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Created by Stéphanie Manel, March 2022 for Landscape genetics lecture : this is a working document that is not exhaustive
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Completed by Brenna Forester
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LG: Landscape genomics methods
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MethodMain AssumptionsPackagepop/indcommentsExampleRef
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AMOVA island hierarchic population*Arlequinpop
Buehler D et al. Evolutionary Ecology 27, 285-300 (2013).
Excoffier L, Hofer T, Foll M. Detecting loci under selection in a hierarchically structured population. Heredity 103, 285-298 (2009).
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Fstisland model*Lositanpop
Sandoval-Castillo et al. Mol Ecol 27,  (2018).
Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G. LOSITAN: A workbench to detect molecular adaptation based on a F(st)-outlier method. Bmc Bioinformatics 9,  (2008).
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Fstisland model*Dfdistpop
Buehler D et al. Evolutionary Ecology 27, 285-300 (2013).
Baumont MA, Nichols RA. Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London, Series B 263, 1619-1626 (1996). 1. Beaumont MA, Balding DJ. Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13, 969-980 (2004).
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Fst multinomial dirichlet model**Bayescanpop
Sandoval-Castillo et al. Mol Ecol 27,  (2018).
Foll M, Gaggiotti O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180,  (2008).
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Fstempirical Fst distributionOutFlankpop
Whitlock MC, Lotterhos KE, Editor: Judith LB. Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST. The American Naturalist 186, S24-S36 (2015).
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Fst Account for coancestry FLKpop
Bonhomme M, et al. Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended. Genetics 186, 241-U406 (2010).
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PCAlinearityPcadaptboth
no underlying population genetic model
Dalongeville et al. BMC Genomics 19,  (2018).
Luu K, Bazin E, Blum MG. Pcadapt: an R package to perform genome scans for selection based on principal component analysis. Mol. Ecol Res 17,  (2017).
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FstTess3
Caye K, Deist TM, Martins H, Michel O, Francois O. 2016. TESS3: fast inference of spatial population structure and genome scans for selection. Molecular Ecology Resources 16:540-548.
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*
evolutionary independance of samples
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**
each population has its own parameter for neutral model ; demes/samples have evolved independently from an ancestral gene pool
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