bio-ecological-genomics-landscape-genomics

name	bio-ecological-genomics-landscape-genomics
description	Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.
tool_type	r
primary_tool	LEA

Version Compatibility

Reference examples tested with: LEA 3.14+ (lfmm2 via LEA 3), pcadapt 4.3+, OutFLANK 0.2+, vegan 2.6+, gradientForest 0.1-32+, terra 1.7+, qvalue 2.34+, BayPass 2.3+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Landscape Genomics

"Find loci associated with environmental adaptation in my populations" -> Genotype-environment association with K-selected latent-factor correction, multivariate RDA for polygenic signal, paired with demography-calibrated FST outliers; genomic-offset prediction with explicit prediction-novelty regime characterization.

• R: LEA::lfmm2() (modern; via LEA 3) for univariate GEA with cross-entropy-elbow K choice
• R: vegan::rda() with Condition() for partial-RDA polygenic GEA
• R: OutFLANK::OutFLANK() for demography-calibrated FST outliers
• R: pcadapt::pcadapt() for PC-based scans without environmental data
• CLI: g_baypass for BayPass Bayesian Core/AUX/C2/IS analyses

The Single Most Important Modern Insight -- GEA is a Four-Confound Problem, Not a Signal-Plus-Noise Problem

The number-one failure mode in landscape genomics is treating "is locus X associated with environment Y" as a simple signal-extraction problem (the NimBios working group consolidated this view in Hoban 2016 Am Nat 188:379-397). GEA has FOUR concurrent confounds:

1. Population structure — IBD-driven allele-frequency gradients track distance, which correlates with most environmental variables
2. Demographic history — range expansion creates allele-frequency clines along the expansion axis that mimic selection (Lotterhos & Whitlock 2014 Mol Ecol 23:2178-2192)
3. Background and linked selection — reduces diversity in low-recombination regions, inflating apparent local-FST signals
4. Sampling design — non-random spatial sampling creates spurious GEA signals (Lotterhos & Whitlock 2015 Mol Ecol 24:1031-1046; paired contrasts > random > transects when demography is concerning)

A second cornerstone: Forester et al. 2018 established RDA as the best polygenic-adaptation detector but with a caveat — RDA performance requires imputed genotypes (no missing data) and is best for linear-gradient environments. For monogenic strong-selection loci, OutFLANK and BayPass-C2 remain competitive.

A third: Genomic offset has three regimes (Lind & Lotterhos 2025 Mol Ecol Resour 25:e14008): works well for interpolation (similar-to-training environments), degrades gracefully for modest extrapolation, FAILS for highly novel future environments. Reporting a single offset map without characterizing prediction-novelty is methodologically incomplete. For the broader eco-evolutionary integration framework, see Aguirre-Liguori 2021 Nat Ecol Evol 5:1350-1360.

Algorithmic Taxonomy

Method	Type	Strength	Fails when
FST outliers (naive)	Univariate per-locus	Simple; widely understood	Inflated FDR under demography (Lotterhos & Whitlock 2014)
OutFLANK (Whitlock & Lotterhos 2015)	Univariate FST with trimmed null	Robust to demography via trimmed-tail null	Conservative; misses weak-effect polygenic
pcadapt (Luu 2017)	PC-based Mahalanobis	Handles continuous structure; no need to define populations	Detects axes-of-divergence loci; not environment-specific
LFMM (Frichot 2013)	MCMC mixed model with latent factors	Original framework	Slow; superseded by LFMM2
LFMM2 (Caye 2019)	LSE-based mixed model with K latent factors	Fast; orders of magnitude faster than LFMM; modern default	K choice is critical; wrong K silently invalidates results
BayPass Core (Gautier 2015)	Bayesian FST with covariance matrix Omega	Explicit shared-history correction via Omega	Computationally heavy; convergence needs care
BayPass AUX	Bayesian env association with binary auxiliary variable	Posterior gives Bayes Factor per locus	Same as Core
BayPass C2	Bayesian contrast between two pre-defined groups	Like Bayesian Fisher exact	Requires pre-defined groups, not continuous env
BayPass IS	Importance-sampling joint Bayesian	Multiple covariates simultaneously	Most computationally expensive
RDA (Forester 2018)	Multivariate constrained ordination	HIGH power and LOW FDR for polygenic adaptation	Requires imputed genotypes; less power for monogenic
pRDA (partial RDA)	RDA conditioning out population structure	Controls for structure explicitly	Conservative; depends on which axes are conditioned out
Gradient forests (Ellis 2012; Ellis-Smith-Pitcher)	Random-forest non-linear GEA	Detects non-linear gene-environment	Less interpretable; no formal p-values
RDA offset (Capblancq 2021)	Linear genomic-offset prediction	Linear gradient assumption	Fails under highly novel future climate (Lind 2025)

