This repository contains code used for data analysis and figures in the following paper.
Inbreeding depression explains killer whale population dynamics
Marty Kardos1*, Yaolei Zhang2,4*, Kim M. Parsons1*, Yunga A2*, Hui Kang3, Xun Xu4, Xin Liu4, Craig O. Matkin5, Peijun Zhang3, Eric J. Ward1, M. Bradley Hanson1, Candice Emmons1, Michael J. Ford1†, Guangyi Fan2,4,6†, Songhai Li3, 7†
1 Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration; Seattle, WA, USA
2BGI-Qingdao, BGI-Shenzhen; Qingdao, 266555, China.
3Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences; Sanya, 572000, China.
4BGI-Shenzhen; Shenzhen 518083, China.
5North Gulf Oceanic Society; Homer, AK, USA.
6State Key Laboratory of Agricultural Genomics, BGI-Shenzhen; Shenzhen 518083, China.
7Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
*These authors contributed equally and are identified as joint first authors.
†Corresponding authors: Songhai Li (lish@idsse.ac.cn), Michael Ford (mike.ford@noaa.gov) and Guangyi Fan (fanguangyi@genomics.cn)
There are several folders that contain code for different analyses:
VariantEffectPredictor: variant effect prediction for analysis of genetic loads
RXY: Analysis of relative genetic loads
ROH: Runs of homozygosity
recombinationRate: Using the R package FastEPRR to estimate recombination rate across the killer whale genome
populationProjections: Individidual-based simulations of futureu population dynamics
SRKWIsolationTime: estimating expected isolation time for the Southern Resident Killer Whale population
Admixture: Analysis of admixture across North Pacific killer whale populations
Genome_assembly_and_annotation: Assembly and annotation of the killer whale genome
NJtree: Neighbor-joining treee for 147 killer whale genomes
PCA: Principle component analysis of 147 killer whale genomes
SNP_calling: variant calling in killer whale genomes
NeEstimator: linkage disequilibrium based analysis of contemporary effective population size
GONE: linkage disequilibrium based analysis of recent (back to 150 generations ago) changes effective population size
archiveFigCode: Code used to make figures
quantPop_0.3.9.tar.gz is an R package used in several analyses
demog_models_code contains the code used in the models of fitness components (survival/fecundity) as a function of inbreeding, sex, age, and year