Population genetic inference using a fixed number of segregating sites: a reassessment

Genetical Research
S E Ramos-OnsinsWolfgang Stephan

Abstract

Coalescent theory is commonly used to perform population genetic inference at the nucleotide level. Here, we examine the procedure that fixes the number of segregating sites (henceforth the FS procedure). In this approach a fixed number of segregating sites (S) are placed on a coalescent tree (independently of the total and internode lengths of the tree). Thus, although widely used, the FS procedure does not strictly follow the assumptions of coalescent theory and must be considered an approximation of (i) the standard procedure that uses a fixed population mutation parameter theta, and (ii) procedures that condition on the number of segregating sites. We study the differences in the false positive rate for nine statistics by comparing the FS procedure with the procedures (i) and (ii), using several evolutionary models with single-locus and multilocus data. Our results indicate that for single-locus data the FS procedure is accurate for the equilibrium neutral model, but problems arise under the alternative models studied; furthermore, for multilocus data, the FS procedure becomes inaccurate even for the standard neutral model. Therefore, we recommend a procedure that fixes the theta value (or alternatively, procedures that con...Continue Reading

References

Apr 1, 1975·Theoretical Population Biology·G A Watterson
Jan 1, 1993·Genetica·F J AyalaD L Hartl
Mar 1, 1993·Genetics·Y X Fu, W H Li
Jan 1, 1995·Annual Review of Genetics·P Donnelly, S Tavaré
Feb 1, 1997·Genetics·S TavaréP Donnelly
Jan 23, 1999·Molecular Biology and Evolution·F Depaulis, M Veuille
Dec 22, 1999·Molecular Biology and Evolution·J K PritchardM W Feldman
Jul 6, 2000·Genetics·J C Fay, C I Wu
Mar 20, 2001·Obstetrical & Gynecological Survey·S Degani
May 24, 2001·Molecular Biology and Evolution·L MarkovtsovaS Tavare
May 24, 2001·Molecular Biology and Evolution·J D Wall, R R Hudson
May 24, 2001·Molecular Biology and Evolution·F DepaulisM Veuille
Mar 20, 2002·Genetics·Molly Przeworski
Nov 26, 2002·Molecular Biology and Evolution·Sebastian E Ramos-Onsins, Julio Rozas
Dec 12, 2003·Bioinformatics·Julio RozasRicardo Rozas
Feb 14, 2004·Molecular Biology and Evolution·Sylvain MoussetMichel Veuille
Mar 11, 2004·Journal of Molecular Evolution·Frantz DepaulisMichel Veuille
Oct 30, 2004·Genetics·Stephen I Wright, Brian Charlesworth
May 28, 2005·Science·Stephen I WrightBrandon S Gaut
Dec 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Benjamin F VoightAnna Di Rienzo
Mar 22, 2006·Molecular Biology and Evolution·Mattias JakobssonMagnus Nordborg

❮ Previous
Next ❯

Citations

Feb 26, 2013·PloS One·Annegret WerznerStefan Laurent
Jul 9, 2010·Genetics·Luca FerrettiSebastian Ramos-Onsins
Oct 2, 2012·Molecular Biology and Evolution·Aida T Miró-Herrans, Connie J Mulligan

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.