX RATIO; SPARROWS;

EID: 84901493693     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12770     Document Type: Article

References (70)

1. Anderson EC, (2005) An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood. Genetics, 170, 955-967.
2. Anderson TR, (2006) Biology of the Ubiquitous House Sparrow-From Genes to Populations. Oxford University Press, New York.
3. Anderson EC, Garza JC, (2009) Estimation of Population Size with Molecular Genetic Data. Technical Memorandum NMFS, NOAA, Santa Cruz, California.
4. Ardren WR, Kapuscinski AR, (2003) Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout. Molecular Ecology, 12, 35-49.
5. Beebee TJC, (2009) A comparison of single-sample effective size estimators using empirical toad (Bufo calamita) population data: genetic compensation and population size-genetic diversity correlations. Molecular Ecology, 18, 4790-4797.
6. Berthier P, Beaumont MA, Cornuet JM, Luikart G, (2002) Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics, 160, 741-751.
7. Billing AM, Lee AM, Skjelseth S, et al,. (2012) Evidence of inbreeding depression but not inbreeding avoidance in a natural house sparrow population. Molecular Ecology, 21, 1487-1499.
8. Burnham KP, Anderson DR, (2002) Model Selection and Multimodal Inference: A Practical Information-Theoretic Approach, 2nd edn. Springer Verlag, New York.
9. Caballero A, (1994) Developments in the prediction of effective population size. Heredity, 73, 657-679.
10. Charlesworth B, (2009) Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics, 10, 195-205.
11. Crow JF, Denniston C, (1988) Inbreeding and variance effective population numbers. Evolution, 42, 482-495.
12. Crow JF, Kimura M, (1970) An Introduction to Population Genetics Theory. Harber and Row, New York.
13. Dawson DA, Horsburgh GJ, Krupa AP, et al,. (2012) Microsatellite resources for Passeridae species: a predicted microsatellite map of the house sparrow Passer domesticus. Molecular Ecology Resources, 12, 501-523.
14. Elphinstone MS, Hinten GN, Anderson MJ, Nock CJ, (2003) An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies. Molecular Ecology Notes, 3, 317-320.
15. Engen S, Lande R, Sæther B-E, (2005) Effective size of a fluctuating age-structured population. Genetics, 170, 941-954.
16. Engen S, Ringsby TH, Sæther B-E, et al,. (2007) Effective size of fluctuating populations with two sexes and overlapping generations. Evolution, 61, 1873-1885.
17. England PR, Cornuet JM, Berthier P, Tallmon DA, Luikart G, (2006) Estimating effective population size from linkage disequilibrium: severe bias in small samples. Conservation Genetics, 7, 303-308.
18. Felsenstein J, (1971) Inbreeding and variance effective numbers in populations with overlapping generations. Genetics, 68, 581-597.
19. Frankham R, (1995) Effective population size/adult population size ratios in wildlife: a review. Genetical Research, 66, 95-107.
20. Frankham R, (1996) Relationship of genetic variation to population size in wildlife. Conservation Biology, 10, 1500-1508.
21. Frankham R, (2010) Challenges and opportunities of genetic approaches to biological conservation. Biological Conservation, 143, 1919-1927.
22. Franklin IR, Frankham R, (1998) How large must populations be to retain evolutionary potential? Animal Conservation, 1, 69-70.
23. Fraser DJ, Hansen MM, Ostergaard S, Tessier N, Legault M, Bernatchez L, (2007) Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems. Molecular Ecology, 16, 3866-3889.
24. Griffith SC, Dawson DA, Jensen H, et al,. (2007) Fourteen polymorphic microsatellite loci characterized in the house sparrow Passer domesticus (Passeridae, Aves). Molecular Ecology Notes, 7, 333-336.
25. Hedrick PW, Fredrickson R, (2010) Genetic rescue guidelines with examples from Mexican wolves and Florida panthers. Conservation Genetics, 11, 615-626.
26. Hedrick PW, Gilpin ME, (1997) Genetic effective size of a metapopulation. In: Metapopulation Biology-Ecology, Genetics, and Evolution (eds, Hanski IA, Gilpin ME,), pp. 165-181. Academic Press, London.
27. Hill WG, (1972) Effective size of populations with overlapping generations. Theoretical Population Biology, 3, 278-289.
28. Hoffman EA, Schueler FW, Blouin MS, (2004) Effective population sizes and temporal stability of genetic structure in Rana pipiens, the northern leopard frog. Evolution, 58, 2536-2545.
29. Husby A, Sæther B-E, Jensen H, Ringsby TH, (2006) Causes and consequences of adaptive seasonal sex ratio variation in house sparrows. Journal of Animal Ecology, 75, 1128-1139.
30. Jensen H, Sæther B-E, Ringsby TH, Tufto J, Griffith SC, Ellegren H, (2003) Sexual variation in heritability and genetic correlations of morphological traits in house sparrow (Passer domesticus). Journal of Evolutionary Biology, 16, 1296-1307.
31. Jensen H, Sæther B-E, Ringsby TH, Tufto J, Griffith SC, Ellegren H, (2004) Lifetime reproductive success in relation to morphology in the house sparrow Passer domesticus. Journal of Animal Ecology, 73, 599-611.
32. Jensen H, Svorkmo-Lundberg T, Ringsby TH, Sæther B-E, (2006) Environmental influence and cohort effects in a sexual ornament in the house sparrow, Passer domesticus. Oikos, 114, 212-224.
33. Jensen H, Steinsland I, Ringsby TH, Sæther B-E, (2008) Evolutionary dynamics of a sexual ornament in the house sparrow (Passer domesticus): the role of indirect selection within and between sexes. Evolution, 62, 1275-1293.