Decision Tree by Scenario

Scenario	Recommended approach	Why
Monogenic local adaptation	OutFLANK or BayPass Core; cross-check with simulations	Demography-calibrated null
Polygenic local adaptation	RDA with environmental matrix; pRDA conditioning on structure	Forester 2018 superior power + lower FDR
Environmental association with structure correction	LFMM2 (K from sNMF cross-entropy elbow)	Modern default; orders of magnitude faster than LFMM
Binary group contrast	BayPass C2	Like Bayesian Fisher exact
Joint multi-covariate Bayesian inference	BayPass IS	Multiple env simultaneously
Quantifying maladaptation under climate change	RDA offset OR gradientForest offset	Report Lind 2025 caveat: works for interpolation, fails for novel
Multi-method consensus	Run OutFLANK + LFMM2 + BayPass; overlap is high-confidence	Method differences = methodological coverage
Mapping landscape resistance	Circuitscape + ResistanceGA optimization	Circuitscape integrates all paths; ResistanceGA optimizes the surface
Distinguishing IBD vs IBE	dbRDA variance partitioning (geographic + env)	Mantel-based methods have known autocorrelation issues
Sampling design optimization	Paired contrasts at environmental endpoints; cite Lotterhos & Whitlock 2015	Most powerful under demographic concern
Polyploid species	polyRAD / fitPoly / updog FIRST; then standard GEA	Diploid-assuming tools give biased FST estimates

LFMM2 with Mandatory K Selection

Goal: Identify loci significantly associated with environmental variables while controlling for unobserved demographic structure via K latent factors.

Approach: Run sNMF on the genotype matrix across K = 1...10 (or higher), compute cross-entropy at each K, pick K at the elbow (where cross-entropy first plateaus), then pass that K to LEA::lfmm2(). Wrong K silently invalidates results — too few K means residual structure confounds environment; too many K absorbs the environmental signal.

library(LEA)
library(qvalue)

# Convert VCF -> LFMM/GENO format
vcf2lfmm('variants.vcf', 'genotypes.lfmm')
vcf2geno('variants.vcf', 'genotypes.geno')

# MANDATORY K selection via sNMF cross-entropy elbow
# Run multiple repetitions per K (5 minimum) for stability
snmf_result <- snmf('genotypes.geno', K = 1:10, repetitions = 5,
                     entropy = TRUE, project = 'new')
ce_values <- sapply(1:10, function(k) min(cross.entropy(snmf_result, K = k)))
plot(1: ce_values xlab   ylab  
     pch   col   type  


best_K  which.mince_values


genotypes  read.lfmm
env_vars  read.env
lfmm_result  lfmm2input  genotypes env  env_vars K  best_K


pvalues  lfmm2.testlfmm_result input  genotypes env  env_vars
                       full   genomic.control  




gif  medianqchisq  pvaluespvalues  df    qchisq df  
cat gif  


qvals  qvaluepvaluespvalues qvalues
candidates  whichqvals  
cat candidates 

RDA — Capblancq & Forester 2021 Swiss-Army-Knife Workflow

Goal: Detect polygenic local adaptation via multivariate constrained ordination, with optional climate-offset prediction.

