Estimating Effective Population Size and Migration Rates From Genetic Samples Over Space and Time

Genetics - Tập 163 Số 1 - Trang 429-446 - 2003
Jinliang Wang1, Michael C. Whitlock2
1Institute of Zoology, Zoological Society of London, London NW1 4RY, United Kingdom
2Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada

Tóm tắt

AbstractIn the past, moment and likelihood methods have been developed to estimate the effective population size (Ne) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of Ne if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of Ne and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of Ne, respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both Ne and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers.

Từ khóa


Tài liệu tham khảo

Anderson, 2000, Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples, Genetics, 156, 2109, 10.1093/genetics/156.4.2109

Arntzen, 1991, Restricted gene flow in a moving hybrid zone of newts (Triturus cristatus, Triturus marmoratus) in western France, Evolution, 45, 805, 10.1111/j.1558-5646.1991.tb04352.x

Beaumont, 1999, Detecting population expansion and decline using microsatellites, Genetics, 153, 2013, 10.1093/genetics/153.4.2013

Beerli, 2001, Maximum likelihood estimation of a migration matrix and effective population size in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci, USA, 98, 4563, 10.1073/pnas.081068098

Caballero, 1994, Developments in the prediction of effective population size, Heredity, 73, 657, 10.1038/hdy.1994.174

Dobzhansky, 1941, Genetics of natural populations. V. Relations between mutation rate and accumulation of lethals in populations of D. pseudoobscura, Genetics, 26, 23, 10.1093/genetics/26.1.23

Ewens, 1979, Mathematical Population Genetics

Feller, 1950, An Introduction to Probability Theory and Its Applications

Fiumera, 1999, Effective population size in the captive breeding program of the Lake Victoria cichlid Paralabidochromis chilotes, Zoo Biol., 18, 215, 10.1002/(SICI)1098-2361(1999)18:3<215::AID-ZOO5>3.0.CO;2-D

Fiumera, 2000, Effective population size and maintenance of genetic diversity in captive-bred populations of a Lake Victoria cichlid, Conserv. Biol., 14, 886, 10.1046/j.1523-1739.2000.97337.x

Frankham, 1995, Effective population-size adult-population size ratios in wildlife—a review, Genet. Res., 66, 95, 10.1017/S0016672300034455

Funk, 1999, Small effective population size in the long-toed salamander, Mol. Ecol., 8, 1633, 10.1046/j.1365-294x.1999.00748.x

Hayward, 2000, Dispersion patterns of young great crested newts (Triturus cristatus), Herpetol. J., 10, 129

Hill, 1981, Estimation of effective population size from data on linkage disequilibrium, Genet. Res., 38, 209, 10.1017/S0016672300020553

Jehle, 2000, High aquatic niche overlap in the newts Triturus cristatus and Triturus marmoratus (Amphibia, Urodela), Hydrobiologia, 437, 149, 10.1023/A:1026554907400

Jehle, 2001, The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T. marmoratus), Mol. Ecol., 10, 839, 10.1046/j.1365-294X.2001.01237.x

Kantanen, 1999, Temporal changes in genetic variation of North European cattle breeds, Anim. Genet., 30, 16, 10.1046/j.1365-2052.1999.00379.x

Krimbas, 1971, The genetics of Dacus oleae. V, Changes of esterase polymorphism in a natural population following insecticide control: Selection or drift? Evolution, 25, 454

Labate, 1999, Temporal changes in allele frequencies in two reciprocally selected maize populations Theor, Appl. Genet., 99, 1166, 10.1007/s001220051321

Luikart, 1999, Estimating the effective number of breeders from heterozygote excess in progeny, Genetics, 151, 1211, 10.1093/genetics/151.3.1211

Lynch, 1998, Genetics and Analysis of Quantitative Traits

Milner, 1985, A genetic model of stock identification in mixed populations of pacific salmon, Oncorhyncus spp, Mar. Fish. Rev., 47, 1

Nei, 1981, Genetic drift and estimation of effective population size, Genetics, 98, 625, 10.1093/genetics/98.3.625

Nielsen, 2001, Distinguishing migration from isolation: an MCMC approach, Genetics, 158, 885, 10.1093/genetics/158.2.885

Pamilo, 1980, On the estimation of population size from allele frequency changes, Genetics, 95, 1055, 10.1093/genetics/95.4.1055

Pollak, 1983, A new method for estimating the effective population size from allele frequency changes, Genetics, 104, 531, 10.1093/genetics/104.3.531

Press, 1996, Numerical Recipes in Fortran 77, Ed. 2

Pudovkin, 1996, On the potential for estimating the effective number of breeders from heterozygote-excess in progeny, Genetics, 144, 383, 10.1093/genetics/144.1.383

Rannala, 1997, Detecting immigration by using multilocus genotypes. Proc. Natl. Acad. Sci, USA, 94, 9197, 10.1073/pnas.94.17.9197

Rousset, 2001, Inferences from spatial population genetics, Handbook of Statistical Genetics, 179

Schwartz, 1999, Using genetics to estimate the size of wild populations: many methods, much potential, uncertain utility, Anim. Conserv., 2, 321, 10.1111/j.1469-1795.1999.tb00079.x

Slatkin, 1987, Gene flow and the geographic structure of natural-populations, Science, 236, 787, 10.1126/science.3576198

Tajima, 1984, Note on genetic drift and estimation of effective population size, Genetics, 106, 569, 10.1093/genetics/106.3.569

Turner, 1999, Temporal genetic variation of mitochondrial DNA and the female effective population size of red drum (Sciaenops ocellatus) in the northern Gulf of Mexico, Mol. Ecol., 8, 1223, 10.1046/j.1365-294x.1999.00662.x

Vitalis, 2001, Estimation of effective population size and migration rate from one- and two-locus identity measures, Genetics, 157, 911, 10.1093/genetics/157.2.911

Wang, 2001, A pseudo-likelihood method for estimating effective population size from temporally spaced samples, Genet. Res., 78, 243, 10.1017/S0016672301005286

Wang, 2001, Optimal marker-assisted selection to increase the effective size of small populations, Genetics, 157, 867, 10.1093/genetics/157.2.867

Wang, 1999, Developments in predicting the effective size of subdivided populations, Heredity, 82, 212, 10.1038/sj.hdy.6884670

Waples, 1989, A generalized approach for estimating effective population size from temporal changes in allele frequency, Genetics, 121, 379, 10.1093/genetics/121.2.379

Whitlock, 1999, Indirect measures of gene flow and migration: FST not equal to 1/(4Nm+1), Heredity, 82, 117, 10.1038/sj.hdy.6884960

Williamson, 1999, Using maximum likelihood to estimate population size from temporal changes in allele frequencies, Genetics, 152, 755, 10.1093/genetics/152.2.755

Wright, 1931, Evolution in Mendelian populations, Genetics, 16, 97, 10.1093/genetics/16.2.97

Thông tin
Thông tin xuất bản

Genetics

Tập 163 Số 1

429-446

Thông tin tác giả