Table 3.

Methodological approaches from empirical seascape genomic studies: elements of experimental design including spatial parameters, analyses, and genetic loci

Organism	Location	Spatial parametersa	Spatial predictor(s)	Genetic response variable(s)	Analytical approachb	Type and numb of locic	Unit genotyped	Number of Pops.	Number of Individuals	Outlier testsd	Number of outlier locie	Reference
Continuous seascape variables with genomic data
cod	North Atlantic—mostly Europe	LAT, LONG, temperature at spawning time, salinity at spawning time	Location-specific values of each of the spatial parameters in turn	Allele frequencies at individual outlier loci	SAM	tSNPs, SNPs (86,12)	Ind	18	708	BayeScan	7	Nielsen et al. (2009a)
cod	Greenland & Iceland	LAT, LONG, distance to nearest coastline, annual maximum, mean and range for annual bottom spring temperature (maximum, mean, and range), surface spring temperature (maximum, mean, and range), and annual mean bottom salinity; initially 24 variables were examined and then reduced to this subset to reduce correlations among variables	Each of the spatial parameters in turn	Allele frequencies of all loci with covariance conditioned on neutral loci	BayEnv	tSNPs (935)	Ind	20	847	BayeScan; Hierarchical	47	Therkildsen et al. (2013)
cod	Greenland	SST (mean, maximum and minimum), sea bottom temperature (mean, maximum and minimum), barotropic stream function	Least cost paths based on ocean climate suitability (created using species distribution modeling based on spatial parameters) between sampled population and spawning grounds	Posterior membership to Icelandic group	Linear model	tSNPs (81)	Ind	6	872	None	NA	Bonanomi et al. (2015)
cod	Baltic and North Sea	SST, temperature at spawning depth, SSS, salinity at spawning depth, dissolved oxygen (both at surface and spawning depth)	Location-specific values of each of the spatial parameters in turn	Population allele frequencies	BayEnv	SNPs (8809)	Ind	7	194	BayeScan; Fdist	326	Berg et al. (2015)
anemonefishes	Red Sea + Oman	Three barriers (arising from circulation or upwelling), OWD, environmental variables: day time SST, SSS, chlorophyll, color dissolved organic matter, particulate organic carbon	Combinations of various putative barriers, overwater distance, first PC of combined environmental variables	Distance matrix based on population pairwise FST values	Linear models with model support assessed by AIC	ddRAD (4559)	Ind	11	144	LFMM	98	Saenz-Agudelo et al. (2015)
			The first PC of the combined environmental variables	Individual genotypes	Latent factor mixed effects model
hake	Europe—mostly Mediterranean	SST, SSS, OWD	Location-specific values of each of the spatial parameters in turn	Allele frequencies at outlier loci with covariance conditioned on neutral loci	BayEnv	tSNPs (381)	Ind	19	850	BayeScan; Hierarchical	17	Milano et al. (2014)
herring	European North Atlantic	SST, mean spawning period surface temperature, SSS, mean spawning period surface salinity, OWD, LAT, LONG	Location-specific values of each of the spatial parameters in turn (excluding OWD), with a covariance matrix estimated from non-outlier loci	Population allele frequencies	BayEnv	tSNPs (281)	Ind	18	607	BayEnv; BayeScan; Hierarchical	10	Limborg et al. (2012)
			Distance matrices based on (1) SST, and (2) SSE with OWD as the additional distance matrix	Distance matrix based on population pairwise FST for each outlier locus	Partial Mantel
sole	European North Atlantic	SST, sea bottom temperature, SSS, mixed layer depth, maximum density gradient, chlorophyll concentration, surface productive layer, OWD, LAT, LONG	Environmental parameters conditioned on LAT and LONG and MEMs based on PcoA of distance matrix of shortest OWDs	Genotypes with analyses performed separately for neutral and outliers	partial RDA	tSNPs (476)	Ind	16	650	Fdist; Bayescan	13	Diopere chap 5, 2014
stickleback	Baltic and North Sea	SST, SSS	Location specific values of each of the spatial parameters in turn	Allele frequencies at outlier loci with covariance conditioned on neutral loci	BayEnv	RADseq (9404)	Pools	10	360	BayeScan; Fst quantile	94	(Guo et al. 2015)
Continuous seascape variables with targeted microsatellites
herring	Baltic and North Sea	Temperature at spawning and in April, salinity at spawning and in April, BPD, OWD, distance to the mouth of the Baltic, fishing pressure, LAT, LONG	Location-specific values of each temperature and salinity parameters in turn using both BPD and OWD as the additional distance matrices	Distance matrix based on population pairwise FST , partitioned for all loci, non-outliers, and the single outlier locus	Mantel and partial Mantel	gl Msats (51,17)	Ind	15	694	BayeScan; Fdist	1	Teacher et al. (2013)
