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fastsimcoal2: demographic inference under complex evolutionary scenarios

Laurent Excofffier, Nina Marchi, David Alexander Marques, Remi Matthey-Doret, Alexandre Gouy, Vitor C Sousa, Russell Schwartz
2021 Bioinformatics  
Motivation fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site  ...  Results Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations  ...  under complex evolutionary scenarios, and the most recent developments have therefore focused on this aspect.  ... 
doi:10.1093/bioinformatics/btab468 pmid:34164653 pmcid:PMC8665742 fatcat:l66enjyxbrayxmxfruvvr2w7gu

fastsimcoal2 : demographic inference under complex evolutionary scenarios

Laurent Excoffier, Nina Marchi, David Alexander Marques, Remi Matthey-Doret, Alexandre Gouy, Vitor C. Sousa
2021
Motivation: fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site  ...  Results: Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations  ...  under complex evolutionary scenarios, and the most recent developments have therefore focused on this aspect.  ... 
doi:10.48350/157985 fatcat:adr5disgmjejfblthgfdwuoq6i

Robust Demographic Inference from Genomic and SNP Data

Laurent Excoffier, Isabelle Dupanloup, Emilia Huerta-Sánchez, Vitor C. Sousa, Matthieu Foll, Joshua M. Akey
2013 PLoS Genetics  
To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations.  ...  Our methodology appears well suited to the study of complex scenarios from large genomic data sets.  ...  The program fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2. Author Contributions  ... 
doi:10.1371/journal.pgen.1003905 pmid:24204310 pmcid:PMC3812088 fatcat:3u66pr5iwvdg7eltykvap4fwo4

The impact of purifying and background selection on the inference of population history: problems and prospects [article]

Parul Johri, Kellen Riall, Jeffrey D. Jensen
2020 biorxiv/medrxiv  
We here examine how the presence of purifying and background selection may bias demographic inference by evaluating two commonly-used methods (MSMC and fastsimcoal2), specifically studying how the underlying  ...  Current procedures for inferring population history are generally performed under the assumption of complete neutrality - that is, neglecting both direct selection and the effects of selection on linked  ...  Under certain scenarios, this resulted in a many-fold mis-inference of population size change.  ... 
doi:10.1101/2020.04.28.066365 pmid:33501439 pmcid:PMC7836109 fatcat:c3cjdb2srjdrbin4l5fwciuiwy

skelesim: an extensible, general framework for population genetic simulation in R

Christian M. Parobek, Frederick I. Archer, Michelle E. DePrenger-Levin, Sean M. Hoban, Libby Liggins, Allan E. Strand
2016 Molecular Ecology Resources  
and marker types, under a variety of demographic conditions. skeleSim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role  ...  Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods.  ...  Acknowledgments This project originated at the Population Genetics in R Hackathon, which was held in March 2015 at the National Evolutionary Synthesis Center (NESCent) in Durham, NC, with the goal of addressing  ... 
doi:10.1111/1755-0998.12607 pmid:27736016 pmcid:PMC5161633 fatcat:35cam4r5drboldvlli7ntubzny

Genomic data support multiple introductions and explosive demographic expansions in a highly invasive aquatic insect

Joaquín Ortego, Vanessa Céspedes, Andrés Millán, Andy J. Green
2021 Molecular Ecology  
Future genomic analyses of native range populations could help to infer the genetic makeup of introduced populations and track invasion routes.  ...  Testing of alternative demographic models indicated that all populations experienced a strong bottleneck followed by a recent and instantaneous demographic expansion that restored a large portion (>30%  ...  | Demographic analyses We used the simulation-based approach implemented in fastsimcoal2 (Excoffier et al., 2013) to infer the evolutionary relationships among the three main genetic groups identified  ... 
doi:10.1111/mec.16050 pmid:34192379 fatcat:ozdb64skdncglicx4yjm4yc24y

The impact of purifying and background selection on the inference of population history: problems and prospects

Parul Johri, Kellen Riall, Hannes Becher, Laurent Excoffier, Brian Charlesworth, Jeffrey D Jensen
2021 Molecular biology and evolution  
We here examine how the presence of direct purifying selection and background selection may bias demographic inference by evaluating two commonly-used methods (MSMC and fastsimcoal2), specifically studying  ...  The results show that, even after masking functional genomic regions, background selection may cause the mis-inference of population growth under models of both constant population size and decline.  ...  Under certain scenarios, this resulted in a manyfold mis-inference of population size change.  ... 
doi:10.1093/molbev/msab050 pmid:33591322 pmcid:PMC8233493 fatcat:rl6cdvrpb5awfag2h32vhi7miy

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)
2020 eLife  
We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing  ...  Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured.  ...  In particular, we simulated data under multi-population models for humans and D. melanogaster and then inferred parameters using ∂a∂i, fastsimcoal2, and smc++.  ... 
doi:10.7554/elife.54967 pmid:32573438 pmcid:PMC7438115 fatcat:swayqkbysrgbfgzdh4yjr4whni

Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus )

Joaquín Ortego, Paul F. Gugger, Victoria L. Sork
2017 New Phytologist  
. • We employed restriction-site-associated DNA sequencing and integrate phylogenomic and population genomic analyses to reconstruct the evolutionary past of these taxa. • Our analyses revealed the presence  ...  Table 2 2 Parameters inferred from coalescent simulations with FASTSIMCOAL2 under the two most supported demographic models.Tableshowspoint estimates under models B1 and C1 (illustrated in Fig.2), model  ...  obtained from our coalescent-based demographic reconstructions in FASTSIMCOAL2.  ... 
doi:10.1111/nph.14951 pmid:29274282 fatcat:dwlxxingqvfpnjd6giynhq5aqm

Genomic evidence of speciation by fusion linked to trophic niche expansion in a recent radiation of grasshoppers [article]

Victor Noguerales, Joaquin Ortego
2021 bioRxiv   pre-print
Genetic clustering analyses and inferences from coalescent-based demographic simulations confirmed that C. s. algoaldensis represents a uniquely evolving lineage and supported the ancient hybrid origin  ...  range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate its long-term persistence through geographic isolation from parental forms in topographically complex  ...  During this work, VN was supported by a postdoctoral contract under the iBioGen project (grant agreement No 810729), which has received funding from the European Union's Horizon 2020 research and innovation  ... 
doi:10.1101/2021.12.26.474180 fatcat:mz6u3xuzuvfi7irqxiwcmdeqkq

Using high-throughput sequencing to investigate the factors structuring genomic variation of a Mediterranean grasshopper of great conservation concern

María José González-Serna, Pedro J. Cordero, Joaquín Ortego
2018 Scientific Reports  
Inferring the demographic history of species is fundamental for understanding their responses to past climate/landscape alterations and improving our predictions about the future impacts of the different  ...  Overall, our study highlights the importance of detailed phylogeographic, demographic and spatiallyexplicit landscape analyses to identify evolutionary significant units and determine the relative impact  ...  Parameters inferred from coalescent simulations with Fastsimcoal2 under the three best supported migration models (see Fig. 4 for details).  ... 
doi:10.1038/s41598-018-31775-x pmid:30194365 pmcid:PMC6128945 fatcat:7aw2xzdttngsfauennzkbfor2a

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

Alexander Nater, Reto Burri, Takeshi Kawakami, Linnéa Smeds, Hans Ellegren
2015 Systematic Biology  
Using genetic data to resolve the evolutionary relationships of species is of major interest in evolutionary and systematic biology.  ...  This allowed us to infer the most likely species tree with high confidence.  ...  inferred over long evolutionary time scales.  ... 
doi:10.1093/sysbio/syv045 pmid:26187295 pmcid:PMC4604831 fatcat:7bwvjpjldffsvowgi6lmzrizqi

The formation of avian montane diversity across barriers and along elevational gradients

José Martín Pujolar, Mozes P. K. Blom, Andrew Hart Reeve, Jonathan D. Kennedy, Petter Zahl Marki, Thorfinn S. Korneliussen, Benjamin G. Freeman, Katerina Sam, Ethan Linck, Tri Haryoko, Bulisa Iova, Bonny Koane (+4 others)
2022 Nature Communications  
In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments.  ...  Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area.  ...  To this end, we maximized the likelihood of the observed AFS under a total of 8 different demographic scenarios applied to each population pair across all species.  ... 
doi:10.1038/s41467-021-27858-5 pmid:35022441 pmcid:PMC8755808 fatcat:ygcn7mbwtzbb7c2o3dfwcvnjwa

Complex patterns of sex-biased demography in canines

Tanya N. Phung, Robert K. Wayne, Melissa A. Wilson, Kirk E. Lohmueller
2019 Proceedings of the Royal Society of London. Biological Sciences  
The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection.  ...  Our results confirm that canine demography has been complex, with opposing sex-biased processes occurring throughout their history.  ...  Inferring sex-biased demography at different timescales under an approximate Bayesian framework. (a) A two-population split model was used to infer demographic parameters.  ... 
doi:10.1098/rspb.2018.1976 pmid:31113325 pmcid:PMC6545087 fatcat:bssdpfz2srhj5np5mccsckrjha

Gene flow as a simple cause for an excess of high‐frequency‐derived alleles

Nina Marchi, Laurent Excoffier
2020 Evolutionary Applications  
Gene flow can either consist in single pulses of admixture or continuous immigration, but different demographic conditions are necessary to observe uSFS in these two scenarios.  ...  Overall, we find that a neutral uSFS occurs under more restrictive conditions in populations having received single pulses of gene flow than in populations exposed to continuous gene flow.  ...  However, Pouyet et al. (2018) recently showed that the uSFS observed in human populations could not be recovered under a complex demographic scenario involving an isolated population, but could be perfectly  ... 
doi:10.1111/eva.12998 pmid:33005222 pmcid:PMC7513730 fatcat:k4dvvp7pancvvp72ppo6elogtu
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