Reference	Study Organism	Ancient dataset	Type of selection focused on	Method description	
Allentoft et al. (2015)	Humans	101 low coverage ancient genomes	Positive selection	Qualitative assessment of selection by tracking allele frequencies of 104 variants putatively under positive selection	
Alves et al. (2019)	Wild European rabbit	Genome-wide data from 91 historical samples	Positive selection	"Test for selection by modelling allele frequency change through time, method by Loog et al (2017) to quantify timing and strength of selection"	
Bollback et al. (2008)	Humans	Dataset from Hummel et al. (2005)	Positive selection	Estimate of 2Nes from allele frequency time series data	
Buckley et al. (2017)	Humans	Dataset from Allentoft et al. (2015	Postive selection	Test for selection by comparing allele frequencies at different periods using a likelihood model	
da Fonseca et al. (2015)	Maize	Exons of 348 genes from 32 ancient samples	Positive selection	"Tajima's D, PBS of populations at different periods"	
Faget et al. (2019)	Horses	"Genome-wide date from 132 samples, 129 genomes with >1x coverage"	Positive selection and negative selection	"PBS selection scan, allele trajectory reconstruction"	
Fehren-Schmitz & Georges (2016)	Humans	Genotypes of 3 SNPs from 109 ancient individuals	Positive selection	Forward simulations with drift and natural selection	
Gamba et al. (2014)	Humans	13 ancient genomes; coverage ranging from high (22.1x) to low (0.10x)	Positive selection	Qualitative assessment of selection by tracking allele frequencies of SNP's in 3 genes associated with pigmentation and in lactase persistence allele	
Gelabert et al. (2017)	Humans	Genome-wide data from 92 ancient individuals	Positive selection	Test for selection in 22 markers associated with Malaria resistance using method by Schraiber et al. (2016)	
Hummel et al. (2005)	Humans	Genotype of 1 locus from 38 historical and 31 ancient individuals	Positive selection	Qualitative assessment of selection by tracking allele frequency of CCR5-D32 gene variant	
Jaenicke-Després et al. (2003)	Maize	3 Loci from 11 ancient samples	Positive selection	Qualitative assessment of selection by tracking allele frequency of 3 variants associated with cob phenotype	
Librado et al. (2017)	Horses	14 ancient genomes; coverage ranging from 1.2x to 10.9x	Positive selection	"Genome-wide scans of selection using multiple methods; Fst, PBS and LSD between samples from different periods and locations"	
Lindo et al. (2016)	Humans	25 ancient exomes	"Balancing, negative and positive selection"	PBS selection scan and forward simulations of highest outlier	
Loog et al. (2017)	Domestic chicken	Genotype of 2 loci from resp. 30 and 59 ancient samples	Positive selection	Bayesian statistical framework to quantify timing and strenght of selection for two loci associated with domestication	
Ludwig et al. (2009)	Horses	8 SNPs in 6 loci from 89 ancient samples	Positive selection	Bollback et al. (2008) method	
Ludwig et al. (2015)	Horses	9 SNPs in 7 loci from 96 ancient samples	Positive and negative selection	Bayesian computational approach to estimate selection coefficients	
Malaspinas et al. (2012)	Horses	Dataset from Ludwig et al. (2009)	Positive selection	Maximum likelihood method to infer selection coefficient and allele age	
Mathieson et al. (2015)	Humans	Genome-wide data from 230 ancient individuals	Positive selection	"Infer selection signals by testing individual SNPs for outlier allele frequencies, test for selection on complex traits"	
Mathieson & Mathieson (2018)	Humans	Genotype of 5 SNPs from 52 Palaeolithic and Mesolithic ancient individuals and genome-wide data of 1078 Holocene ancient individuals	Positive selection	Mathieson and McVean (2013) method	
Ollivier et al. (2016)	Dogs	1 locus from 13 ancient samples	Positive selection	Qualitative assessment of selection by tracking changes in copy number	
Ramos-Madrigal et al. (2016)	Maize	Whole-genome shotgun data and data from a library enriched for 348 loci of 1 ancient sample	Positive selection	Qualitiative assessment of timing of selection by inferring domestication status of a set of SNPs	
Sandoval-Castellanos et al. (2017)	Horses	Genotypes of 9 loci from 27 ancient samples	Positive selection	"Infer selection coefficients using S-MCMC and ABC simulations, and path augmentation method"	
Schraiber et al. (2016)	Horses	Dataset from Ludwig et al. (2009)	Positive selection	Bayesian method to infer selection coefficients and allele age from time-series data	
Schubert et al. (2014)	Horses	2 ancient samples; average coverage of 24.3x and 7.4x	Positive selection	"Genome-wide scans of selection using multiple methods; ? ratio, Watterson estimator and Tajima’s D statistic, Hidden Markov Model, and coalescent genotypes"	
Steinrücken et al. (2014)	Horses	Dataset from Ludwig et al. (2009)	Balancing selection	Maximum likelihood method to infer selection coefficient 	
Swarts et al. (2017)	Maize	15 ancient samples; coverage ranging from 5x to 20x	Positive selection	"Test for selection by calculating Fst for 10,000 differentiated SNPs"	
Sverrisdottir et al. (2014)	Humans	Genotype of 1 loci from 8 ancient samples	Positive selection	Forward simulations with drift and natural selection	
Wilde et al. (2014)	Humans	Genotypes of 3 SNPs from 63 ancient individuals	Positive selection	Forward simulations with drift and natural selection	
Wutke et al. (2016)	Horses	Genotypes of 8 SNPs from 107 ancient samples	Positive and negative selection	Bayesian method with simulations to infer selection coefficients	
Ye et al. (2017)	Humans	325 ancient samples	Positive selection	"Multiple Methods; Mathieson et al. (2015) to test for recent selection, Schraiber et al. (2016), and Ferrer-Admetlla et al. (2016) to test for ancient selection"	
					
PBS: Population Branch Statistic					
LSD: Levels of exclusively Shared Differences					
"S-MCMC: Simulation Markov
chain Monte Carlo"					
					
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