The dynamics of alternative pathways to compensatory substitution
The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have received considerable attention, most studies have focused on the case when natural selection i...
Gespeichert in:
Veröffentlicht in: | BMC bioinformatics 2013, Vol.14 Suppl 15 (S15), p.S2-S2, Article S2 |
---|---|
1. Verfasser: | |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | S2 |
---|---|
container_issue | S15 |
container_start_page | S2 |
container_title | BMC bioinformatics |
container_volume | 14 Suppl 15 |
creator | Nasrallah, Chris A |
description | The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have received considerable attention, most studies have focused on the case when natural selection is very strong against deleterious intermediates. In the biologically-plausible scenario of weak to moderate selection there exist two alternate pathways for compensatory substitution. In one pathway, a deleterious mutation becomes fixed prior to occurrence of the compensatory mutation. In the other, the two loci are simultaneously polymorphic. The rates of compensatory substitution along these two pathways and their relative probabilities are functions of the population size, selection strength, mutation rate, and recombination rate. In this paper these rates and path probabilities are derived analytically and verified using population genetic simulations. The expected time durations of these two paths are similar when selection is moderate, but not when selection is weak. The effect of recombination on the dynamics of the substitution process are explored using simulation. Using the derived rates, a phylogenetic substitution model of the compensatory evolution process is presented that could be used for inference of population genetic parameters from interspecific data. |
doi_str_mv | 10.1186/1471-2105-14-S15-S2 |
format | Article |
fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3852009</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1502330328</sourcerecordid><originalsourceid>FETCH-LOGICAL-b529t-75c23c6d5cd9f0eb8be45534534140daf795c38f602e4647d98c8891ea98eea13</originalsourceid><addsrcrecordid>eNqFkl1LwzAUhoMobn78AkEK3nhTzWeb3ghj-AWCF9PrkKanLqNtZpNO9u9tnQ4VRAjkkPPk5c2bg9AJwReEyOSS8JTElGAREx7PiIhndAeNt6e73-oROvB-gTFJJRb7aES5SLjkdIwmT3OIinWja2t85MpIVwHaRge7gmipw_xNr30UXGRcvYTG6-DadeS73AcbumBdc4T2Sl15OP7cD9HzzfXT9C5-eLy9n04e4lzQLMSpMJSZpBCmyEoMucyBC8F4vwjHhS7TTBgmywRT4AlPi0waKTMCOpMAmrBDdLXRXXZ5DYWBJrS6UsvW1rpdK6et-tlp7Fy9uJViUlCMs17gZiOQW_eHwM9O_2Q1RKiGCPtK9SGrGe2Fzj-dtO61Ax9Ubb2BqtINuM4rIjBlDDMq_0c5l5SSNBvQs1_ownX9T1QfFKUiSXHSU2xDmdZ530K59U-wGsbiD8en37Pb3vmaA_YOfCGz_g</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1442256706</pqid></control><display><type>article</type><title>The dynamics of alternative pathways to compensatory substitution</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>SpringerNature Journals</source><source>PubMed Central Open Access</source><source>Springer Nature OA Free Journals</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Nasrallah, Chris A</creator><creatorcontrib>Nasrallah, Chris A</creatorcontrib><description>The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have received considerable attention, most studies have focused on the case when natural selection is very strong against deleterious intermediates. In the biologically-plausible scenario of weak to moderate selection there exist two alternate pathways for compensatory substitution. In one pathway, a deleterious mutation becomes fixed prior to occurrence of the compensatory mutation. In the other, the two loci are simultaneously polymorphic. The rates of compensatory substitution along these two pathways and their relative probabilities are functions of the population size, selection strength, mutation rate, and recombination rate. In this paper these rates and path probabilities are derived analytically and verified using population genetic simulations. The expected time durations of these two paths are similar when selection is moderate, but not when selection is weak. The effect of recombination on the dynamics of the substitution process are explored using simulation. Using the derived rates, a phylogenetic substitution model of the compensatory evolution process is presented that could be used for inference of population genetic parameters from interspecific data.