Recombination as a point process along sequences

Theoretical Population Biology
C Wiuf, J Hein

Abstract

Histories of sequences in the coalescent model with recombination can be simulated using an algorithm that takes as input a sample of extant sequences. The algorithm traces the history of the sequences going back in time, encountering recombinations and coalescence (duplications) until the ancestral material is located on one sequence for homologous positions in the present sequences. Here an alternative algorithm is formulated not as going back in time and operating on sequences, but by moving spatially along the sequences, updating the history of the sequences as recombination points are encountered. This algorithm focuses on spatial aspects of the coalescent with recombination rather than on temporal aspects as is the case of familiar algorithms. Mathematical results related to spatial aspects of the coalescent with recombination are derived.

References

May 2, 2013·Heredity·S PeischlM Kirkpatrick
Sep 20, 2006·Nature Reviews. Genetics·Paul Marjoram, Simon Tavaré
May 10, 2013·Nature Reviews. Genetics·Vitor Sousa, Jody Hey
Oct 27, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Laxmi Parida
Apr 20, 2010·Bioinformatics·Ingo BullaMario Stanke
Dec 16, 2010·Bioinformatics·Bernhard HauboldPeter Pfaffelhuber
Jul 29, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Gilean A T McVean, Niall J Cardin
Aug 13, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Maria De IorioMichael P H Stumpf
Nov 26, 2008·Genome Research·Gary K ChenJeffrey D Wall
Oct 6, 2009·Genome Research·Adam Siepel
Mar 5, 2011·BMC Bioinformatics·Laxmi ParidaAsif Javed
Mar 17, 2006·BMC Genetics·Paul Marjoram, Jeff D Wall
May 23, 2013·PLoS Computational Biology·Haipeng Li, Thomas Wiehe
Oct 17, 2006·PLoS Genetics·Haipeng Li, Wolfgang Stephan
Jun 12, 2013·PLoS Genetics·Kelley Harris, Rasmus Nielsen
Feb 11, 2009·Genetics·Simon BoitardAndreas Futschik
Aug 16, 2011·Genetics·Olivier C Martin, Frédéric Hospital
May 17, 2014·PLoS Genetics·Matthew D RasmussenAdam Siepel
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Peter Calabrese
Nov 22, 2001·Proceedings of the National Academy of Sciences of the United States of America·D Posada, K A Crandall
Aug 26, 2014·Theoretical Population Biology·Shai CarmiItsik Pe'er
Feb 4, 2014·Theoretical Population Biology·Asger Hobolth, Jens Ledet Jensen
Sep 25, 2014·Annual Review of Genetics·Thomas MailundMikkel Heide Schierup
Jan 16, 2010·Journal of Mathematical Biology·Stephanie Leocard, Etienne Pardoux
Jun 12, 2013·Theoretical Population Biology·John Wakeley
Sep 27, 2012·Theoretical Population Biology·Matthias SteinrückenYun S Song
May 22, 2010·Trends in Ecology & Evolution·Katalin CsilléryOlivier François
May 13, 2009·Theoretical Population Biology·Anders ErikssonB Mehlig
Nov 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yufeng Wu
Dec 1, 1999·American Journal of Human Genetics·A G Clark
Jul 11, 2006·Theoretical Population Biology·Ola Hössjer
Nov 11, 2015·Nature Reviews. Genetics·Joshua G Schraiber, Joshua M Akey
Apr 23, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Shuo YangItsik Pe'er
Jun 10, 2014·Theoretical Population Biology·J KelleherN H Barton
Aug 7, 2004·Journal of Bioinformatics and Computational Biology·Nadia el-Mabrouk

Citations

Apr 1, 1975·Theoretical Population Biology·G A Watterson
Dec 1, 1985·Theoretical Population Biology·N Kaplan, R R Hudson

Related Concepts

Genetics, Population
Recombination, Genetic
Phylogeny
Underpopulation
Homologous Gene
Determination, Sequence Homology
Genealogical Tree

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.

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.

Related Papers

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Gilean A T McVean, Niall J Cardin
Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
R C Griffiths, P Marjoram
© 2020 Meta ULC. All rights reserved