Joint inference of population assignment and demographic history

Sang Chul Choi, Jody Hey


A new approach to assigning individuals to populations using genetic data is described. Most existing methods work by maximizing Hardy-Weinberg and linkage equilibrium within populations, neither of which will apply for many demographic histories. By including a demographic model, within a likelihood framework based on coalescent theory, we can jointly study demographic history and population assignment. Genealogies and population assignments are sampled from a posterior distribution using a general isolation-with-migration model for multiple populations. A measure of partition distance between assignments facilitates not only the summary of a posterior sample of assignments, but also the estimation of the posterior density for the demographic history. It is shown that joint estimates of assignment and demographic history are possible, including estimation of population phylogeny for samples from three populations. The new method is compared to results of a widely used assignment method, using simulated and published empirical data sets.


Mar 15, 2014·Systematic Biology·Adam D LeachéRemco R Bouckaert
Aug 30, 2013·Systematic Biology·Noah M ReidBryan C Carstens
Feb 27, 2016·Journal of Theoretical Biology·Elina NumminenJukka Corander
Jul 17, 2013·Molecular Ecology·Bryan C CarstensJordan D Satler
Dec 30, 2014·Ecology and Evolution·Alexander I Putman, Ignazio Carbone
Aug 16, 2013·Systematic Biology·Adam D LeachéZiheng Yang


Jun 1, 1995·Molecular Ecology·D PaetkauC Strobeck
Aug 19, 1997·Proceedings of the National Academy of Sciences of the United States of America·Bruce Rannala, J L Mountain
Jun 29, 2004·The Journal of Heredity·L BaudouinJ M Cornuet
Oct 16, 2004·Molecular Biology and Evolution·Yong-Jin Won, Jody Hey
Nov 3, 2004·Genetics·Gilles GuillotJean François Cosson
Mar 5, 2005·Bioinformatics·Dmitry A KonovalovNigel Bajema
Oct 11, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Mikhail Matz, Rasmus Nielsen
Mar 2, 2006·Systematic Biology·Rasmus Nielsen, Mikhail Matz
Jun 7, 2006·Current Biology : CB·Anne FischerSvante Pääbo
Jan 24, 2007·Genetics·John P Huelsenbeck, Peter Andolfatto
Feb 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jody Hey, Rasmus Nielsen
Apr 24, 2007·PLoS Genetics·Celine BecquetDavid Reich
Feb 26, 2008·Bioinformatics·Yu Zhang
Apr 19, 2008·PLoS Genetics·Jennifer L CaswellDavid Reich
Oct 2, 2009·Molecular Biology and Evolution·Jared L Strasburg, Loren H Rieseberg
Dec 4, 2009·Molecular Biology and Evolution·Jody Hey
May 5, 2010·Proceedings of the National Academy of Sciences of the United States of America·Ziheng Yang, Bruce Rannala
Mar 1, 2010·Molecular Ecology Resources·Johan FogelqvistMartin Lascoux

Related Concepts

In Silico
Genetics, Population
Linkage Disequilibrium
Genetic Linkage
Posterior Pituitary Disease
Sampling - Surgical Action

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.

Sexual Dimorphism in Neurodegeneration

There exist sex differences in neurodevelopmental and neurodegenerative disorders. For instance, multiple sclerosis is more common in women, whereas Parkinson’s disease is more common in men. Here is the latest research on sexual dimorphism in neurodegeneration

HLA Genetic Variation

HLA genetic variation has been found to confer risk for a wide variety of diseases. Identifying these associations and understanding their molecular mechanisms is ongoing and holds promise for the development of therapeutics. Find the latest research on HLA genetic variation here.

Super-resolution Microscopy

Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Here are the latest discoveries pertaining to super-resolution microscopy.

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.

Brain Lower Grade Glioma

Low grade gliomas in the brain form from oligodendrocytes and astrocytes and are the slowest-growing glioma in adults. Discover the latest research on these brain tumors here.

CD4/CD8 Signaling

Cluster of differentiation 4 and 8 (CD8 and CD8) are glycoproteins founds on the surface of immune cells. Here is the latest research on their role in cell signaling pathways.

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.

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.