			Location-specific values of each temperature and salinity parameters along with distance to the mouth of the Baltic, LAT, LONG	By locus allele frequencies (all loci)	MatSAM
			Combinations of location specific values of each temperature and salinity parameters along with distance to the mouth of the Baltic, fishing pressure	Population heterozygosity and allelic richness partitioned for all loci, non-outliers, and the single outlier locus	GLMs
sticklebacks	Baltic and North Sea	SST, SSS, BPD, OWD, LAT, LONG	SST and SSS in turn	Population allele frequencies for outlier loci	SAM	gl Msats (20, 20)	Ind	38	973	BayeScan; Fdist	9	DeFaveri et al. (2013)
			SST and SSS in turn with OWD as the additional distance matrix	Distance matrices based on population pairwise FST for outlier loci (individually and as a group)	Partial Mantel tests
			Combinations of SST, SSS, LAT, LONG	Population allele frequencies separately for genic and non genic loci	GESTE with Bayesian model selection
turbot	Europe (not Med)	Habitat variables: SST, sea bottom temperature, SSS, sea bottom salinity, oxygen concentration, primary production; Hydrodynamic variables: bottom shear stress, depth of pycnocline, density-based stratification index; LAT, LONG	All habitat and hydrodynamic variables, a matrix representing sampling year, and distance-based MEMs using a truncated distance matrix (PCNM approach)	Genotypes, with analyses performed separately for neutral and outliers and for different geographical partitions	RDA and partial RDA with dbMEM/PCNM to describe geographic distance and spatial correlations	gl Msats (12, 6)	Ind	290	999 (466 for some analyses)	BayeScan; Fdist	3	Vandamme et al. (2014)
Nominal seascape variable(s), with genomic data
anchovy	Europe (Atlantic, Mediterranean)	Open water versus coastal; nested sampling design with 2 habitats in 2 locations	Habitat	Joint allele frequency spectrum between pairs of populations	Custom model	RADseq (5628)	Ind	4	128	δαδι	431	{LeMoan: 2016be}
litorinid snail	Europe (Sweden, UK, Spain)	habitat: wave versus crab; nested sampling design with 2 habitat sites in 3 locations	Habitat	Proportion of shared outlier loci	Identifying sets of loci that are outliers in multiple habitat comparisons	RNAseq (6790)	pools	6	∼480	Fst quantile	NA	Westram et al. (2014)
			Habitat	Allele frequencies of SNPs from outlier contigs	Determining whether allele frequency changes between habitats are consistent across locations
litorinid snail	Sweden—3 island locations <10 km distant	habitat: wave versus crab; nested sampling design with 2 habitat sites in 3 locations	Habitat	Proportion of shared outlier loci	Identifying sets of loci that are outliers in multiple habitat comparisons	RADseq (4187)	Ind	6	130	Fdist	4-636 (depending on comparison)	Ravinet et al. (2016)
			Habitat	Individual genotype (presence/absence of alleles)	Binomial GLM
seagrass	Wadden Sea, North Sea (50 kms)	tidal position: tidal flat (exposed to air twice per day) or tidal creek (permanently submerged)	OWD	Distance matrix based on population pairwise FST	Mantel	gl Msats (14, 11)	Ind	6	485	DetSel; Fdist	3	Oetjen and Reusch (2007)
			OWD and habitat category	Distance matrix based on population pairwise FST	Partial Mantel
			Marker type and habitat	Distance matrix based on population pairwise FST	2-way ANOVA

^aLAT =  latitude; LONG  =  longitude, SST =  mean annual surface temperature; SSS  = mean annual surface salinity, OWD = overwater distance, BPD = biophysical distance. Many studies simply report “temperature” or “salinity” in which case we assume that SST and SSS, respectively, are implied.

^bBayEnv (Günther and Coop 2013); GESTE (Foll and Gaggiotti 2006); GLM is a general linear model; SAM/ matSAM (Joost et al. 2008).

^ctSNPs: Transcriptome-derived SNPs; gl Msats: gene linked microsatellites. In parentheses is the number of loci included in analyses (post filtering); if study includes both gene linked loci and non-gene linked loci then 2 numbers are reported, respectively.

^dBayEnv is the method of Coop et al. (2010); BayeScan is the method of Foll and Gaggiotti (2008); DetSel is from the method of Vitalis et al. (2003); Fdist is the method of Beaumont and Nicols (1996) regardless of which program was used for the analysis; LFMM is based on the method of Frichot et al. (2013) ; δαδι is the method of Gutenkunst et al. (2009).

^eAs defined by authors.