@article{3380, abstract = {Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds.}, author = {Logeswaran, Sayanthan and Barton, Nicholas H}, journal = {Genetical Research}, number = {3}, pages = {221 -- 232}, publisher = {Cambridge University Press}, title = {{Mapping Mendelian traits in asexual progeny using changes in marker allele frequency}}, doi = {10.1017/S0016672311000115}, volume = {93}, year = {2011}, } @article{3390, abstract = {What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a 'pedigree' of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual's reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction analogous to the Wright-Fisher model, an individual's reproductive value is determined within ~10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it, and that conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual's genetic contribution to the population can be summarized through a single number: its reproductive value.}, author = {Barton, Nicholas H and Etheridge, Alison}, journal = {Genetics}, number = {4}, pages = {953 -- 973}, publisher = {Genetics Society of America}, title = {{The relation between reproductive value and genetic contribution}}, doi = {10.1534/genetics.111.127555}, volume = {188}, year = {2011}, } @article{3391, abstract = {Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time}, author = {de Vladar, Harold and Barton, Nicholas H}, journal = {Trends in Ecology and Evolution}, number = {8}, pages = {424 -- 432}, publisher = {Cell Press}, title = {{The contribution of statistical physics to evolutionary biology}}, doi = {10.1016/j.tree.2011.04.002}, volume = {26}, year = {2011}, } @article{3394, abstract = {Random genetic drift shifts clines in space, alters their width, and distorts their shape. Such random fluctuations complicate inferences from cline width and position. Notably, the effect of genetic drift on the expected shape of the cline is opposite to the naive (but quite common) misinterpretation of classic results on the expected cline. While random drift on average broadens the overall cline in expected allele frequency, it narrows the width of any particular cline. The opposing effects arise because locally, drift drives alleles to fixation—but fluctuations in position widen the expected cline. The effect of genetic drift can be predicted from standardized variance in allele frequencies, averaged across the habitat: 〈F〉. A cline maintained by spatially varying selection (step change) is expected to be narrower by a factor of relative to the cline in the absence of drift. The expected cline is broader by the inverse of this factor. In a tension zone maintained by underdominance, the expected cline width is narrower by about 1 – 〈F〉relative to the width in the absence of drift. Individual clines can differ substantially from the expectation, and we give quantitative predictions for the variance in cline position and width. The predictions apply to clines in almost one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or along a coast line and give a guide to what patterns to expect in two dimensions.}, author = {Polechova, Jitka and Barton, Nicholas H}, journal = {Genetics}, number = {1}, pages = {227 -- 235}, publisher = {Genetics Society of America}, title = {{Genetic drift widens the expected cline but narrows the expected cline width}}, doi = {10.1534/genetics.111.129817}, volume = {189}, year = {2011}, } @article{3395, abstract = {Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data.}, author = {Palero, Ferran and Abello, Pere and Macpherson, Enrique and Beaumont, Mark and Pascual, Marta}, journal = {Biological Journal of the Linnean Society}, number = {2}, pages = {407 -- 418}, publisher = {Wiley-Blackwell}, title = {{Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas}}, doi = {10.1111/j.1095-8312.2011.01728.x}, volume = {104}, year = {2011}, } @article{3778, author = {Barton, Nicholas H}, journal = {Heredity}, number = {2}, pages = {205 -- 206}, publisher = {Nature Publishing Group}, title = {{Estimating linkage disequilibria}}, doi = {10.1038/hdy.2010.67}, volume = {106}, year = {2011}, } @article{3784, abstract = {Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus.}, author = {Palero, Ferran and Guerao, Guillermo and Clark, Paul and Abello, Pere}, journal = {Journal of the Marine Biological Association of the United Kingdom}, number = {2}, pages = {485 -- 492}, publisher = {Cambridge University Press}, title = {{Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description}}, doi = {10.1017/S0025315410000287}, volume = {91}, year = {2011}, } @article{3393, abstract = {Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.}, author = {Barton, Nicholas H and Turelli, Michael}, issn = {1537-5323}, journal = {American Naturalist}, number = {3}, pages = {E48 -- E75}, publisher = {University of Chicago Press}, title = {{Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects}}, doi = {10.1086/661246}, volume = {178}, year = {2011}, } @article{3375, abstract = {By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states.