bio-ecological-genomics-conservation-genetics

name	bio-ecological-genomics-conservation-genetics
description	Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.
tool_type	mixed
primary_tool	hierfstat

Version Compatibility

Reference examples tested with: hierfstat 0.5+, adegenet 2.1+, detectRUNS 2.0+, poppr 2.9+, NeEstimator V2.1+, GONE2, SNeP 1.1+, SLiM 4+, msprime 1.3+, bcftools 1.19+

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.

Conservation Genetics

"Assess the genetic health of my endangered population" -> Estimate Ne by time horizon (contemporary LD, recent trajectory, deep demographic history), measure inbreeding via F_ROH with length-class thresholds, decompose realized vs masked genetic load, and interpret against the modern 100/1000 Ne rule.

• R: hierfstat::basic.stats() for F-statistics and diversity
• R: detectRUNS::consecutiveRUNS.run() or bcftools roh -G30 for ROH detection
• CLI: Ne2.exe option_file.ne2 for NeEstimator V2 contemporary Ne (option-file driven, NOT CLI flags)
• CLI: gone2 for recent Ne trajectory from genome-wide LD (requires populated cM map)

The Single Most Important Modern Insight -- There is No Single Best Ne Estimator

The most common methodological failure in conservation genetics is treating "Ne" as one quantity. It is not. Each Ne estimator captures a different time horizon with different biases:

• LD-based (NeEstimator V2, Waples 2006): Last 1-few generations; biased downward at small N
• GONE / GONE2 (Santiago 2020): Recent 100-200 generations trajectory; requires populated cM genetic map
• Heterozygote-excess: Last 1 generation only; very low power
• Temporal (Jorde-Ryman): Between two time-sampled cohorts
• Stairway Plot 2 / dadi / fastsimcoal2: 10^3 to 10^5 generations from SFS
• PSMC: 10^4 to 10^6 generations from single high-coverage genome

A second cornerstone: Ne/Nc ratio is NOT 0.1 universally. Frankham 1995 reported a median of 0.1 in vertebrates, but Hauser & Carvalho 2008 Fish Fish 9:333-362 documented Ne/Nc spanning 2-6 orders of magnitude smaller than census (i.e., 10^-2 to 10^-6) in marine fish with sex-biased and sweepstakes-recruitment reproduction. Conservation papers that assume Ne/Nc = 0.1 are wrong for many taxa.

A third: the 50/500 rule was revised to 100/1000 by Frankham et al. 2014 Biol Conserv 170:56-63. The 50/500 numbers came from 1980 and underestimate the Ne needed for adaptive maintenance. The modern thresholds are Ne >= 100 for short-term inbreeding-fitness protection and Ne >= 1000 for long-term adaptive potential.

Algorithmic Taxonomy

Method	Time horizon	Strength	Bias mode
LDNe (NeEstimator V2 LD method)	Last 1-few generations	Single sample; SNP-friendly	Biased downward at small N; sensitive to physical linkage
SNeP (LD with physical-linkage correction)	Last 1-few generations	Corrects LDNe for chromosomal linkage in genomic data	Requires phased genotypes
GONE / GONE2	Recent 100-200 generations	Detects bottleneck/expansion trajectory	Requires populated cM genetic map column (NOT physical position)
Heterozygote-excess	Last 1 generation	Detects recent bottleneck	Very low power; requires high heterozygosity
Temporal (Jorde-Ryman, Pollak)	Between two cohorts	Direct drift estimate	Requires temporal samples
Sibship (Wang COLONY)	Current generation	Pedigree-based from kinship	Computationally expensive
dadi (Gutenkunst 2009)	10^3 - 10^5 generations	Diffusion SFS-based; analytical	Local-optima trap; <=3 populations practical
fastsimcoal2 (Excoffier 2013)	10^3 - 10^5 generations	Simulation-based composite-likelihood	Optimization needs >= 50 replicates
moments (Jouganous 2017)	10^3 - 10^5 generations	Moment-based ODE; faster than dadi	Same dimensionality limits
momi2 (Kamm 2020)	10^3 - 10^5 generations	Analytical SFS via moments	Stiff at very recent times
Stairway Plot 2	10^3 - 10^5 generations	Folded SFS; no parametric model	Requires explicit mutation rate and generation time
PSMC	10^4 - 10^6 generations	Whole-genome pairwise coalescent	Requires >= 20x WGS coverage
MSMC2	Multi-individual deep coalescent	Better recent resolution than PSMC	Requires phased data; computational
msprime (Kelleher 2016)	Simulation (not inference)	Gold-standard neutral simulator	Used to generate data under a fitted model
SLiM 3/4 (Haller & Messer 2019)

