Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree

Zongfeng YangHaipeng Li


Many population genomic studies have been conducted in the past to search for traces of recent events of positive selection. These traces, however, can be obscured by temporal variation of population size or other demographic factors. To reduce the confounding impact of demography, the coalescent tree topology has been used as an additional source of information for detecting recent positive selection in a population or a species. Based on the branching pattern at the root, we partition the hypothetical coalescent tree, inferred from a sequence sample, into two subtrees. The reasoning is that positive selection could impose a strong impact on branch length in one of the two subtrees while demography has the same effect on average on both subtrees. Thus, positive selection should be detectable by comparing statistics calculated for the two subtrees. Simulations demonstrate that the proposed test based on these principles has high power to detect recent positive selection even when DNA polymorphism data from only one locus is available, and that it is robust to the confounding effect of demography. One feature is that all components in the summary statistics ([Formula: see text]) can be computed analytically. Moreover, misinferen...Continue Reading


Apr 1, 1975·Theoretical Population Biology·G A Watterson
Aug 9, 2002·Theoretical Population Biology·Alexandre SibertEvelyne Heyer
Dec 6, 2002·Genome Research·Joshua M AkeyMark D Shriver
Jan 30, 2003·Systematic Biology·Andy Purvis, Paul-Michael Agapow
Mar 11, 2004·Journal of Molecular Evolution·Frantz DepaulisMichel Veuille
Jul 29, 2004·Genetics·Yuseob Kim, Rasmus Nielsen
May 25, 2005·Genetics·Jeffrey D JensenCarlos D Bustamante
May 28, 2005·Science·Stephen I WrightBrandon Gaut
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos D Bustamante
Mar 10, 2006·PLoS Biology·Catriona MacCallum, Emma Hill
May 12, 2006·Genome Research·Kosuke M TeshimaMolly Przeworski
Jun 17, 2006·Science·Pardis C SabetiEric S Lander
Sep 15, 2006·Systematic Biology·Frederick A Matsen
Oct 17, 2006·PLoS Genetics·Haipeng Li, Wolfgang Stephan
Jun 5, 2007·Molecular Biology and Evolution·Ryan D HernandezCarlos D Bustamante
Jul 28, 2007·Molecular Biology and Evolution·Ryan D HernandezCarlos D Bustamante
Oct 26, 2007·Trends in Genetics : TIG·Jeffrey D JensenCharles F Aquadro
Jun 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Feng TianEdward S Buckler
Aug 6, 2009·Heredity·Joachim Hermisson
Dec 8, 2009·Science·Michael GoreEdward S Buckler
Apr 1, 2009·Systematic Biology·Daniel FordTanja Stadler
Jul 9, 2010·Genetics·Luca FerrettiSebastian E Ramos-Onsins
Jun 5, 2012·Nature Genetics·Jer-Ming ChiaDoreen Ware
Oct 2, 2012·Trends in Genetics : TIG·Matthew B HuffordJeffrey Ross-Ibarra
Nov 13, 2012·Mathematical Biosciences·Arnau MirLucı A Rotger
May 23, 2013·PLoS Computational Biology·Haipeng Li, Thomas Wiehe
Jun 19, 2013·Genetics·Roy RonenVineet Bafna
Jul 10, 2013·Annual Review of Genomics and Human Genetics·Wenqing Fu, Joshua M Akey
Sep 3, 2013·Mathematical Biosciences·Filippo DisantoThomas Wiehe
Sep 21, 2013·Nature Reviews. Genetics·Laura B Scheinfeldt, Sarah A Tishkoff
Nov 28, 2013·Annual Review of Genetics·Joseph J VittiPardis C Sabeti
Jun 10, 2014·Theoretical Population Biology·M RafajlovićB Mehlig
Apr 8, 2015·Nature Genetics·Xiaoming Liu, Yun-Xin Fu
Jun 15, 2015·Trends in Genetics : TIG·Jeffrey R AdrionBrandon S Cooper
Jun 21, 2015·Molecular Biology and Evolution·Haley Hunter-Zinck, Andrew G Clark
Mar 16, 2016·PLoS Genetics·Daniel R Schrider, Andrew D Kern
May 7, 2016·Bioinformatics·Michael DeGiorgioRasmus Nielsen
Mar 1, 1975·Evolution; International Journal of Organic Evolution·Masatoshi NeiRanajit Chakraborty
Jul 7, 2017·Genetics·Luca FerrettiSebastian E Ramos-Onsins


Oct 2, 2018·Genes & Genetic Systems·Naoko T FujitoNaoyuki Takahata
Jan 25, 2020·G3 : Genes - Genomes - Genetics·Matthew Hartfield, Thomas Bataillon
Nov 12, 2019·PLoS Computational Biology·Yichen Zheng, Thomas Wiehe

Related Concepts

Biological Adaptation
Zea luxurians
Population Spatial Distribution
Genetics, Population
Selection, Genetic
Two-Parameter Models
Quantitative Trait Loci
Trees (plant)

Trending Feeds


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.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

Pediculosis pubis

Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.

Rh Isoimmunization

Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.

Enzyme Evolution

This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.

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.

Pharmacology of Proteinopathies

This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.