Article

Maximum Likelihood Estimation of Population Growth Rates Based on the Coalescent

Department of Genetics, University of Washington, Seattle, Washington 98195, USA.
Genetics (Impact Factor: 4.87). 06/1998; 149(1):429-34.
Source: PubMed

ABSTRACT We describe a method for co-estimating 4Nemu (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling. Population growth (or decline) is assumed to be exponential. The estimates of growth rate are biased upwards, especially when 4Nemu is low; there is also a slight upwards bias in the estimate of 4Nemu itself due to correlation between the parameters. This bias cannot be attributed solely to Metropolis-Hastings sampling but appears to be an inherent property of the estimator and is expected to appear in any approach which estimates growth rate from genealogy structure. Sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus.

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    • "Estimates of genetic diversity (θ) with 95% CIs obtained from simulations using the ML coalescent-based approach of Kuhner et al. (1998); long-term effective population sizes (Ne) were derived from θ "
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    ABSTRACT: Genetic variation was examined in two endangered mussel species, Epioblasma brevidens and Epioblasma capsaeformis, and in a non-listed species, Lampsilis fasciola, in the Clinch River, Tennessee, USA, by screening mitochondrial DNA (mtDNA) sequences and nuclear DNA microsatellites. Patterns of mtDNA polymorphism exhibited different trends in long-term population sizes for each species during the late Pleistocene and Holocene (∼20 000 ya to present); namely, E. brevidens has declined over time, E. capsaeformis has remained demographically stable, and L. fasciola has expanded. However, analyses using microsatellites did not exhibit similar trends, perhaps because homoplasy had eliminated long-term population signatures for the loci examined. For both marker types, long-term effective population size (Ne) was low in E. brevidens, intermediate in E. capsaeformis, and high in L. fasciola. Moderately diverged mtDNA lineages, perhaps indicative of secondary contact, were observed in E. brevidens and E. capsaeformis. Perhaps the most surprising result of this study was the high level of genetic variation observed at both mtDNA and microsatellite DNA markers for L. fasciola, variation seemingly contrary to the relatively small demes that currently reside in the Clinch River. However, the data are consistent with known demographic and life-history traits of these three mussel species and their fish hosts, namely that they each use hosts with different dispersal capabilities, ranging from low, moderate, and high, respectively. The low divergence of mtDNA sequence variation reported in this and other recent mussel studies indicates that considerable extant population genetic variation probably originated during the late Pleistocene and Holocene. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.
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    • "Table S5. Assessment of past changes in N e within local populations based on maximum-likelihood estimates of g, the exponential growth parameter, calculated using FLUCTUATE (Kuhner et al. 1998). Table S6. "
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    • "Y. H. Qu et al. and upper bounds of the 95% confidence intervals, were estimated for mtDNA using fluctuate 1.4 (Kuhner et al., 1998) and scaled to Ne using a mutation rate of 1 9 10 À8 per year. Divergence times, which were converted to numbers of generations, were set to be the lower and upper bounds of the ABC estimated divergence times (Table 2). "
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