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SWEEPFINDER2: Increased sensitivity, robustness, and flexibility [article]

Michael DeGiorgio, Christian D. Huber, Melissa J. Hubisz, Ines Hellmann, Rasmus Nielsen
<span title="2015-05-26">2015</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection, as well as increased  ...  Moreover, SweepFinder2 enables the use of invariant sites for sweep detection, increasing both its power and precision relative to SweepFinder.  ...  Additionally, it incorporates novel features that provide the user with increased flexibility.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1505.07142v1">arXiv:1505.07142v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ub4x37obyzflllgf6sbokqtv3m">fatcat:ub4x37obyzflllgf6sbokqtv3m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200929174343/https://arxiv.org/ftp/arxiv/papers/1505/1505.07142.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/07/94/0794d510ea71384a80a51c884e9703a77316c929.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1505.07142v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

A survey of methods and tools to detect recent and strong positive selection

Pavlos Pavlidis, Nikolaos Alachiotis
<span title="2017-04-08">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kga3wj5jurhgflm5yjfqv2bnyy" style="color: black;">Journal of Biological Research - Thessaloniki</a> </i> &nbsp;
Additionally, we summarize the results of comparisons among four open-source software releases (SweeD, SweepFinder, Sweep-Finder2, and OmegaPlus) regarding sensitivity, specificity, and execution times  ...  The frequency of the favored allele increases in the population and due to genetic hitchhiking the neighboring linked variation diminishes, creating so-called selective sweeps.  ...  Thus, it exhibits increased sensitivity and robustness to background selection and mutation rate variations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40709-017-0064-0">doi:10.1186/s40709-017-0064-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28405579">pmid:28405579</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5385031/">pmcid:PMC5385031</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7cj43lhkkfemtm64huiurk7mjq">fatcat:7cj43lhkkfemtm64huiurk7mjq</a> </span>
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Detecting Positive Selection in Populations Using Genetic Data [chapter]

Angelos Koropoulis, Nikolaos Alachiotis, Pavlos Pavlidis
<span title="">2020</span> <i title="Springer US"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
We also summarize the results of comparisons among five open-source software releases (SweeD, SweepFinder, SweepFinder2, OmegaPlus, and RAiSD) regarding sensitivity, specificity, and execution times.  ...  The frequency of the favored allele increases in the population and, due to genetic hitchhiking, neighboring linked variation diminishes, creating so-called selective sweeps.  ...  Thus, it exhibits increased sensitivity and robustness to background selection and mutation rate variations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-0716-0199-0_5">doi:10.1007/978-1-0716-0199-0_5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31975165">pmid:31975165</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jyr6mrkeefa2dpiymxnvqxly3m">fatcat:jyr6mrkeefa2dpiymxnvqxly3m</a> </span>
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Classic and introgressed selective sweeps shape mimicry loci across a butterfly adaptive radiation [article]

Markus Moest, Steven M Van Belleghem, Jennifer E James, Camilo Salazar, Simon H Martin, Sarah L Barker, Gilson R P Moreira, Claire Mérot, Mathieu Joron, Nicola J Nadeau, Florian M Steiner, Chris D Jiggins
<span title="2019-06-28">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, consistent with patterns found in some populations.  ...  Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution.  ...  Acknowledgements We thank John Davey and Richard Wallbank for assistance with the capture design and Joe Hanly and Erica Westerman for providing aristaless CRE coordinates.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/685685">doi:10.1101/685685</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4a45ot7tondbpkvvjmgvnvljg4">fatcat:4a45ot7tondbpkvvjmgvnvljg4</a> </span>
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Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation

Markus Moest, Steven M. Van Belleghem, Jennifer E. James, Camilo Salazar, Simon H. Martin, Sarah L. Barker, Gilson R. P. Moreira, Claire Mérot, Mathieu Joron, Nicola J. Nadeau, Florian M. Steiner, Chris D. Jiggins (+1 others)
<span title="2020-02-06">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tsaumnzpkvdmvdi3blhl5clb24" style="color: black;">PLoS Biology</a> </i> &nbsp;
Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic ofsweeps of introgressed variation and consistent  ...  Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution.  ...  Acknowledgments We thank John Davey and Richard Wallbank for assistance with the capture design and Joe Hanly and Erica Westerman for providing aristaless CRE coordinates.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.3000597">doi:10.1371/journal.pbio.3000597</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32027643">pmid:32027643</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4dx4qtqfmjfvbiwmjfwo6zg3fq">fatcat:4dx4qtqfmjfvbiwmjfwo6zg3fq</a> </span>
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VolcanoFinder: Genomic scans for adaptive introgression