</description><identifier>ISSN: 1471-2105</identifier><identifier>EISSN: 1471-2105</identifier><identifier>DOI: 10.1186/1471-2105-14-S15-S2</identifier><identifier>PMID: 24564842</identifier><language>eng</language><publisher>England: BioMed Central</publisher><subject>Age ; Evolution ; Evolution, Molecular ; Gene expression ; Genetics, Population ; Haplotypes ; Models, Genetic ; Molecular biology ; Mutation ; Phylogenetics ; Phylogeny ; Population ; Probability ; Proceedings ; Selection, Genetic ; Studies</subject><ispartof>BMC bioinformatics, 2013, Vol.14 Suppl 15 (S15), p.S2-S2, Article S2</ispartof><rights>2013 Nasrallah; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>Copyright © 2013 Nasrallah; licensee BioMed Central Ltd. 2013 Nasrallah; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b529t-75c23c6d5cd9f0eb8be45534534140daf795c38f602e4647d98c8891ea98eea13</citedby><cites>FETCH-LOGICAL-b529t-75c23c6d5cd9f0eb8be45534534140daf795c38f602e4647d98c8891ea98eea13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852009/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852009/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,4024,27923,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24564842$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nasrallah, Chris A</creatorcontrib><title>The dynamics of alternative pathways to compensatory substitution</title><title>BMC bioinformatics</title><addtitle>BMC Bioinformatics</addtitle><description>The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have received considerable attention, most studies have focused on the case when natural selection is very strong against deleterious intermediates. In the biologically-plausible scenario of weak to moderate selection there exist two alternate pathways for compensatory substitution. In one pathway, a deleterious mutation becomes fixed prior to occurrence of the compensatory mutation. In the other, the two loci are simultaneously polymorphic. The rates of compensatory substitution along these two pathways and their relative probabilities are functions of the population size, selection strength, mutation rate, and recombination rate. In this paper these rates and path probabilities are derived analytically and verified using population genetic simulations. The expected time durations of these two paths are similar when selection is moderate, but not when selection is weak. The effect of recombination on the dynamics of the substitution process are explored using simulation. Using the derived rates, a phylogenetic substitution model of the compensatory evolution process is presented that could be used for inference of population genetic parameters from interspecific data.</description><subject>Age</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Gene expression</subject><subject>Genetics, Population</subject><subject>Haplotypes</subject><subject>Models, Genetic</subject><subject>Molecular biology</subject><subject>Mutation</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Population</subject><subject>Probability</subject><subject>Proceedings</subject><subject>Selection, Genetic</subject><subject>Studies</subject><issn>1471-2105</issn><issn>1471-2105</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkl1LwzAUhoMobn78AkEK3nhTzWeb3ghj-AWCF9PrkKanLqNtZpNO9u9tnQ4VRAjkkPPk5c2bg9AJwReEyOSS8JTElGAREx7PiIhndAeNt6e73-oROvB-gTFJJRb7aES5SLjkdIwmT3OIinWja2t85MpIVwHaRge7gmipw_xNr30UXGRcvYTG6-DadeS73AcbumBdc4T2Sl15OP7cD9HzzfXT9C5-eLy9n04e4lzQLMSpMJSZpBCmyEoMucyBC8F4vwjHhS7TTBgmywRT4AlPi0waKTMCOpMAmrBDdLXRXXZ5DYWBJrS6UsvW1rpdK6et-tlp7Fy9uJViUlCMs17gZiOQW_eHwM9O_2Q1RKiGCPtK9SGrGe2Fzj-dtO61Ax9Ubb2BqtINuM4rIjBlDDMq_0c5l5SSNBvQs1_ownX9T1QfFKUiSXHSU2xDmdZ530K59U-wGsbiD8en37Pb3vmaA_YOfCGz_g</recordid><startdate>2013</startdate><enddate>2013</enddate><creator>Nasrallah, Chris A</creator><general>BioMed Central</general><general>BioMed Central Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QO</scope><scope>7SC</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AL</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K7-</scope><scope>K9.