SEARCH

SEARCH BY CITATION

Literature cited

  • Altukhov, Y. P., E. A. Salmenkova, and V. T. Omelchenko 2000. Management of Salmonid Fisheries in the British Isles: Towards a Practical Approach Based on Population Genetics. Blackwell Science, Oxford.
  • Baglinière, J., and A. Champigneulle 1986. Populations estimates of juvenile Atlantic salmon, Salmo salar, as indices of smolt production in the river Scorff, Brittany. Journal of Fish Biology 29:467482.
  • Baglinière, J., and G. Maisse 1985. Precocious maturation and smoltification in wild Atlantic salmon in the armoricain massif, France. Aquaculture 45:249263.
  • Baglinière, J., G. Maisse, and A. Nihouarn 1993. Comparison of two methods of estimating Atlantic salmon, Salmo salar, wild smolt production. In R. J. Gibson, and R. E. Cuting, eds. Production of Juvenile Atlantic Salmon, Salmo salar, in Natural Waters, Vol. 118, pp. 189201. Canadian Special Publication of Fisheries and Aquatic Sciences, Ottawa, ON, Canada.
  • Baglinière, J., F. Marchand, and V. Vauclin 2005. Interannual changes in recruitment of Atlantic salmon (Salmo salar) population in the river Oir (lower Normandy, France): relationship with spawners and in-stream habitat. Journal of Marine Science 62:69707.
  • Beaumont, M. 1999. Detecting population expansion and decline using microsatellites. Genetics 153:20132029.
  • Butler, J. 2004. Moray Firth Seal Management Plan: A Pilot Project for Managing Interactions Between Seals and Salmon in Scotland, Vol. 64. Moray Firth Seal Management Plan, The HDH Wills 1965 Charitable Trust, Aberlour, Morayshire.
  • Butler, J., S. Middlemas, S. McKelvey, I. McMyn, B. Leyshon, I. Walker, P. M. Thompson et al. 2008. The Moray Firth Seal Management Plan: an adaptive framework for balancing the conservation of seals, salmon, fisheries and wildlife tourism in the UK. Aquatic Conservation: Marine and Freshwater Ecosystems 18:10251038.
  • Chevalet, C. 2000. The number of lines of descent and fixation probabilities of alleles in the pure genetic drift process. Theoretical Population Biology 57:167175.
  • Chevalet, C., and N. Nikolic 2010. Distribution of coalescent times and distances between microsatellite alleles with changing effective population size. Theoretical Population Biology 77:152163.
  • Chikhi, L., V. Sousa, P. Luisi, B. Goossens, and M. Beaumont 2010. The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186:983995.
  • Cornuet, J., and G. Luikart 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:20012014.
  • Cornuet, J. M., F. Santos, M. A. Beaumont, C. P. Robert, J.-M. Marin, D. J. Balding, T. Guillemaud et al. 2008. Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24:27132719.
  • Debowski, P., and R. Bartel 1995. Homing sea trout (Salmo trutta L.) smolts released into polish rivers. Archives of Polish Fisheries 3:107122.
  • Di Rienzo, A., A. C. Peterson, J. C. Garza, A. M. Valdes, M. Slatkin, and N. B. Freimer. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America 91:31663170.
  • Drummond, A., A. Rambaut, B. Shapiro, and O. Pybus 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution 22:11851192.
  • Frankham, R. 1995. Effective population size/adult population size ratios in wildlife: a review. Genetics Research 66:95107.
  • Garcia-Vazquez, E., P. Moran, J. Martinez, J. Perez, B. de Gaudemar and E. Beall. 2001. Alternative mating strategies in Atlantic salmon and brown trout. Journal of Heredity 92:146149.
  • Gelman, A., and D. B. Rubin 1992. Inference from iterative simulation using multiple sequences. Statistical Science 7:457511.
  • Geyer, C. 2009. A Markov Chain Monte Carlo package for R. http://www.stat.umn.edu/geyer/mcmc/ (accessed on 23 May 2014).
  • Griffiths, R. C., and S. Tavaré 1994. Sampling theory for neutral alleles in a varying environment. Philosophical Transactions of the Royal Society of London B: Biological Sciences 344:403410.
  • Hare, M. P., L. Nunney, M. K. Schwartz, D. E. Ruzzante, M. Burford, R. S. Waples, K. Ruegg et al. 2011. Understanding and estimating effective population size for practical application in marine species management. Conservation Biology 25:438449.
  • Hawkins, A. 2000. Problems facing salmon in the sea summing up. In D. H. Mills, ed. The Ocean Life of Atlantic Salmon: Environmental and Biological Factors Influencing Survival, pp. 211222. Fishing News Books, Oxford.
  • Hedrick, P., and S. Kalinowski 2000. Inbreeding depression in conservation biology. Annual Review of Ecology, Evolution, and Systematics 31:139162.
  • Hoffman, J. I., S. M. Grant, J. Forcada, and C. D. Phillips 2011. Bayesian inference of a historical bottleneck in a heavily exploited marine mammal. Molecular Ecology 20:39894008.
  • Johns, M., and J. Hutchings 2001. The influence of male parr body size and mate competition on fertilization success and effective population size in Atlantic salmon. Heredity 86:675684.
  • Johns, M., and J. Hutchings 2002. Individual variation in Atlantic salmon fertilization success: implications for effective population size. Ecological Applications 12:184193.
  • Jonsson, B., and N. Jonsson 2004. Factors affecting marine production of Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 61:23692383.
  • Jonsson, B., N. Jonsson, and L. Hansen 2003. Atlantic salmon straying from river Imsa. Journal of Fish Biology 62:641657.
