@article{4260,
abstract = {We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles. },
author = {Johnson, Toby and Nicholas Barton},
journal = {Genetics},
number = {1},
pages = {395 -- 411},
publisher = {Genetics Society of America},
title = {{The effect of deleterious alleles on adaptation in asexual populations}},
volume = {162},
year = {2002},
}
@article{4261,
abstract = {Until recently, it was impracticable to identify the genes that are responsible for variation in continuous traits, or to directly observe the effects of their different alleles. Now, the abundance of genetic markers has made it possible to identify quantitative trait loci (QTL) — the regions of a chromosome or, ideally, individual sequence variants that are responsible for trait variation. What kind of QTL do we expect to find and what can our observations of QTL tell us about how organisms evolve? The key to understanding the evolutionary significance of QTL is to understand the nature of inherited variation, not in the immediate mechanistic sense of how genes influence phenotype, but, rather, to know what evolutionary forces maintain genetic variability.},
author = {Nicholas Barton and Keightley, Peter D},
journal = {Nature Reviews Genetics},
pages = {11 -- 21},
publisher = {Nature Publishing Group},
title = {{Understanding quantitative genetic variation}},
doi = {10.1038/nrg700},
volume = {3},
year = {2002},
}
@article{4262,
abstract = {Natural populations are structured spatially into local populations and genetically into diverse ‘genetic backgrounds’ defined by different combinations of selected alleles. If selection maintains genetic backgrounds at constant frequency then neutral diversity is enhanced. By contrast, if background frequencies fluctuate then diversity is reduced. Provided that the population size of each background is large enough, these effects can be described by the structured coalescent process. Almost all the extant results based on the coalescent deal with a single selected locus. Yet we know that very large numbers of genes are under selection and that any substantial effects are likely to be due to the cumulative effects of many loci. Here, we set up a general framework for the extension of the coalescent to multilocus scenarios and we use it to study the simplest model, where strong balancing selection acting on a set of n loci maintains 2n backgrounds at constant frequencies and at linkage equilibrium. Analytical results show that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. However, simulation results reveal that the structured coalescent approach breaks down when the number of backgrounds approaches the population size, because of stochastic fluctuations in background frequencies. A new method is needed to extend the structured coalescent to cases with large numbers of backgrounds.},
author = {Nicholas Barton and Navarro, Arcadio},
journal = {Genetical Research},
number = {2},
pages = {129 -- 139},
publisher = {Cambridge University Press},
title = {{Extending the coalescent to multilocus systems: the case of balancing selection}},
doi = {10.1017/S0016672301005493},
volume = {79},
year = {2002},
}
@article{4263,
abstract = {We introduce a general recursion for the probability of identity in state of two individuals sampled from a population subject to mutation, migration, and random drift in a two-dimensional continuum. The recursion allows for the interactions induced by density-dependent regulation of the population, which are inevitable in a continuous population. We give explicit series expansions for large neighbourhood size and for low mutation rates respectively and investigate the accuracy of the classical Malécot formula for these general models. When neighbourhood size is small, this formula does not give the identity even over large scales. However, for large neighbourhood size, it is an accurate approximation which summarises the local population structure in terms of three quantities: the effective dispersal rate, σe; the effective population density, ρe; and a local scale, κ, at which local interactions become significant. The results are illustrated by simulations.},
author = {Nicholas Barton and Depaulis, Frantz and Etheridge, Alison M},
journal = {Theoretical Population Biology},
number = {1},
pages = {31 -- 48},
publisher = {Academic Press},
title = {{Neutral evolution in spatially continuous populations}},
doi = {10.1006/tpbi.2001.1557},
volume = {61},
year = {2002},
}
@article{4347,
abstract = {Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.},
author = {Huelsenbeck, John P and Jonathan Bollback and Levine, Amy M},
journal = {Systematic Biology},
number = {1},
pages = {32 -- 43},
publisher = {Oxford University Press},
title = {{Inferring the root of a phylogenetic tree}},
doi = {10.1080/106351502753475862},
volume = {51},
year = {2002},
}