Decision Tree by Scenario

Scenario	Recommended approach	Why
Contemporary Ne from a single SNP sample	NeEstimator V2 LD method with Pcrit = 0.02	Standard; widely accepted by conservation reviewers
LDNe applied to RAD-seq / WGS	Use SNeP (Barbato 2015) OR thin SNPs to >= 1 cM apart	LDNe assumes inter-locus r^2 reflects demography only; physical linkage inflates it
Recent Ne trajectory (bottleneck detection)	GONE2 with populated cM genetic-map column	GONE2 fails silently if cM column is zero (PLINK default uses physical position)
Deep demographic history (mammal/vertebrate)	PSMC with >= 20x WGS or Stairway Plot 2 from SFS	PSMC requires high coverage; Stairway Plot 2 needs only the SFS
Multi-population demographic inference	dadi / fastsimcoal2 with >= 50 independent optimization replicates	Likelihood surfaces have local optima; single-replicate inference is unreliable
Inbreeding from genomic data	F_ROH with length-class thresholds (bcftools roh OR detectRUNS)	F_IS is genome-averaged; F_ROH partitions inbreeding by time
Genetic-load assessment	Decompose realized vs masked via Bertorelle 2022 framework	Single "load" estimate hides the dynamics
Define management unit (MU) or ESU	Moritz 1994 reciprocal monophyly + nuclear divergence	Do NOT use BPP/BFD* species-delimitation methods (Sukumaran-Knowles 2017 oversplitting)
Forward simulation of selection + demography	SLiM 4 with tree-sequence recording + pyslim/tskit	Tree-sequence recording is 5-100x faster than mutation tracking
Comparing Ne across species	Cite Ne/Nc taxonomic variation (Hauser & Carvalho 2008)	The Ne/Nc = 0.1 default is wrong for many taxa
Genetic rescue decision	Frankham 2015 meta-analysis; usually favors rescue	Outbreeding-depression fear is overstated for most cases

Genetic Diversity and F-Statistics

Goal: Compute standard population-genetic metrics with Weir-Cockerham estimators and bootstrap confidence intervals.

Approach: Convert VCF to genind via adegenet, then to hierfstat format. Run basic.stats for Fis/Fst/Ho/He and pairwise.WCfst with bootstrapping for population differentiation.

library(hierfstat)
library(adegenet)
library(poppr)

# VCF/genepop/PLINK -> genind via adegenet
data_genind <- read.genepop('populations.gen')
data_hf <- genind2hierfstat(data_genind)

# F-statistics with Weir-Cockerham estimators
bstats <- basic.stats(data_hf)
cat('Overall Fis:', bstats$overall['Fis'], '\n')
cat('Overall Fst:', bstats$overall['Fst'], '\n')

# Pairwise FST with bootstrap CIs
pw_fst <- pairwise.WCfst(data_hf)
boot_fst <- boot.ppfst(data_hf, nboot = 1000)

# Rarefied allelic richness (corrects for unequal sample sizes)
ar <- allelic.richness(data_hf)


pa  private_allelesdata_genind count.alleles  

Runs of Homozygosity with Length-Class Dating

Goal: Detect autozygous segments and date the inbreeding events by ROH length class.

