Related papers: Tread lightly interpreting group differences in ge…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Selection bias is a serious potential problem for inference about relationships of scientific interest based on samples without well-defined probability sampling mechanisms. Motivated by the potential for selection bias in (a) estimated…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…
Mendelian randomization is the use of genetic variants as instrumental variables to assess whether a risk factor is a cause of a disease outcome. Increasingly, Mendelian randomization investigations are conducted on the basis of summarized…
Microarray data are often used to determine which genes are differentially expressed between groups, for example, between treatment and control groups. There are methods of determining which genes have a high probability of differential…
This paper shows that differentiating the lifetimes of two phenotypes independently from their fertility can lead to a qualitative change in the equilibrium of a population: since survival and reproduction are distinct functional aspects of…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
There is active debate over whether to consider patient race and ethnicity when estimating disease risk. By accounting for race and ethnicity, it is possible to improve the accuracy of risk predictions, but there is concern that their use…
The use of population descriptors like race, ethnicity, and ancestry in science, medicine and public health has a long, complicated, and at times dark history, particularly for genetics, given the field's perceived importance for…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
A key goal in studies of ecology and evolution is understanding the causes of phenotypic diversity in nature. Most traits of interest, such as those relating to morphology, life-history, immunity and behaviour are quantitative, and…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be…
When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are…
In microbial communities, each species often has multiple, distinct phenotypes, but studies of ecological stability have largely ignored this subpopulation structure. Here, we show that such implicit averaging over phenotypes leads to…
We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population…
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,…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
Inference with population genetic data usually treats the population pedigree as a nuisance parameter, the unobserved product of a past history of random mating. However, the history of genetic relationships in a given population is a…