Frequency spectrum neutrality tests: one for all and all for one

Guillaume Achaz


Neutrality tests based on the frequency spectrum (e.g., Tajima's D or Fu and Li's F) are commonly used by population geneticists as routine tests to assess the goodness-of-fit of the standard neutral model on their data sets. Here, I show that these neutrality tests are specific instances of a general model that encompasses them all. I illustrate how this general framework can be taken advantage of to devise new more powerful tests that better detect deviations from the standard model. Finally, I exemplify the usefulness of the framework on SNP data by showing how it supports the selection hypothesis in the lactase human gene by overcoming the ascertainment bias. The framework presented here paves the way for constructing novel tests optimized for specific violations of the standard model that ultimately will help to unravel scenarios of evolution.


Apr 1, 1975·Theoretical Population Biology·G A Watterson
Oct 1, 1995·Theoretical Population Biology·Y X Fu
Aug 1, 1993·Genetics·Y X Fu, W H Li
Jan 23, 1999·Molecular Biology and Evolution·F Depaulis, M Veuille
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
Nov 13, 2001·American Journal of Human Genetics·J WakeleyK Ardlie
Nov 26, 2002·Molecular Biology and Evolution·Sebastian E Ramos-Onsins, Julio Rozas
Oct 28, 2005·Genome Research·Andrew G ClarkRasmus Nielsen
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos Bustamante
Dec 13, 2006·Nature Genetics·Sarah A TishkoffPanos Deloukas
Jan 23, 2008·Genetical Research·Sebastian E Ramos-OnsinsWolfgang Stephan
Jun 20, 2008·Genetics·Guillaume Achaz


Jan 31, 2012·Nature Genetics·Erik C AndersenLeonid Kruglyak
Sep 28, 2010·BMC Evolutionary Biology·Iderval S Sobrinho, Reinaldo A de Brito
Mar 19, 2013·PloS One·Nadia Mhedbi-HajriMarie-Agnès Jacques
Jul 9, 2010·Genetics·Luca FerrettiSebastian E Ramos-Onsins
Jun 5, 2012·Genetics·Luca FerrettiSebastian E Ramos-Onsins
Nov 30, 2013·Molecular Biology and Evolution·Eunjung HanJohn Novembre
Apr 18, 2014·Molecular Biology and Evolution·Bastian PfeiferMartin J Lercher
May 10, 2011·Theoretical Population Biology·Paul A Jenkins, Yun S Song
Mar 5, 2016·Molecular Biology and Evolution·Marguerite LapierreEduardo P C Rocha
May 7, 2015·Molecular Ecology·Anna Fijarczyk, Wiesław Babik
Jul 16, 2015·Molecular Biology and Evolution·Walter SanseverinoJosep Maria Casacuberta
May 15, 2015·Molecular Biology and Evolution·Elsa G GuillotMurray P Cox
Jun 10, 2014·Theoretical Population Biology·M RafajlovićB Mehlig
Aug 21, 2013·American Journal of Human Genetics·Dan ZhouGabriel G Haddad
Dec 17, 2014·Theoretical Population Biology·Franz Baumdicker
Mar 27, 2018·Disasters·Paul Knox Clarke, Leah Campbell
Mar 21, 2018·BMC Genomics·Alexander L GreningerKeith R Jerome
Oct 14, 2017·Molecular Biology and Evolution·Julio RozasAlejandro Sánchez-Gracia
Sep 28, 2017·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·Priti AzadGabriel G Haddad
Sep 13, 2017·Evolutionary Bioinformatics Online·Javier NavarroSebastian E Ramos-Onsins
Dec 31, 2015·Genetics·Daniel A SkellyEric A Stone
Jul 7, 2017·Genetics·Luca FerrettiSebastian E Ramos-Onsins
Feb 5, 2020·Genome Biology and Evolution·Katherine M Siewert, Benjamin F Voight
Mar 9, 2017·Genetics·Sònia Casillas, Antonio Barbadilla
Jul 8, 2020·Pathogens·Paul A Fuerst, Gregory C Booton
Nov 12, 2017·Genetics·Sebastian MatuszewskiJeffrey D Jensen
Nov 9, 2018·Frontiers in Genetics·Luca FerrettiSebastian E Ramos-Onsins
Jun 19, 2013·Genetics·Roy RonenVineet Bafna
Feb 23, 2018·Frontiers in Microbiology·Eric DuchaudPierre Nicolas
Nov 8, 2015·G3 : Genes - Genomes - Genetics·Nicolas AlcalaSéverine Vuilleumier
Oct 8, 2020·Journal of Fungi·Daniel Wagner C L SantosConceição de Maria Pedrozo E Silva de Azevedo
Sep 9, 2020·Molecular Biology and Evolution·Joaquin C B NunezDavid M Rand
Sep 13, 2019·Zoology : Analysis of Complex Systems, ZACS·Manoj Kumar Gupta, Ramakrishna Vadde
Nov 15, 2017·Theoretical Population Biology·Ilana M ArbisserNoah A Rosenberg

Related Concepts

In Silico
Genetic Equilibrium
Genetics, Population
Variation (Genetics)
Truncation Biases
Single Nucleotide Polymorphism
Evolution, Neutral
Biological Evolution

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.