Approach: Use bcftools roh -G30 (HMM-based, density-independent) for VCF input OR detectRUNS::consecutiveRUNS.run() for PLINK. Bin ROH by length to date inbreeding events: > 16 Mb means parents/grandparents; 4-16 Mb means ~5 generations; 1-4 Mb means ~10-20 generations; < 1 Mb is deep background.

library(detectRUNS)

# detectRUNS: SNP-by-SNP scanning from PLINK files
runs <- consecutiveRUNS.run(
    genotypeFile = 'genotypes.ped',
    mapFile = 'genotypes.map',
    minSNP = 20,        # Minimum SNPs per run; prevents short-stretch false positives
    minLengthBps = 1e6, # 1 Mb minimum; shorter ROH usually not IBD-derived
    maxGap = 1e6,
    maxOppRun = 1,
    maxMissRun = 2
)

# F_ROH per individual = sum(ROH length) / autosomal genome length
# > 16 Mb ROH: parents/grandparents inbreeding (very recent)
# 4-16 Mb: ~5 generations back
# 1-4 Mb: ~10-20 generations (historical bottleneck)
# < 1 Mb: deep background, ancient homozygosity
froh <- Froh_inbreeding(runs, mapFile = 'genotypes.map', genome_wide = TRUE)

# Bin ROH by length to estimate inbreeding timing
runs_summary <- summaryRuns(runs, genotypeFile = 'genotypes.ped'
                            mapFile  
plot_DistributionRunsruns

# Alternative: bcftools roh with HMM (density-independent; better for low-density data)
# -G30: per-sample genotype likelihood threshold (30 = high-quality calls)
# --AF-tag AF: use AF tag from VCF for allele frequencies (else --AF-file)
bcftools roh -G30 --AF-tag AF -o roh_results.txt input.vcf.gz

NeEstimator V2 — Option-File API

Goal: Estimate contemporary Ne via LD method from a single sample (Do et al. 2014 Mol Ecol Resour 14:209-214).

Approach: NeEstimator V2 is option-file driven, NOT CLI-flag driven. Create a .ne2 text option file specifying input format, methods (LD/HetExcess/Coancestry/Temporal), Pcrit thresholds, and output. Run with Ne2.exe option_file.ne2.

# Example NeEstimator V2 option file (option_file.ne2)
# Line order matters; defaults can cause silent failures
# See NeEstimator V2 documentation: https://github.com/bunop/NeEstimator2.X

# Input format
1 0                                   # 1=GenePop, 2=FSTAT; second value reserved
input_genotypes.gen

# Methods (1 = run; 0 = skip)
1 0 0 0                               # LD only; others (HetExcess, Coancestry, Temporal) off

# Pcrit cutoffs (allele frequencies below threshold excluded)
3                                     # number of Pcrit values
0.05 0.02 0.01                        # 0.02 is standard; 0.05 conservative; 0.01 sensitive

# Mating system: 0 = random mating; 1 = monogamy
0

# Output
output_results.txt

# Run NeEstimator V2 (Java-based)
java -jar NeEstimator.jar option_file.ne2
# Verify INFO output line: confirms which methods ran and which were skipped

# Common failure: "Ne = infinity" reported
# Diagnosis: insufficient drift signal (population larger than method can detect)
# Try multiple Pcrit; with genomic data add SNeP physical-linkage correction

GONE2 — Recent Ne Trajectory with the cM-Column Trap

Goal: Estimate the Ne trajectory over the last ~100-200 generations from genome-wide LD across recombination rates.

Approach: GONE2 requires a genetic map with POPULATED cM positions (not just physical position). PLINK MAP files default to cM=0; if this is not corrected, GONE2 will silently produce nonsense. Verify the cM column is populated from a genetic-map file or use Hi-C-derived recombination map.