Approach: Apply the Capblancq & Forester 2021 RDA workflow: (1) variable selection via forward selection with adjusted R^2; (2) variance partitioning into pure-environment / pure-spatial / shared; (3) GEA outlier identification at SD > 3 on RDA axes 1-3; (4) adaptive-index computation; (5) genomic-offset prediction with the Lind 2025 three-regime caveat. CRITICAL: genotypes must be imputed before RDA (no missing data); cite Forester 2018 for the polygenic-power result.

library(vegan)

# CRITICAL: impute missing genotypes BEFORE RDA (Forester 2018 benchmark requirement)
# Column-mean imputation per locus is the simplest valid choice;
# population-stratified mean imputation is preferred when populations are known.
# For LEA-generated data, LEA::impute() is the canonical option.
for (j in seq_len(ncol(allele_freq))) {
    col_mean <- mean(allele_freq[, j], na.rm = TRUE)
    allele_freq[is.na(allele_freq[, j]), j] <- col_mean
}

# Partial RDA conditioning on population structure (e.g., Q-matrix from sNMF)
# This is pRDA per Capblancq 2021
rda_result <- rda(allele_freq ~ temperature + precipitation + altitude +
                  Condition(as.matrix(q_matrix)), data  env_data


anovarda_result permutations  


vp  varpartallele_freq env_data q_matrix
vppartfract  



loadings  scoresrda_result choices   display  
zscores  applyloadings  x x  meanx  sdx
rda_candidates  whichapplyzscores    
cat rda_candidates 

BayPass — Core, AUX, C2, IS Models

Goal: Bayesian Genotype-Environment Association with explicit population-history correction via covariance matrix Omega.

Approach: Convert VCF to BayPass's space-separated allele-count format. Run Core (estimates Omega; like Bayesian FST); use AUX for binary env-association testing; C2 for two-group contrast; IS for joint multi-covariate.

# BayPass input: space-separated allele counts, NOT VCF
# Use vcf2baypass.pl OR bcftools query to convert

# Core model: estimate Omega (population covariance from genome-wide SNPs)
g_baypass -gfile geno_BayPass.txt -outprefix core_run -nthreads 4

# AUX (binary auxiliary variable): test environmental association
# omegafile from Core run; covariates is samples x env file
g_baypass -gfile geno_BayPass.txt -efile env_BayPass.txt \
          -omegafile core_run_mat_omega.out \
          -outprefix aux_run -auxmodel -nthreads 4

# C2 (contrast between two pre-defined groups)
# contrasts.txt: 1 = group 1, -1 = group 2, 0 = excluded
g_baypass -gfile geno_BayPass.txt -contrastfile contrasts.txt \
          -omegafile core_run_mat_omega.out \
          -outprefix c2_run -nthreads 4

# Bayes Factor > 20 dB: strong evidence
# Bayes Factor > 30 dB: decisive evidence
# Convert: BFis (decibel scale) = 10 * log10(BF)

Genomic Offset — Lind & Lotterhos 2025 Three-Regime Framework

Goal: Predict maladaptation under future climate using genomic-offset methods (gradientForest, RDA-offset, LFMM2offset, RONA) while characterizing prediction-novelty. For the broader genomic-prediction review (foundation of the offset literature), see Capblancq et al. 2020 Annu Rev Ecol Evol Syst 51:245-269.

Approach: Compute offset per location as the distance in transformed genomic-environmental space between current and future predicted climate. CRITICAL: characterize whether each prediction falls into regime 1 (interpolation), regime 2 (modest extrapolation), or regime 3 (highly novel, where offset is uninformative or misleading). Report offset alongside prediction-novelty mapping.

library(gradientForest)
library(terra)

# Fit gradient forests on candidate loci x environment
gf <- gradientForest(cbind(env_predictors, allele_data),
                     predictor.vars = colnames(env_predictors),
                     response.vars = colnames(allele_data),
                     ntree = 500, trace = FALSE)

# Variable importance (which env drives most allele turnover)
plot(gf, plot.type = 'Overall.Importance')

# Predict genetic offset under current vs future
current <- rast('bioclim_current.tif')
future <- rast('bioclim_2070_ssp585.tif')
current_vals <- extract(current, sampling_coords)
future_vals <- extract(future, sampling_coords)

# Genomic offset = Euclidean distance in transformed space
current_transformed  predictgf current_vals
future_transformed  predictgf future_vals
genetic_offset  rowSumscurrent_transformed  future_transformed

Per-Method Failure Modes

LFMM2 with wrong K silently invalidates results

Trigger: Running LFMM2 with K too small (residual structure confounds environment) or K too large (latent factors absorb the environmental signal).

Mechanism: LFMM2 uses K latent factors to capture unobserved population structure. Wrong K means structure is either undercorrected (false positives) or overcorrected (false negatives), with no error message.