}, author = {de Vladar, Harold and Barton, Nicholas H}, journal = {Journal of the Royal Society Interface}, number = {58}, pages = {720 -- 739}, publisher = {Royal Society}, title = {{The statistical mechanics of a polygenic character under stabilizing selection mutation and drift}}, doi = {10.1098/rsif.2010.0438}, volume = {8}, year = {2011}, } @article{474, abstract = {Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.}, author = {Barton, Nicholas H and Kelleher, Jerome and Etheridge, Alison}, journal = {Evolution}, number = {9}, pages = {2701 -- 2715}, publisher = {Wiley-Blackwell}, title = {{A new model for extinction and recolonization in two dimensions: Quantifying phylogeography}}, doi = {10.1111/j.1558-5646.2010.01019.x}, volume = {64}, year = {2010}, } @misc{9764, author = {Rosas, Ulises and Barton, Nicholas H and Copsey, Lucy and Barbier De Reuille, Pierre and Coen, Enrico}, publisher = {Public Library of Science}, title = {{Heterosis and the drift load}}, doi = {10.1371/journal.pbio.1000429.s003}, year = {2010}, } @article{3303, abstract = {Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. }, author = {Weissman, Daniel and Feldman, Marcus and Fisher, Daniel}, journal = {Genetics}, number = {4}, pages = {1389 -- 1410}, publisher = {Genetics Society of America}, title = {{The rate of fitness-valley crossing in sexual populations}}, doi = {10.1534/genetics.110.123240}, volume = {186}, year = {2010}, } @article{3604, abstract = {We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales.}, author = {Senn, Helen and Goodman, Simon and Swanson, Graeme and Barton, Nicholas H and Pemberton, Josephine}, journal = {Molecular Ecology}, number = {5}, pages = {910 -- 924}, publisher = {Wiley-Blackwell}, title = {{Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland}}, doi = {10.1111/j.1365-294X.2009.04497.x}, volume = {19}, year = {2010}, } @article{3772, author = {Barton, Nicholas H}, journal = {PLoS Genetics}, number = {6}, publisher = {Public Library of Science}, title = {{Understanding adaptation in large populations}}, doi = {10.1371/journal.pgen.1000987}, volume = {6}, year = {2010}, } @article{3773, abstract = {If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry.}, author = {Barton, Nicholas H}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1547}, pages = {1825 -- 1840}, publisher = {Royal Society}, title = {{What role does natural selection play in speciation?}}, doi = {10.1098/rstb.2010.0001}, volume = {365}, year = {2010}, } @article{3774, abstract = {1. Hybridisation with an invasive species has the potential to alter the phenotype and hence the ecology of a native counterpart. 2. Here data from populations of native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland is used to assess the extent to which hybridisation between them is causing phenotypic change. This is done by regression of phenotypic traits against genetic hybrid scores. 3. Hybridisation is causing increases in the body weight of sika-like deer and decreases in the body weight of red-like females. Hybridisation is causing increases in jaw length and increases in incisor arcade breadth in sika-like females. Hybridisation is also causing decreases in incisor arcade breadth in red-like females. 4. There is currently no evidence that hybridisation is causing changes in the kidney fat weight or pregnancy rates of either population. 5. Increased phenotypic similarity between the two species is likely to lead to further hybridisation. The ecological consequences of this are difficult to predict.}, author = {Senn, Helen and Swanson, Graeme and Goodman, Simon and Barton, Nicholas H and Pemberton, Josephine}, journal = {Journal of Animal Ecology}, number = {2}, pages = {414 -- 425}, publisher = {Wiley-Blackwell}, title = {{Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)}}, doi = {10.1111/j.1365-2656.2009.01633.x}, volume = {79}, year = {2010}, } @article{3776, abstract = {The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps.}, author = {Barton, Nicholas H}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1552}, pages = {2559 -- 2569}, publisher = {Royal Society}, title = {{Genetic linkage and natural selection}}, doi = {10.1098/rstb.2010.0106}, volume = {365}, year = {2010}, } @article{3777, abstract = {Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.}, author = {Barton, Nicholas H}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1544}, pages = {1281 -- 1294}, publisher = {Royal Society}, title = {{Mutation and the evolution of recombination}}, doi = {10.1098/rstb.2009.0320}, volume = {365}, year = {2010}, } @article{3779, abstract = {Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity.}, author = {Rosas, Ulises and Barton, Nicholas H and Copsey, Lucy and Barbier De Reuille, Pierre and Coen, Enrico}, journal = {PLoS Biology}, number = {7}, publisher = {Public Library of Science}, title = {{Cryptic variation between species and the basis of hybrid performance}}, doi = {10.1371/journal.pbio.1000429}, volume = {8}, year = {2010}, } @article{3783, abstract = {MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/.}, author = {Palero, Ferran and González Candelas, Fernando and Pascual, Marta}, journal = {Journal of Heredity}, number = {2}, pages = {247 -- 249}, publisher = {Oxford University Press}, title = {{Microsatelight – Pipeline to expedite microsatellite analysis}}, doi = {10.1093/jhered/esq111}, volume = {102}, year = {2010}, }