# GONE2 input: PLINK BED/BIM/FAM or VCF + populated MAP
# CRITICAL: BIM/MAP cM column must be populated; default cM=0 produces silent failure

# Check cM column populated
head genotypes.bim   # column 3 should NOT be all zeros

# Run GONE2
# -t 4: threads
# -u 0.05: upper recombination rate bound (exclude pairs with r > 0.05)
# Smaller -u focuses on more recent generations
./gone2 -t 4 -u 0.05 genotypes.vcf

# Output: OUTPUT_GONE2 with generation, Ne, CI_low, CI_high

# Parse GONE2 output and plot Ne trajectory
gone_out <- read.table('OUTPUT_GONE2', header = TRUE, sep = '\t')

pdf('gone2_ne_trajectory.pdf', width = 8, height = 5)
plot(gone_out$generation, gone_out$Ne,
     type = 'l', lwd = 2, col = 'blue',
     xlab = 'Generations ago', ylab = 'Effective population size (Ne)',
     main = 'Recent Ne Trajectory (GONE2)', log = 'y')
polygon(c(gone_out$generation, rev(gone_out$generation))
        gone_outCI_low revgone_outCI_high
        col  adjustcolor alpha   border  
dev.off

SNeP — Physical-Linkage-Corrected LDNe for Genomic Data

Goal: Apply physical-linkage correction to LDNe when SNPs come from RAD-seq or WGS (where inter-locus r^2 reflects chromosomal linkage, not just demography).

Approach: SNeP (Barbato 2015 Front Genet 6:109) implements Waples & Do's physical-linkage correction. Use when SNPs are not pre-thinned to >= 1 cM apart.

# SNeP input: PLINK PED/MAP or VCF + map file
# Multi-threaded; supports several corrections (sample size, mutation, phasing, recombination)
./SNeP1.1 -ped genotypes.ped -map genotypes.map -threads 4 \
          -mutationrate 1.4e-8 -out snep_results.txt

# Output: Ne estimates per recombination-rate bin

Deep Demographic History

Goal: Reconstruct Ne trajectory over thousands of generations from genome-wide variation.

Approach: Pick the appropriate tool by data type. PSMC for a single high-coverage diploid genome. Stairway Plot 2 for SFS from population samples. dadi or fastsimcoal2 for multi-population history with composite likelihood.

# --- PSMC: single high-coverage WGS (>= 20x) ---
bcftools mpileup -C50 -Q 30 -q 30 -f reference.fa sample.bam | \
    bcftools call -c | vcfutils.pl vcf2fq -d 10 -D 100 > consensus.fq
fq2psmcfa -q20 consensus.fq > consensus.psmcfa
psmc -N25 -t15 -r5 -p '4+25*2+4+6' -o sample.psmc consensus.psmcfa
psmc_plot.pl -u 1.4e-8 -g 5 -p sample_psmc_plot sample.psmc

# --- Stairway Plot 2: SFS-based (works with RAD-seq or WGS) ---
# Build SFS from VCF (use easySFS or vcf2sfs)
# Create blueprint.txt specifying nseq, L, mu, generation time
java -cp stairway_plot_v2.jar Stairbuilder blueprint.txt
bash blueprint.sh

# --- fastsimcoal2: multi-population composite-likelihood SFS ---
# REQUIRES >= 50 independent optimization replicates; single-run is unreliable
for i in {1..50}; do
    fsc27 -t template.tpl -e template.est -m -L 50 -n 100000 -q
done
# Compare likelihoods across replicates; report best AND distribution

Genetic Load — Realized vs Masked Decomposition

Goal: Decompose total genetic load into realized (currently expressed) and masked (heterozygous, potential) components per Bertorelle 2022 framework.

Approach: Use SnpEff/VEP to annotate variants for predicted functional effect. Compute realized load from homozygous-derived-allele counts at deleterious positions; compute masked load from heterozygous counts. Hedrick & Garcia-Dorado 2016 distinguish purging vs drift dynamics; report both.

