Data and computer code used in the research paper "Female lineages and changing kinship patterns in Neolithic Çatalhöyük"

This repo contains custom code and tables Z1-24 of the paper "Female lineages and changing kinship patterns in Neolithic Çatalhöyük" Also see doi:10.5281/zenodo.6373390

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Molecular Sex Assignement

Code described in Supplementary Materials and Methods section 5 'Molecular sex assignment' are available in https://github.com/mskilic/SexDetermineR

Haplotype diversity

Code described in Supplementary Materials and Methods section 8.7 'Testing change in pairwise haplotype diversity over time' are available in "haplotype diversity", by Gözde Atağ

Downsampling experiments to test the effect of imputation

Code described in Supplementary Materials and Methods section 11.2.2 'Downsampling experiments to test the effect of imputation on kinship estimates' in https://github.com/MerveNurGuler/Haploidize-VCF

Evaluating variation in kinship estimates

Code described in 11.4 'Evaluating variation in kinship estimates'are available in "estimating_variation.zip", by Merve Nur Güler

Pedigree reconstruction

Code described in Supplementary Materials and Methods section 12 'Pedigree reconstruction' are available in "pedigree_visualizations", by Ekin Sağlıcan

ROH analyses

Code described in Supplementary Materials and Methods section 13 'Runs of Homozygosity (ROH)' are available in "roh_analyses", by Elifnaz Eker

Genealogy simulations for measuring inbreeding

Code described in Supplementary Materials and Methods section 14 'Genealogy simulations for measuring inbreeding under random mating' are available in https://github.com/BusraKatircioglu/inbreedingSimulation

Residence simulations

Code described in Supplementary Materials and Methods section 16 'Calculating the matrilocality rate posterior probability' are available in "residence_simulations", by Muhammed Sıddık Kılıç

Simulations of house co-burial relatedness

Code described in Supplementary Materials and Methods section 18 'Simulations of house co-burial relatedness' are available in "relatedness_simulations", by Eren Yüncü

Metagenomic analyses

Code described in Supplementary Materials and Methods section 19 'Metagenomic analysis' are available in "metagenomic_analyses", by Arda Sevkar

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