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Table 1 Description of the genome scan methods used to detect candidate outlier SNPs

From: Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus)

Method

R package

Categories

Correction for spatial or population structure

Data

# outliers detected (# unique)

Reference

Linear regression (LM)

LM

Linear model

No

Allele frequencies

129 (78)

R development Core Team

Redundancy Analysis (RDA)

vegan

Multivariate method

Yes

Allele frequencies

11 (0)

Legendre & Legendre 2012 [73]

Generalized linear spatial mixed models (gINLAnd)

gINLAnd

Mixed model

Yes

Read counts

7 (0)

Guillot et al. 2013 [49]

Latent factor mixed models (LFMMs)

LEA

Mixed model

Yes

Read counts

0

-

Frichot et al. 2013 [50]

Moran spectral outlier detection (MSOD)

PCNM and adespatial

Multivariate method

Yes

Allele frequencies

7 (1)

Wagner et al. 2017 [43]

Principal Component Analysis (PCadapt)

pcadapt

Multivariate method

No

Allele frequencies

88 (43)

Duforet-Frebourg et al. 2015 [74]