# Conceptual workflow (Bertorelle et al. 2022 NRG 23:492-503)
# Realized load: count_homozygous_deleterious / total_deleterious_sites
# Masked load: count_heterozygous_deleterious / total_deleterious_sites
# Total load = realized + 0.5 * masked (assuming partial dominance)

# Annotate VCF with SnpEff or VEP first to classify deleterious vs neutral
# Then per individual:
# realized_load <- sum(genotype == 2 & severity == 'HIGH') / sum(severity == 'HIGH')
# masked_load <- sum(genotype == 1 & severity == 'HIGH') / sum(severity == 'HIGH')

# Cite Hedrick & Garcia-Dorado 2016 TREE 31:940-952 for purging vs drift:
# Strong-s alleles purge under inbreeding (potentially good)
# Weak-s alleles fix by drift (definitely bad)
# Net effect depends on selection-coefficient distribution
# Empirical purging example: Robinson 2018 Curr Biol 28:3487-3494 (Channel Island foxes)
# Simulation-based load assessment: Kyriazis 2021 Evol Lett 5:33-47

Forward Simulation with Tree-Sequence Recording

Goal: Simulate selection and non-Wright-Fisher demography efficiently using SLiM 4 with tskit tree-sequence recording.

Approach: SLiM 4 with treeSeqOutput() records the genealogy; pyslim + tskit adds neutral mutations a posteriori. This is 5-100x faster than mutation-tracking (Haller, Galloway, Kelleher, Messer, Ralph 2019 Mol Ecol Resour 19:552-566). The Eidos scripting language is NOT Python.

# Reference: SLiM 4+, pyslim 1.0+, tskit 0.5+, msprime 1.3+
# Note: SLiM scripts (.slim files) use Eidos, not Python.
# See https://messerlab.org/slim/ for full Eidos syntax.

# After running a SLiM simulation with treeSeqOutput():
import tskit
import pyslim
import msprime

ts = tskit.load('simulation.trees')
ts = pyslim.update(ts)  # update to current SLiM/pyslim conventions

# Recapitate: add coalescence above the SLiM tree root (neutral burn-in)
ts_recap = pyslim.recapitate(ts, recombination_rate=1e-8,
                              ancestral_Ne=10000, random_seed=42)

# Add neutral mutations after-the-fact via msprime
ts_mut = msprime.sim_mutations(ts_recap, rate=1e-8, random_seed=42)

# Export VCF for downstream analyses
with open('simulation.vcf', 'w') as f:
    ts_mut.write_vcf(f)

Per-Method Failure Modes

LDNe applied to RAD-seq SNPs without physical-linkage correction

Trigger: Running NeEstimator V2 LD method on RAD-seq or WGS genotypes thinned only by MAF, with multiple SNPs per chromosome at close physical distance. For RAD-seq biases more broadly, see Andrews 2016 Nat Rev Genet 17:81-92.

Mechanism: LDNe assumes inter-locus r^2 reflects only demographic LD (drift, random mating). With physically linked SNPs, much r^2 is chromosomal, NOT demographic. The estimator interprets this as "more drift has happened" and reports a smaller Ne.

Symptom: LDNe estimate dramatically lower than ecologically reasonable; downward bias compared with temporal or other estimators on the same population.

Fix: Thin SNPs to >= 1 cM apart OR use SNeP (Barbato 2015) which corrects for physical linkage explicitly. NeEstimator V2 has a Chrom flag for chromosome-aware LDNe; document its use.

GONE2 silent failure with PLINK MAP cM=0 (the default)

Trigger: Running GONE/GONE2 on PLINK output where the MAP file's cM column was never populated (defaults to 0 because PLINK uses physical position).

Mechanism: GONE/GONE2 use the cM positions to interpret recombination distances; cM=0 for all loci means the algorithm cannot distinguish linked from unlinked SNPs and produces nonsense.

Symptom: GONE2 output shows extreme Ne values or completely flat trajectory; results inconsistent across runs or with other methods.

Fix: Populate the cM column from a species-specific genetic map, OR build one from Hi-C data, OR use the linkage-rate approximation from PLINK --cm-map. Verify with head genotypes.bim — column 3 should not be all zeros.

