Related papers: Reconstructing pedigrees using probabilistic analy…
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…
We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and…
Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for system cell transplants. Haplotype sharing detection requires imputation of donor and recipient. We show that even in high-resolution…
Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…
The ``sample amplification'' problem formalizes the following question: Given $n$ i.i.d. samples drawn from an unknown distribution $P$, when is it possible to produce a larger set of $n+m$ samples which cannot be distinguished from $n+m$…
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…
The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
A large offspring number diploid biparental multilocus population model of Moran type is our object of study. At each timestep, a pair of diploid individuals drawn uniformly at random contribute offspring to the population. The number of…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
Randomness is one of the important key concepts of statistics. In epidemiology or medical science, we investigate our hypotheses and interpret results through this statistical randomness. We hypothesized by imposing some conditions to this…
The Coefficient of Parentage (COP) between two individuals is the expected inbreeding of their offspring. Originally exploited by animal breeders, is now a routine calculation among plant breeders as part of crop improvement programs. Here…
In a reinforced Galton-Watson process with reproduction law $\boldsymbol{\nu}$ and memory parameter $q\in(0,1)$, the number of children of a typical individual either, with probability $q$, repeats that of one of its forebears picked…
Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model…
Let $W_1,\ldots,W_N$ be a sample of $\mathrm{Pareto}(\alpha)$ random variables normalized by their sum, such that $\sum_i W_i=1$. The $W_i$ may represent the weights of valleys in a spin glass (if $0<\alpha<1$), or the frequency of…
Motivation: The reconstruction of gene networks from gene expression microarrays is gaining popularity as methods improve and as more data become available. The reliability of such networks could be judged by the probability that a…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
We present methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
Applications such as the analysis of microbiome data have led to renewed interest in statistical methods for compositional data, i.e., multivariate data in the form of probability vectors that contain relative proportions. In particular,…