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dc.contributor.authorPatton, Austin H
dc.contributor.authorMargres, Mark J
dc.contributor.authorStahlke, Amanda R
dc.contributor.authorHendricks, Sarah
dc.contributor.authorLewallen, Kevin
dc.contributor.authorHamede, Rodrigo K
dc.contributor.authorRuiz-Aravena, Manuel
dc.contributor.authorRyder, Oliver A.
dc.contributor.authorMcCallum, Hamish I
dc.contributor.authorJones, Menna E
dc.contributor.authorHohenlohe, Paul A
dc.contributor.authorStorfer, Andrew
dc.date.accessioned2021-03-19T17:31:21Z
dc.date.available2021-03-19T17:31:21Z
dc.date.issued2019
dc.identifier.issn0737-4038
dc.identifier.doi10.1093/molbev/msz191
dc.identifier.urihttp://hdl.handle.net/20.500.12634/961
dc.description.abstractReconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ?300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species’ effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
dc.language.isoen
dc.relation.urlhttps://doi.org/10.1093/molbev/msz191
dc.rightsThe Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/ licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectTASMANIAN DEVILS
dc.subjectPOPULATIONS
dc.subjectEVOLUTION
dc.subjectADAPTATION
dc.subjectEXPERIMENTAL METHODS
dc.subjectGENOMICS
dc.subjectGEOLOGY
dc.titleContemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian devils
dc.typeArticle
dc.source.journaltitleMolecular Biology and Evolution
dc.source.volume36
dc.source.issue12
dc.source.beginpage2906
dc.source.endpage2921
refterms.dateFOA2021-03-19T18:24:58Z
html.description.abstractReconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ?300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species’ effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
dc.source.conference


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The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/
licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is
properly cited.
Except where otherwise noted, this item's license is described as The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/ licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.