NeEstimator silently fails with malformed option file

Trigger: Modifying line order in the .ne2 option file or omitting expected parameters.

Mechanism: NeEstimator V2 reads the option file by line order with rigid parsing. Reordered lines or skipped parameters cause the program to misinterpret subsequent lines without raising clear errors.

Symptom: "INFO" output line shows fewer methods running than expected; results file is empty or has impossible values.

Fix: Strictly follow the documented option-file format. The INFO line confirms which methods actually ran. Cross-reference with the official documentation (https://github.com/bunop/NeEstimator2.X).

dadi/fastsimcoal2 single-replicate inference at local optimum

Trigger: Running dadi or fastsimcoal2 with only 1-5 optimization replicates and reporting the result.

Mechanism: Likelihood surfaces for demographic inference have local optima. A single optimization may converge to a local maximum that is much worse than the global maximum.

Symptom: Reviewer asks "how many replicates?"; parameter estimates inconsistent across studies; demographic events implausible.

Fix: Run >= 50 independent replicates with random starting parameters; report the best-likelihood replicate AND the spread; flag if the top replicates disagree.

Ne/Nc = 0.1 assumption applied to fish or other high-fecundity taxon

Trigger: Converting Ne to Nc via ratio = 0.1 for a marine fish, broadcast spawner, or other species with high reproductive skew.

Mechanism: Frankham 1995 median Ne/Nc = 0.1 was derived from primarily terrestrial vertebrates. Hauser & Carvalho 2008 documented Ne/Nc spanning 2-6 orders of magnitude smaller than census (10^-2 to 10^-6) in marine fish with sex-biased and sweepstakes recruitment. The 0.1 default produces wildly wrong Nc estimates.

Symptom: Census size estimate disagrees with field observations by orders of magnitude.

Fix: Use taxon-specific Ne/Nc ratios from the literature. For marine fish with sweepstakes recruitment, Hauser & Carvalho 2008 documented Ne/Nc spanning 2-6 orders of magnitude smaller than census (10^-2 to 10^-6). For long-lived mammals, 0.1 - 0.3 is typical. Cite Hauser & Carvalho 2008 when discussing Ne/Nc.

Quantitative Thresholds

Threshold	Value	Source / rationale
Modern Ne for inbreeding protection	Ne >= 100	Frankham 2014 Biol Conserv 170:56-63 (revised from 50)
Modern Ne for adaptive maintenance	Ne >= 1000	Frankham 2014 (revised from 500)
F_ROH for very recent inbreeding	ROH > 16 Mb	Parents/grandparents-scale; standard ROH-length-class convention
F_ROH for historical bottleneck	1-4 Mb ROH	~10-20 generations back
LDNe Pcrit (allele frequency cutoff)	0.02 standard; 0.05 conservative; 0.01 sensitive	NeEstimator V2 convention
GONE2 minimum SNPs	10,000	Reliable trajectory inference
GONE2 minimum N	50 diploids	Statistical power floor
PSMC minimum coverage	>= 20x WGS	Single-genome SMC requires high coverage
dadi / fsc2 optimization replicates	>= 50	Local-optima trap below this
Ne/Nc default (use cautiously)	0.1 vertebrate median	Hauser & Carvalho 2008 documented 2-6 orders of magnitude variation in marine fish (10^-2 to 10^-6)
SLiM forward-sim with tree sequences	treeSeqOutput() mandatory for speed	5-100x faster than mutation tracking

Common errors

Error	Cause	Solution
LDNe reports Ne = infinity	Population too large for method to detect drift	Try multiple Pcrit; switch to SNeP for genomic data; acknowledge "Ne very large"
GONE2 nonsense trajectory	cM column = 0 in BIM/MAP file (PLINK default)	Populate cM with species genetic map or Hi-C inference
NeEstimator silent skip	Malformed option file or wrong method index	Check INFO line in output; align with documented format
bcftools roh empty output	Missing -G30 flag or --AF-tag	Add -G30 --AF-tag AF
detectRUNS missing F_ROH	Wrong mapFile path or chromosome naming mismatch	Verify map file format matches PED file
dadi numerical error at recent times	Mixing float32 in SFS construction	Use numpy float64 explicitly
SLiM script error "Eidos not Python"	Trying to use Python syntax	SLiM uses Eidos; consult SLiM manual
msprime PopulationConfiguration deprecation	Old msprime <1.0 API in newer install	Use msprime.Demography() constructor

