Related papers: An exploratory analysis of combined genome-wide SN…
The description of complex human mobility patterns is at the core of many important applications ranging from urbanism and transportation to epidemics containment. Data about collective human movements, once scarce, has become widely…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace…
Oceania and Island Southeast Asia have a rich, yet understudied, human genomic landscape. This region encompasses some of the first areas inhabited by humans following the out-of-Africa expansion, includes populations with the highest…
Here we present the first genome wide statistical test for recessive selection. This test uses explicitly non-equilibrium demographic differences between populations to infer the mode of selection. By analyzing the transient response to a…
The Roma people, living throughout Europe, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1000-1500 years…
There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case--control…
Populations evolving under the joint influence of recombination and resampling (traditionally known as genetic drift) are investigated. First, we summarise and adapt a deterministic approach, as valid for infinite populations, which assumes…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
Here we present an Italian criminal case that shows how statistical methods can be used to extract information from a series of mixed DNA profiles. The case involves several different individuals and a set of different DNA traces. The case…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about…
Genetic data are now routinely used to study the history of population size, subdivision, and gene flow. A variety of formal statistical methods is available for testing hypotheses and fitting models to data. Yet it is often unclear which…
When long-lived, balancing selection can lead to trans-species polymorphisms that are shared by two or more species identical by descent. In this case, the gene genealogies at the selected sites cluster by allele instead of by species and,…
Among the evolutionary methods, one that is quite prominent is Genetic Programming, and, in recent years, a variant called Geometric Semantic Genetic Programming (GSGP) has shown to be successfully applicable to many real-world problems.…
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…
We examine the problem of family size statistics (the number of individuals carrying the same surname, or the same DNA sequence) in a given size subsample of an exponentially growing population. We approach the problem from two directions.…
Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and population size remains constant over time. However, it is unclear how such tests are affected if the last…
Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no…