Advertisement

Topics

An empirical approach to demographic inference with genomic data.

08:00 EDT 9th April 2019 | BioPortfolio

Summary of "An empirical approach to demographic inference with genomic data."

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 fixed, unobserved object, and so an alternative approach is to treat this network of relationships as a complex object we wish to learn about, by observing how genomes have been noisily passed down through it. This paper explores this point of view, showing how to translate questions about population genetic data into calculations with a Poisson process of mutations on all ancestral genomes. This method is applied to give a robust interpretation to the f statistic used to identify admixture, and to design a new statistic that measures covariances in mean times to most recent common ancestor between two pairs of sequences. The method more generally interprets population genetic statistics in terms of sums of specific functions over ancestral genomes, thereby providing concrete, broadly interpretable interpretations for these statistics. This provides a method for describing demographic history without simplified demographic models. More generally, it brings into focus the population pedigree, which is averaged over in model-based demographic inference.

Affiliation

Journal Details

This article was published in the following journal.

Name: Theoretical population biology
ISSN: 1096-0325
Pages:

Links

DeepDyve research library

PubMed Articles [20622 Associated PubMed Articles listed on BioPortfolio]

Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data.

Restriction-site associated DNA sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods of...

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets.

One common method of minimizing errors in large DNA sequence datasets is to drop variable sites with a minor allele frequency below some specified threshold. Though widespread, this procedure has the ...

Bayesian phylodynamic inference with complex models.

Population genetic modeling can enhance Bayesian phylogenetic inference by providing a realistic prior on the distribution of branch lengths and times of common ancestry. The parameters of a populatio...

Towards an accurate and efficient heuristic for species/gene tree co-estimation.

Species and gene trees represent how species and individual loci within their genomes evolve from their most recent common ancestors. These trees are central to addressing several questions in biology...

Genomic inference using diffusion models and the allele frequency spectrum.

Evolutionary, biological, and demographic processes together shape observed variation in populations. Understanding how these processes influence variation allows us to infer past demography and the n...

Clinical Trials [5464 Associated Clinical Trials listed on BioPortfolio]

Demographic, Metabolic, and Genomic Description of Neonates With Severe Hyperbilirubinemia

The purpose of this study is to compare the demographic, metabolic, and genomic characteristics of patients who develop severe hyperbilirubinemia to patients who never developed a signific...

Return of Actionable Variants Empirical Study

This is a genomic implementation project with ancillary studies to understand the impact on patients' health and well-being of returning genomic results to them and depositing those result...

Rady Children's Institute Genomic Biorepository

Rady Children's Institute for Genomic Medicine (RCI) will collect biological samples (such as blood), derived genomic sequences (from DNA and RNA), and clinical features in a Biorepository...

GRADE-SRM: Genomic Risk Assessment and Decisional Evaluation for Small Renal Masses

Purpose: The purpose of this study is to evaluate the role of renal mass biopsy on decision-making for patients presenting with clinical T1 kidney tumors. This study also incorporates inte...

Genomic Analysis of Peritoneal Mesothelioma by CGH Arrays

Peritoneal mesothelioma is a rare disease representing one third of all mesothelioma and nothing is known about molecular characteristics of this disease. As main cancers, genetic heteroge...

Medical and Biotech [MESH] Definitions

The generation of theories from analysis of empirical data.

Detailed account or statement or formal record of data resulting from empirical inquiry.

Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.

Various units or machines that operate in combination or in conjunction with a computer but are not physically part of it. Peripheral devices typically display computer data, store data from the computer and return the data to the computer on demand, prepare data for human use, or acquire data from a source and convert it to a form usable by a computer. (Computer Dictionary, 4th ed.)

Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.

Advertisement
Quick Search
Advertisement
Advertisement

 


DeepDyve research library

Searches Linking to this Article