Derek Setter, Sylvain Mousset, Xiaoheng Cheng, Rasmus Nielsen, Michael DeGiorgio, Joachim Hermisson, Alex Buerkle
<span title="2020-06-18">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j6fzfstrmzcj3aeps7bx6tpoy4" style="color: black;">PLoS Genetics</a> </i> &nbsp;
and TCHH-RPTN in Africans.  ...  We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.  ...  a flexible scheme to match simulated volcano footprints for both hard and soft introgression sweeps.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1008867">doi:10.1371/journal.pgen.1008867</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32555579">pmid:32555579</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vceb5vio75hvfpm23ii3jbo2o4">fatcat:vceb5vio75hvfpm23ii3jbo2o4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201105051904/https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1008867&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d6/db/d6db07e4254d2916f9dffb956936e7d448636448.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1008867"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

VolcanoFinder: genomic scans for adaptive introgression [article]

Derek Setter, Sylvain Mousset, Xiaoheng Cheng, Rasmus Nielsen, Michael DeGiorgio, Joachim Hermisson
<span title="2019-07-11">2019</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
and TCHH-RPTN in Africans.  ...  We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.  ...  a flexible scheme to match simulated volcano footprints for both hard and soft introgression sweeps.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/697987">doi:10.1101/697987</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mqyv7nojhrb33p4xqwhisb7tvy">fatcat:mqyv7nojhrb33p4xqwhisb7tvy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201106181714/https://www.pure.ed.ac.uk/ws/files/154433191/journal.pgen.1008867.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/37/94/3794283f37b803bf530cba8be4b1cac5f7ed6481.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/697987"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Evidence for widespread selection in shaping the genomic landscape during speciation of Populus [article]

Jing Wang, Nathaniel Street, Eung-Jun Park, Pär K Ingvarsson, Jianquan Liu
<span title="2019-10-28">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Increasing our understanding of how various evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation.  ...  However, the genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance.  ...  ., & Nielsen, R. (2016). 8 2 3 SweepFinder2: increased sensitivity, robustness and flexibility. Bioinformatics, 8 2 4 32(12), 1895-1897. 8 2 5 Degnan, J. H., & Salter, L. A. (2005).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/819219">doi:10.1101/819219</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tmbu6thaongttowy2sp3zodo6i">fatcat:tmbu6thaongttowy2sp3zodo6i</a> </span>
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In the presence of population structure: From genomics to candidate genes underlying local adaptation [article]

Nicholas Price, Lua Lopez, Adrian E. E. Platts, Jesse R. Lasky, John K. McKay
<span title="2019-05-19">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
These include a negative regulator of abscisic-acid (FLDH) and flowering time genes PIF3, FIO1, and COL5.  ...  Finally, SNPs that showed significantly high Fst and LD, were enriched along fitness QTL peaks and cis-regulatory/nonsynonymous sites showing significant functional constraint.  ...  Methods in Ecology and Evolution 6:1248-1258. 598 DeGiorgio M, Huber CD, Hubisz MJ, Hellmann I, Nielsen R. 2016. SweepFinder2: increased 599 sensitivity, robustness and flexibility.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/642306">doi:10.1101/642306</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rqbqlugbl5ekhgmrwpwk6msima">fatcat:rqbqlugbl5ekhgmrwpwk6msima</a> </span>
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Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation

Markus Moest, Steven M Van Belleghem, Jennifer E James, Camilo Salazar, Simon H Martin, Sarah L Barker, Gilson R P Moreira, Claire Mérot, Mathieu Joron, Nicola J Nadeau, Florian M Steiner, Chris D Jiggins (+2 others)
<span title="2020-03-10">2020</span>
Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent  ...  Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution.  ...  Acknowledgments We thank John Davey and Richard Wallbank for assistance with the capture design and Joe Hanly and Erica Westerman for providing aristaless CRE coordinates.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17863/cam.50320">doi:10.17863/cam.50320</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ycslumcn4bd2rl47r4hjruy4sy">fatcat:ycslumcn4bd2rl47r4hjruy4sy</a> </span>
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A community-maintained standard library of population genetic models

Jeffrey R Adrion, Christopher B Cole, Noah Dukler, Jared G Galloway, Ariella L Gladstein, Graham Gower, Christopher C Kyriazis, Aaron P Ragsdale, Georgia Tsambos, Franz Baumdicker, Jedidiah Carlson, Reed A Cartwright (+17 others)
<span title="2020-06-23">2020</span> <i title="eLife Sciences Publications, Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/en4qj5ijrbf5djxx7p5zzpjyoq" style="color: black;">eLife</a> </i> &nbsp;
Re-cent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone  ...  The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations.  ...  Sweepfinder2: increased sensitivity, robustness and flexibility. Blanco, et al. African genomes illuminate the early history and transition to 648 selfing in Arabidopsis thaliana.  ... 
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