  • Jordan, W., T. Cross, W. Crozier, A. Ferguson, P. Galvin, R.H. Hurell, P. McGinnity et al. 2005. Allozyme variation in Atlantic salmon from the British Isles: associations with geography and the environment. Journal of Zoology 65(Suppl A):146168.
  • Kimmel, M., R. Chakraborty, J. P. King, M. Bamshad, W. S. Watkins, and L. B. Jorde 1998. Signatures of population expansion in microsatellite repeat data. Genetics 148:19211930.
  • Kingman, J. 1982a. On the genealogy of large populations. Journal of Applied Probability 19:2743.
  • Kingman, J. 1982b. The coalescent. Stochastic Processes and Their Applications 13:235248.
  • Kuhner, M., J. Yamoto, and J. Felsenstein 1998. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149:429434.
  • Laughton, R. 1991. The Movements of Adult Atlantic Salmon (Salmo salar L.) in the River Spey, as Determined by Radio Telemetry During 1988–1989. Scottish Fisheries, Research Report 50, Aberdeen.
  • Li, H., and R. Durbin 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493496.
  • Lohse, K., R. J. Harrison, and N. H. Barton 2011. A general method for calculating likelihoods under the coalescent process. Genetics 189:977987.
  • Nielsen, R., and M. Beaumont 2009. Statistical inferences in phylogeography. Molecular Ecology 18:10341047.
  • Nielsen, R., and J. Wakeley 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885896.
  • Nikolic, N., J. Butler, J. Baglinière, R. Laughton, I. McMyn and C. Chevalet 2009a. An examination of genetic diversity and effective population size in Atlantic salmon. Genetics Research 91:118.
  • Nikolic, N., F. Fève, C. Chevalet, B. Hoyheim, and J. Riquet 2009b. A set of 37 microsatellite DNA markers for genetic diversity and structure analysis of Atlantic salmon (Salmo salar) populations. Journal of Fish Biology 74:458466.
  • Parrish, D., J. Behnke, S. Gephard, S. McCormick, and G. Reeves 1998. Why aren't there more Atlantic salmon (Salmo salar)? Canadian Journal of Fisheries and Aquatic Sciences 55(Suppl 1):281287.
  • Peter, B., D. Wegmann, and L. Excoffier 2010. Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Molecular Ecology 19:46484660.
  • Pritchard, J., and M. Feldman 1996. Statistics for microsatellite variation based on coalescence. Theoretical Population Biology 50:325344.
  • Ptak, S., and M. Przeworski 2002. Evidence for population growth in humans is confounded by fine-scale population structure. Trends in Genetics 18:559563.
  • Pybus, O. G., A. Rambault, and P. H. Harvey 2000. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155:14291437.
  • Quinn, T. 1993. A review of homing and straying of wild and hatchery-produced salmon. Fisheries Research 17:2944.
  • R Development Core Team. 2008. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org (accessed on 23 May 2014).
  • Reich, D., and D. Goldstein 1998. Genetic evidence for a paleolithic human population expansion in Africa. Proceedings of the National Academy of Sciences of the United States of America 95:81198123.
  • Rogers, A. 1995. Genetic evidence for a pleistocene population explosion. Evolution 49:608615.
  • Rogers, A., and H. Harpending 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9:552569.
  • Rosenberg, N. A., J. K. Pritchard, J. L. Weber, H. M. Cann, K. K. Kidd, L. A. Zhivotovsky, and M. W. Feldman 2002. Genetic structure of human populations. Science 298:23812385.
  • Shaffer, M. L., L. Hood-Watchman, W. J. I. Snape, and I. Latchis 2000. Population viability analysis and conservation policy. In S. R. Beissinger, and D. R. McCullough, eds. Population Viability Analysis, pp. 123146. University of Chicago Press, Chicago, IL.
  • Shriver, M., L. Jin, R. Ferrell, and R. Deka 1997. Microsatellite data support an early population expansion in Africa. Genome Research 7:586591.
  • Skaala, O., and G. Naevdal 1989. Genetic differentiation between freshwater resident and anadromous brown trout (Salmo trutta), within watercourses. Journal of Fish Biology 34:597605.
  • Slatkin, M., and R. Hudson 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555562.
  • Stabell, O. 1984. Homing and olfaction in salmonids: a critical review with special reference to the Atlantic salmon. Biological Reviews of the Cambridge Philosophical Society 59:333338.
  • Stewart, D., G. Smith, and A. Youngson 2002. Tributary-specific variation in timing of return of adult Atlantic salmon (Salmo salar) to freshwater has a genetic component. Canadian Journal of Fisheries and Aquatic Sciences 59:276281.
  • Tishkoff, S. A., F. A. Reed, F. R. Friedlaender, C. Ehret, A. Ranciaro, A. Froment, J.B. Hirbo et al. 2009. The genetic structure and history of Africans and African Americans. Science 324:10351044.
  • Wakeley, J. 1999. Nonequilibrium migration in human history. Genetics 153:18631871.
  • Watkins, J. 2006. Microsatellite evolution: Markov transition functions for a suite of models. Theoretical Population Biology 71:147159.
  • Weiss, G., and A. von Haeseler 1998. Inference of population history using a likelihood approach. Genetics 149:15391546.
  • Whittaker, J., R. Harbord, N. Boxall, I. Mackay, R. Dawson and R. M. Sibly. 2003. Likelihood-based estimation of microsatellite mutation rates. Genetics 164:781787.
  • Wilson, I., and D. Balding 1998. Genealogical inference from microsatellite data. Genetics 150:499510.
  • Wu, C. H., and A. J. Drummond 2011. Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo. Genetics 188:151164.