References

• Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium. Conserv Genet 7(2):167-184. doi:10.1007/s10592-005-9100-y
• Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR (2014) NeEstimator V2. Mol Ecol Resour 14(1):209-214. doi:10.1111/1755-0998.12157
• Santiago E, Novo I, Pardiñas AF, Saura M, Wang J, Caballero A (2020) Recent demographic history inferred by high-resolution analysis of linkage disequilibrium (GONE). Mol Biol Evol 37(12):3642-3653. doi:10.1093/molbev/msaa169
• Barbato M, Orozco-terWengel P, Tapio M, Bruford MW (2015) SNeP: physical-linkage-corrected LDNe. Front Genet 6:109. doi:10.3389/fgene.2015.00109
• Frankham R, Bradshaw CJA, Brook BW (2014) Revised 100/1000 Ne rules. Biol Conserv 170:56-63. doi:10.1016/j.biocon.2013.12.036
• Hauser L, Carvalho GR (2008) Paradigm shifts in marine fisheries genetics. Fish Fish 9(4):333-362. doi:10.1111/j.1467-2979.2008.00299.x
• Hedrick PW, García-Dorado A (2016) Understanding inbreeding depression, purging, and genetic rescue. Trends Ecol Evol 31(12):940-952. doi:10.1016/j.tree.2016.09.005
• Bertorelle G, Raffini F, Bosse M, Bortoluzzi C, Iannucci A, Trucchi E, Morales HE, van Oosterhout C (2022) Genetic load. Nat Rev Genet 23(8):492-503. doi:10.1038/s41576-022-00448-x
• Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring joint demographic history with dadi. PLoS Genet 5(10):e1000695. doi:10.1371/journal.pgen.1000695
• Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M (2013) Robust demographic inference (fastsimcoal2). PLoS Genet 9(10):e1003905. doi:10.1371/journal.pgen.1003905
• Jouganous J, Long W, Ragsdale AP, Gravel S (2017) Inferring the joint demographic history of multiple populations: beyond the diffusion approximation (moments). Genetics 206(3):1549-1567. doi:10.1534/genetics.117.200493
• Kamm J, Terhorst J, Durbin R, Song YS (2020) Efficiently inferring the demographic history of many populations with allele count data (momi2). J Am Stat Assoc 115(531):1472-1487. doi:10.1080/01621459.2019.1635482
• Kelleher J, Etheridge AM, McVean G (2016) Efficient coalescent simulation (msprime). PLoS Comput Biol 12(5):e1004842. doi:10.1371/journal.pcbi.1004842
• Haller BC, Messer PW (2019) SLiM 3: forward genetic simulation beyond Wright-Fisher. Mol Biol Evol 36(3):632-637. doi:10.1093/molbev/msy228
• Haller BC, Galloway J, Kelleher J, Messer PW, Ralph PL (2019) Tree-sequence recording in SLiM. Mol Ecol Resour 19(2):552-566. doi:10.1111/1755-0998.12968
• Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016) Harnessing RADseq for population genomics. 17(2):81-92. doi:10.1038/nrg.2015.28

Related Skills

• ecological-genomics/landscape-genomics - Adaptive variation and genotype-environment associations
• ecological-genomics/species-delimitation - Taxonomic unit definition (cite Sukumaran-Knowles caveat for ESU/MU vs species)
• population-genetics/population-structure - Population stratification and STRUCTURE/ADMIXTURE
• population-genetics/selection-statistics - Genome-wide selection signatures
• variant-calling/vcf-basics - VCF preparation from RAD-seq or WGS