Symptom: Thousands of significant SNPs (too small K) OR almost none (too large K); genomic inflation factor lambda far from 1.0.

Fix: Use sNMF cross-entropy elbow as the primary K choice; run LFMM2 at K-1, K, K+1 and report sensitivity; flag loci detected at only one K as lower-confidence.

RDA on un-imputed genotypes silently degrades

Trigger: Running RDA on an allele-frequency matrix with NA values without imputation.

Mechanism: RDA cannot handle missing data internally; default behavior is to use na.omit which drops loci AND samples. Forester 2018's RDA-dominance benchmark assumed imputed genotypes.

Symptom: Effective sample size much smaller than expected; results sensitive to which loci have missing data.

Fix: Impute missing genotypes (mean within population, kNN, or snmf::impute()) BEFORE running RDA.

Genomic offset reported without prediction-novelty characterization

Trigger: Producing a country-wide genomic-offset map without indicating which areas are inside vs outside the training-data envelope.

Mechanism: Per Lind & Lotterhos 2025, genomic-offset accuracy declines with novelty of the predicted environment. Highly novel future climates fall in "regime 3" where offset is uninformative.

Symptom: Map shows highest predicted maladaptation in geographically extreme areas; cross-validation with multiple methods shows divergent predictions.

Fix: Compute prediction novelty per location (e.g., Mahalanobis distance to training envelope); annotate offset values with their regime; report cross-method consensus rather than single-method offset.

OutFLANK applied to continuous sampling design

Trigger: Running OutFLANK on continuous-gradient samples treated as a single "population".

Mechanism: OutFLANK assumes distinct, well-defined populations for FST calculation. Continuous sampling does not have natural population delimitation; the FST distribution depends arbitrarily on how samples are binned.

Symptom: OutFLANK results unstable to alternative population definitions; very few or impossibly many outliers.

Fix: Use LFMM2 or RDA for continuous gradient data; OutFLANK is appropriate when distinct populations are defined a priori.

LDNe physical-linkage trap on RAD-seq SNPs

Trigger: Running LFMM2 / RDA / OutFLANK on RAD-seq SNPs without LD pruning.

Mechanism: Physical linkage among RAD-seq SNPs creates correlated test statistics; outlier counts are inflated by chromosomal clustering rather than independent adaptation signal.

Symptom: Outliers cluster in large blocks along the genome; individual-locus inference is dominated by linkage.

Fix: LD-prune SNPs (PLINK --indep-pairwise 50 5 0.2) before GEA; OR thin to >= 1 cM apart with a genetic map.

Quantitative Thresholds

Threshold	Value	Source / rationale
LFMM2 K selection	Cross-entropy elbow from sNMF (LEA)	Caye 2019; sensitivity check at K-1, K+1
Genomic inflation factor target	Lambda ~ 1.0	> 1.5 = under-correction; < 0.5 = over-correction
FDR threshold	q < 0.05 (Storey)	qvalue package; more powerful than BH for genomic data
RDA outlier threshold	abs(z) > 3 on RDA axes 1-3	Capblancq & Forester 2021 conservative; 2.5 for polygenic
BayPass Bayes Factor	BF > 20 dB strong; > 30 dB decisive	Gautier 2015 convention
OutFLANK trim fractions	LeftTrim = RightTrim = 0.05	Whitlock & Lotterhos 2015 default
OutFLANK Hmin	0.1	Exclude low-heterozygosity unreliable FST
Forester 2018 RDA imputation	Required (no missing data)	RDA performance benchmark assumed imputed genotypes
Lind & Lotterhos 2025 offset regimes	Regime 1 (interpolation) / 2 (modest extrapolation) / 3 (highly novel)	Characterize per location
Lotterhos & Whitlock 2015 sampling design	Paired contrasts > random > transects under demographic concern	Genome-scan power

