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Data from: The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions
- 负责人：
- DOI：
- doi:10.5061/dryad.584m3
- 摘要：
- by regions of low posterior density. Markov chain Monte Carlo (MCMC) algorithms are the most widely used numerical method for generating samples from these
Data from: Bayesian analysis of biogeography when the number of areas is large
- 负责人：
- DOI：
- doi:10.5061/dryad.8346r
- 摘要：
- . We develop this approach in a Bayesian framework, marginalizing over all possible biogeographic histories using Markov chain Monte Carlo (MCMC). Besi
Data from: Bayesian tests of topology hypotheses with an example from diving beetles
- 负责人：
- DOI：
- doi:10.5061/dryad.s631d
- 摘要：
- We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.
Data from: Identifying loci under selection against gene flow in isolation with migration models
- 负责人：
- 关键词：
- Oryctolagus cuniculus;MCMC;demographic history;coalescent;Isolation with Migration;natural selection
- DOI：
- doi:10.5061/dryad.vr7bb
- 摘要：
- When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).
Data from: Heterozygosity-fitness correlations in a migratory bird: an analysis of inbreeding and single-locus effects
- 负责人：
- Harrison, Xavier
- DOI：
- doi:10.5061/dryad.52dk8
- 摘要：
- Studies in a multitude of taxa have described a correlation between heterozygosity and fitness, and usually conclude that this is evidence for inbreeding depression. Here we have used multi-locus heterozygosity estimates from 15 microsatellite markers to show evidence of heterozygosity-fitness correlations (HFCs) in a long-distance migratory bird, the light-bellied Brent goose. We found significant, positive heterozygosity-heterozygosity correlations between random subsets of the markers we employ, and no evidence that a model containing all loci as individual predictors in a multiple regression explained significantly more variation than a model with multi-locus heterozygosity as a single predictor. Collectively these results lend support to the hypothesis that the HFCs we have observed are a function of inbreeding depression. However, we do find that fitness correlations are only detectable in years where population-level productivity is high enough for the reproductive asymmetry between high and low heterozygosity individuals to become apparent. We suggest that lack of evidence of heterozygosity-fitness correlations in animal systems may be because heterozygosity is a poor proxy measure of inbreeding, especially when employing low numbers of markers, but alternatively because the asymmetries between individuals of different heterozygosities may only be apparent when environmental effects on fitness are less pronounced.
Data from: Estimating uncertainty in multivariate responses to selection
- 负责人：
- DOI：
- doi:10.5061/dryad.384nf
- 摘要：
- esponses to selection to be distinguished, and if implemented in a Bayesian-MCMC framework, statistically robust estimates of uncertainty on all of these parameters
Data from: Worldwide phylogeny of three-spined sticklebacks
- 负责人：
- 关键词：
- Pleistocene to Holocene.;SNP;Gasterosteus;coalescent;RAD-seq;phylogenomics;Gasterosteus aculeatus
- DOI：
- doi:10.5061/dryad.2529hr1
- 摘要：
- of extant G. aculeatus populations, as well their ancestral geographic distributions using Statistical-Dispersal Vicariance and Bayesian Binary MCMC analyses
Data from: Divergent natural selection drives the evolution of reproductive isolation in an Australian wildflower
- 负责人：
- 关键词：
- MCMCglmm;ecological speciation;postzygotic isolation;Senecio lautus;Senecio;reciprocal transplant
- DOI：
- doi:10.5061/dryad.17h0t
- 摘要：
- Ecological speciation occurs when reproductive isolation evolves between populations adapting to contrasting environments. A key prediction of this process is that the fitness of hybrids between divergent populations should be reduced in each parental environment as a function of the proportion of local genes they carry, a process resulting in ecologically dependent reproductive isolation (RI). To test this prediction, we use reciprocal transplant experiments between adjacent populations of an Australian wildflower, Senecio lautus, at two locations to distinguish between ecologically dependent and intrinsic genetic reproductive barriers. These barriers can be distinguished by observing the relative fitness of reciprocal backcross hybrids, as they differ in the contribution of genes from either parent while controlling for any intrinsic fitness effects of hybridization. We show ecologically dependent fitness effects in establishment and survival of backcrosses in one transplant experiment, and growth performance in the second transplant experiment. These results suggests natural selection can create strong reproductive barriers that maintain differentiation between populations with the potential to interbreed, and implies a significant role for ecology in the evolutionary divergence of S. lautus.
Data from: Estimation of individual growth trajectories when repeated measures are missing
- 负责人：
- DOI：
- doi:10.5061/dryad.r6j80
- 摘要：
- repeated measures and observation error. This method is much faster than MCMC methods, allowing more models to be tested in a shorter time. For the scenarios
Data from: Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation
- 负责人：
- DOI：
- doi:10.5061/dryad.r2rn0
- 摘要：
- procedure that allows users to assess which model (e.g. with or without an environment effect) is most suited. We code all our MCMC algorithms in a mix