</scope><scope>L7M</scope><scope>LK8</scope><scope>L~C</scope><scope>L~D</scope><scope>M0N</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>2013</creationdate><title>The dynamics of alternative pathways to compensatory substitution</title><author>Nasrallah, Chris A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b529t-75c23c6d5cd9f0eb8be45534534140daf795c38f602e4647d98c8891ea98eea13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Age</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Gene expression</topic><topic>Genetics, Population</topic><topic>Haplotypes</topic><topic>Models, Genetic</topic><topic>Molecular biology</topic><topic>Mutation</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Population</topic><topic>Probability</topic><topic>Proceedings</topic><topic>Selection, Genetic</topic><topic>Studies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nasrallah, Chris A</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Computing Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Computer Science Collection</collection><collection>Computer Science Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>ProQuest Biological Science Collection</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Computing Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nasrallah, Chris A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The dynamics of alternative pathways to compensatory substitution</atitle><jtitle>BMC bioinformatics</jtitle><addtitle>BMC Bioinformatics</addtitle><date>2013</date><risdate>2013</risdate><volume>14 Suppl 15</volume><issue>S15</issue><spage>S2</spage><epage>S2</epage><pages>S2-S2</pages><artnum>S2</artnum><issn>1471-2105</issn><eissn>1471-2105</eissn><abstract>The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have received considerable attention, most studies have focused on the case when natural selection is very strong against deleterious intermediates. In the biologically-plausible scenario of weak to moderate selection there exist two alternate pathways for compensatory substitution. In one pathway, a deleterious mutation becomes fixed prior to occurrence of the compensatory mutation. In the other, the two loci are simultaneously polymorphic. The rates of compensatory substitution along these two pathways and their relative probabilities are functions of the population size, selection strength, mutation rate, and recombination rate. In this paper these rates and path probabilities are derived analytically and verified using population genetic simulations. The expected time durations of these two paths are similar when selection is moderate, but not when selection is weak. The effect of recombination on the dynamics of the substitution process are explored using simulation. Using the derived rates, a phylogenetic substitution model of the compensatory evolution process is presented that could be used for inference of population genetic parameters from interspecific data.</abstract><cop>England</cop><pub>BioMed Central</pub><pmid>24564842</pmid><doi>10.1186/1471-2105-14-S15-S2</doi><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1471-2105 |
ispartof | BMC bioinformatics, 2013, Vol.14 Suppl 15 (S15), p.S2-S2, Article S2 |
issn | 1471-2105 1471-2105 |
language | eng |
recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3852009 |
source | MEDLINE; DOAJ Directory of Open Access Journals; SpringerNature Journals; PubMed Central Open Access; Springer Nature OA Free Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central |
subjects | Age Evolution Evolution, Molecular Gene expression Genetics, Population Haplotypes Models, Genetic Molecular biology Mutation Phylogenetics Phylogeny Population Probability Proceedings Selection, Genetic Studies |
title | The dynamics of alternative pathways to compensatory substitution |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T22%3A15%3A38IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20dynamics%20of%20alternative%20pathways%20to%20compensatory%20substitution&rft.jtitle=BMC%20bioinformatics&rft.au=Nasrallah,%20Chris%20A&rft.date=2013&rft.volume=14%20Suppl%2015&rft.issue=S15&rft.spage=S2&rft.epage=S2&rft.pages=S2-S2&rft.artnum=S2&rft.issn=1471-2105&rft.eissn=1471-2105&rft_id=info:doi/10.1186/1471-2105-14-S15-S2&rft_dat=%3Cproquest_pubme%3E1502330328%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1442256706&rft_id=info:pmid/24564842&rfr_iscdi=true |