MQU_PopGenomics

Montezuma Quail Population Genomics

This repository contains scripts for the publication:

Samarth Mathur, J. Andrew DeWoody. Genetic load has potential in large populations but is realized in small inbred populations. Evolutionary Applications. (in press) https://doi.org/10.1111/eva.13216

Folders

This repository contains the following scripts within each folder

Map_ReadProcess

Scripts for aligning MQU reads to a reference genome and processing reads according to GATK Best Practices

• alignment.sh

  • Aligning reads to a reference assembly, sorting, marking dupicates, realinging around indels, and base quality score recalibration

• genic_alignment.sh

  • Extracting genic reads and mapping it to MQU genic regions (as annotated in Mathur et al. 2019)

Mitogenome

Scripts for assembling individual mitogenomes and getting phylogenetic trees

• Mitogenome_alignment.sh

  • Identify NUMTs, remove NUMT reads, and map mitogenome reads to reference mitochondrial genome

• Mito_haplotypes.sh

  • Identify SNPs, filter SNPs, and create concensus mitogenome haplotypes for each individual

• mtDNA_tree.sh

  • Create mulitple sequence alignment and phylogenetic trees using clustalW

Pop_Gen

Scripts for population genomic metric estimations using ANGSD

• genotype_likelihoods.sh

  • Estimate genotype likelihoods from populations

• relatedness.sh

  • Estimating relatedness between a pair of individuals

• inbreeding_pca.sh

  • Estimating per-site inbreeding coefficients (F) and performing PCA on all individuals

• admxiture.sh

  • To estimate admixture proportions for different number of ancestral populations (K)

• SFS.sh

  • Estimate the site frequency spectrum (sfs) and bootstrap it

• theta.sh

  • Estimate nucleotide diversity (theta) and calculate Tajima's D and various other neutrality test statistics for whole genome

• fst.sh

  • Estimate global and sliding-window Fst between populations from SFS

• genic_theta.sh

  • Estimate nucleotide diversity (theta) and calculate Tajima's D and various other neutrality test statistics for genic regions

• genic_fst.sh

  • Estimate global and sliding-window Fst between populations from SFS for genic regions

• heterozygosity.sh

  • Estimate observed heterozygosity for each individual from SFS

Denomgraphy

Scripts for demographic history analyses

• mu_rate.sh

  • Estimate the whole-genomic mutation rate (μ) for effective population size (Ne) and for demographic reconstruction

• smc.sh

  • Reconstructing historic population demography by running sequential Markov coalescent simulations (SMCs) in SMC++.

Genetic Load

Scripts for calling genotypes, functionally annotating genic SNPs, and calculating their population frequencies

• genotype_calling.sh

  • To call SNP genotypes from whole genome data

• SNPeff.sh

  • To functionally annotate SNPs as high, moderate, low, and no-impact variants

• genetic_load.sh

  • Filter annotated SNPs and estimate minor allele frequency (MAF) for all impact class variants