34. Jensen H, Moe R, Hagen IJ, et al,. (2013) Genetic variation and structure of house sparrow populations: is there an island effect? Molecular Ecology, 22, 1792-1805.
35. Kalinowski ST, Waples RS, (2002) Relationship of effective to census size in fluctuating populations. Conservation Biology, 16, 129-136.
36. Kekkonen J, Seppä P, Hanski IK, Jensen H, Väisänen RA, Brommer JE, (2011) Low genetic differentiation in a sedentary bird: house sparrow population genetics in a contiguous landscape. Heredity, 106, 183-190.
37. Kimura M, Crow JF, (1963) The measurement of effective population number. Evolution, 17, 279-288.
38. Leberg P, (2005) Genetic approaches for estimating the effective size of populations. Journal of Wildlife Management, 69, 1385-1399.
39. Luikart G, Ryman N, Tallmon DA, Schwartz MK, Allendorf FW, (2010) Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics, 11, 355-373.
40. Nunney L, (1993) The influence of mating system and overlapping generations on effective population size. Evolution, 47, 1329-1341.
41. Nunney L, (1995) Measuring the ratio of effective population size to adult numbers using genetic and ecological data. Evolution, 49, 389-392.
42. Ovaskainen O, Hanski IA, (2004) Metapopulation dynamics in highly fragmented landscapes. In: Ecology, Genetics, and Evolution of Metapopulations (eds, Hanski IA, Gaggiotti OE,), pp. 73-103. Elsevier Academic Press, San Diego, California.
43. Palstra FP, Ruzzante DE, (2011) Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish. Heredity, 107, 444-455.
44. Pärn H, Jensen H, Ringsby TH, Sæther B-E, (2009) Sex-specific fitness correlates of dispersal in a house sparrow metapopulation. Journal of Animal Ecology, 78, 1216-1225.
45. Pärn H, Ringsby TH, Jensen H, Sæther B-E, (2012) Spatial heterogeneity in the effects of climate and density-dependence on dispersal in a house sparrow metapopulation. Proceedings of the Royal Society Biological Sciences, 279, 144-152.
46. Phillipsen IC, Funk WC, Hoffman EA, Monsen KJ, Blouin MS, (2011) Comparative analyses of effective population size within and among species: Ranid frogs as a case study. Evolution, 65, 2927-2945.
47. Pinheiro J, Bates D, DebRoy S, Sarkar D, (2011) nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-102. Available from: http://CRAN.R-project.org/package=nlme.
48. R Development Core Team (ed.) (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
49. Ringsby TH, Sæther B-E, Tufto J, Jensen H, Solberg EJ, (2002) Asynchronous spatiotemporal demography of a house sparrow metapopulation in a correlated environment. Ecology, 83, 561-569.
50. Ringsby TH, Sæther B-E, Jensen H, Engen S, (2006) Demographic characteristics of extinction in a small, insular population of house sparrows in northern Norway. Conservation Biology, 20, 1761-1767.
51. Sæther B-E, Ringsby TH, Bakke Ø, Solberg EJ, (1999) Spatial and temporal variation in demography of a house sparrow metapopulation. Journal of Animal Ecology, 68, 628-637.
52. Schwartz MK, Luikart G, Waples RS, (2007) Genetic monitoring as a promising tool for conservation and management. Trends in Ecology & Evolution, 22, 25-33.
53. Tallmon DA, Koyuk A, Luikart G, Beaumont MA, (2008) ONeSAMP: a program to estimate effective population size using approximate Bayesian computation. Molecular Ecology Resources, 8, 299-301.
54. Templeton AR, Read B, (1984) Factors eliminating inbreeding depression in a captive herd of speke's gazelle (Gazella spekei). Zoo Biology, 3, 177-199.
55. Tufto J, Ringsby TH, Dhondt AA, Adriaensen F, Matthysen E, (2005) A parametric model for estimation of dispersal patterns applied to five passerine spatially structured populations. American Naturalist, 165, E13-E26.
56. Wang JL, (2001) A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research, 78, 243-257.
57. Wang JL, (2005) Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society B-Biological Sciences, 360, 1395-1409.
58. Wang JL, (2009) A new method for estimating effective population sizes from a single sample of multilocus genotypes. Molecular Ecology, 18, 2148-2164.
59. Wang JL, Caballero A, (1999) Developments in predicting the effective size of subdivided populations. Heredity, 82, 212-226.
60. Wang JL, Whitlock MC, (2003) Estimating effective population size and migration rates from genetic samples over space and time. Genetics, 163, 429-446.
61. Waples RS, (1989) A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics, 121, 379-391.
62. Waples RS, (2005) Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Molecular Ecology, 14, 3335-3352.
63. Waples RS, (2010) Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size. Molecular Ecology Resources, 10, 785-796.
64. Waples RS, Do C, (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8, 753-756.
65. Waples RS, Do C, (2010) Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications, 3, 244-262.
66. Waples RS, England PR, (2011) Estimating contemporary effective population size on the basis of linkage disequilibrium. Genetics, 189, 633-644.
67. Waples RS, Yokota M, (2007) Temporal estimates of effective population size in species with overlapping generations. Genetics, 175, 219-233.
68. Whitlock MC, Barton NH, (1997) The effective size of a subdivided population. Genetics, 146, 427-441.
69. Wright S, (1931) Evolution in Mendelian populations. Genetics, 16, 98-159.
70. Wright S, (1938) Size of population and breeding structure in relation to evolution. Science, 87, 430-431.