Common errors

Error	Cause	Solution
LFMM2 returns thousands of significant SNPs	K too small	Increase K via sNMF cross-entropy elbow
LFMM2 returns no significant SNPs	K too large; signal absorbed	Decrease K
Lambda (GIF) >> 1.5	Insufficient structure correction	Increase K or add structure covariate
RDA effective N much smaller than total	NA values in allele matrix	Impute before RDA
pcadapt screeplot shows no elbow	Continuous population structure or single-cline data	Switch to LFMM2 or RDA
OutFLANK error about populations	Continuous sampling, no defined populations	Use LFMM2 / RDA instead
BayPass "format error"	Passing VCF directly	Convert to space-separated allele counts via vcf2baypass.pl
Gradient-forest plot blank	Insufficient SNPs in candidate set	Increase candidate-locus pool
Genomic offset highest in intermediate climate	PC axes capture environment; structure absorbing signal	pRDA conditioning on geographic distance

References

• Frichot E, Schoville SD, Bouchard G, François O (2013) LFMM. Mol Biol Evol 30(7):1687-1699. doi:10.1093/molbev/mst063
• Caye K, Jumentier B, Lepeule J, François O (2019) LFMM 2: fast LSE estimator. Mol Biol Evol 36(4):852-860. doi:10.1093/molbev/msz008
• Gain C, François O (2021) LEA 3 package. Mol Ecol Resour 21(8):2738-2748. doi:10.1111/1755-0998.13366
• Gautier M (2015) BayPass. Genetics 201(4):1555-1579. doi:10.1534/genetics.115.181453
• Forester BR, Lasky JR, Wagner HH, Urban DL (2018) Multilocus adaptation methods: RDA superior. Mol Ecol 27(9):2215-2233. doi:10.1111/mec.14584
• Capblancq T, Forester BR (2021) RDA Swiss-army-knife for landscape genomics. Methods Ecol Evol 12(12):2298-2309. doi:10.1111/2041-210X.13722
• Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, Keller SR (2020) Genomic prediction of (mal)adaptation. Annu Rev Ecol Evol Syst 51:245-269. doi:10.1146/annurev-ecolsys-020720-042553
• Whitlock MC, Lotterhos KE (2015) OutFLANK. Am Nat 186(S1):S24-S36. doi:10.1086/682949
• Lotterhos KE, Whitlock MC (2014) Demographic confounders of FST outlier tests. Mol Ecol 23(9):2178-2192. doi:10.1111/mec.12725
• Lotterhos KE, Whitlock MC (2015) Sampling-design optimization for genome scans. Mol Ecol 24(5):1031-1046. doi:10.1111/mec.13100
• Lind BM, Lotterhos KE (2025) Accuracy of predicting maladaptation. Mol Ecol Resour 25:e14008. doi:10.1111/1755-0998.14008
• Wang IJ, Bradburd GS (2014) Isolation by environment (IBD vs IBE). Mol Ecol 23(23):5649-5662. doi:10.1111/mec.12938
• McRae BH, Dickson BG, Keitt TH, Shah VB (2008) Circuitscape circuit-theory. Ecology 89(10):2712-2724. doi:10.1890/07-1861.1
• Peterman WE (2018) ResistanceGA. Methods Ecol Evol 9(6):1638-1647. doi:10.1111/2041-210X.12984
• Ellis N, Smith SJ, Pitcher CR (2012) Gradient forests. Ecology 93(1):156-168. doi:10.1890/11-0252.1
• Aguirre-Liguori JA, Ramírez-Barahona S, Gaut BS (2021) Evolutionary genomics of climate response. Nat Ecol Evol 5(10):1350-1360. doi:10.1038/s41559-021-01526-9
• Hoban S, Kelley JL, Lotterhos KE et al. (2016) Finding the genomic basis of local adaptation. Am Nat 188(4):379-397. doi:10.1086/688018
• Luu K, Bazin E, Blum MGB (2017) pcadapt: an R package to perform genome scans for selection based on principal component analysis. Mol Ecol Resour 17(1):67-77. doi:10.1111/1755-0998.12592
• Legendre P, Fortin M-J (2010) Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships. 10(5):831-844. doi:10.1111/j.1755-0998.2010.02866.x

Related Skills

• ecological-genomics/conservation-genetics - Population genetic health (Ne, F_ROH); use ESU/MU framework not species delimitation for management units
• ecological-genomics/community-ecology - Environmental gradient analysis for species composition (analog of GEA for community data)
• population-genetics/selection-statistics - Selection scans in human population genetics
• population-genetics/population-structure - STRUCTURE / ADMIXTURE for substructure inference
• variant-calling/vcf-basics - VCF preparation from RAD-seq or WGS