Ct_pop_gen_project

This repository contains scripts and files used to perform the analyses and make the figures and tables associated with the Caenorhabditis tropicalis population genetics manuscript

The "data" folder contains the raw datasets from public database (e.g. CaeNDR)
The "plots" folder contains all the figures generated by the scripts
The "processed_data" folder contains all the intermediate results files generated during the analysis
The "scripts" folder contains all the codes used for generating figures and tables
The "tables" folder contains all the tables generated by the scripts

How to use the scripts in this repository to plot figures and generate tables in the manuscript

This section shows the names and order of the scripts used to plot figures and generate tables.
Notes: The "→" reprensents the order of scripts. The “+” means you should use them both/all in that step.

Main Figures & Tables

Figure 1. Global distribution of 518 C. tropicalis isotype reference strains

Figure 1 a-f: Plot_isotype_tropicalis_global_map.R
Figure 1 g-i: Plot_PCA_vcf.R

Figure 2. The ML tree of 518 C. tropicalis isotype reference strains generated from variants pruned with LD r² values less than or equal to 0.9

Figure 2: Calculate_C_tro_vcf_to_pyh.sh + vcf2phylip.py →
Calculate_C_tro_LD_pruned_0.9_pyh_to_tree.sh →
Plot_tree_in_lat_with_label.R
Notes: The vcf2phylip.py can be found in https://github.com/edgardomortiz/vcf2phylip

Figure 3. Diversity statistic calculated across global C. tropicalis isotypes

Figure 3: Plot_tro_pi_theta_d.R

Figure 4. LD decay for all C. tropicalis isotype reference strains across all autosomes

Figure 4: Calculate_LD_per_Mb_all.sh + Calculate_LD_per_Mb_geo.sh →
Plot_LD_geo_all.R

Figure 5. Hyper-variable regions (HVRs) in C. tropicalis

Figure 5 b, c: Calculate_HVRs_TajimasD_bed_file.R →
Calculate_vcf_to_zarr_HVRs.sh →
Calculate_zarr_to_pi_theta_d_HVRs.sh →
Plot_HVRs_TajimasD.R

Figure 6. Relatedness and frequency of 518 C. tropicalis isotype reference strains at the Medea regions

Figure 6: Calculate_C_tro_Medea_vcf.sh →
Plot_Medea_vcf2tree.R

Figure 7. Human Impact Index of nematode sampling sites

Figure 7: Calculate_download_and_unzip_tif_files.sh →
Calculate_human_footprint_index.R →
Plot_human_footprint_index.R

Table 1. Effective population size (N_e) for Caenorhabditis spp. samples from different studies

Table 1:
C. tropicalis: Calculate_vcf_to_zarr_geo.sh →
Calculate_zarr_to_pi_theta_d_geo.sh
C. elegans: Calculate_Ce_vcf_to_zarr.sh →
Calculate_Ce_zarr_to_pi_theta_d.sh
C. briggsae: trim-fq-nf workflow: https://github.com/andersenlab/trim-fq-nf →
alignment-nf workflow: https://github.com/andersenlab/alignment-nf →
wi-gatk workflow: https://github.com/andersenlab/wi-gatk →
Calculate_Cb_vcf_to_zarr.sh →
Calculate_Cb_zarr_to_pi_theta_d.sh
Then, use all the output above and this R script to generate the table: Table_isotypes_Ne_Outcrossing rate.R

Table 2. Outcrossing rate of isotype reference strains from different sampling sites

Table 2:
C. tropicalis: Calculate_vcf_to_zarr_geo.sh →
Calculate_zarr_to_pi_theta_d_geo.sh + Calculate_LD_per_Mb_all.sh + Calculate_LD_per_Mb_geo.sh
C. elegans: Calculate_Ce_vcf_to_zarr.sh →
Calculate_Ce_zarr_to_pi_theta_d.sh + Calculate_Ce_LD_per_Mb.sh
C. briggsae: trim-fq-nf workflow: https://github.com/andersenlab/trim-fq-nf →
alignment-nf workflow: https://github.com/andersenlab/alignment-nf →
wi-gatk workflow: https://github.com/andersenlab/wi-gatk →
Calculate_Cb_vcf_to_zarr.sh →
Calculate_Cb_zarr_to_pi_theta_d.sh + Calculate_Cb_LD_per_Mb.sh
Then, use all the output above and this R script to generate the table: Table_isotypes_Ne_Outcrossing rate.R

Supplemental Figures & Tables

Figure S1. Global distribution of 690 C. tropicalis strains

Figure S1: Plot_strains_tropicalis_global_map.R

Figure S2. Geographical distance between strains within an isotype

Figure S2 a: Plot_Vincenty_geo_Ce.R
Figure S2 b: Plot_Vincenty_geo_Ct.R

Figure S3-S5. The ML trees of 518 C. tropicalis isotype reference strains generated from LD-pruned variants with r² values less than or equal to 0.7-0.9

Figure S3-S5: Calculate_C_tro_vcf_to_pyh.sh + vcf2phylip.py →
Calculate_C_tro_LD_pruned_0.6_pyh_to_tree.sh + Calculate_C_tro_LD_pruned_0.7_pyh_to_tree.sh + Calculate_C_tro_LD_pruned_0.8_pyh_to_tree.sh →
Plot_tree_in_lat_with_label.R
Notes: The vcf2phylip.py can be found in https://github.com/edgardomortiz/vcf2phylip

Figure S6. Unrooted maximum likelihood trees of 518 C. tropicalis isotype reference strains generated from LD-pruned variants

Figure S6: Plot_equal angle_unrooted_tree.R

Figure S7. Scatter plot shows significant positive correlation between geographic distance and phylogenetic distance

Figure S7: Plot_phy_geo.R

Figure S8. Genetic distance (D_xy) correlation with geographic distance and regional variation

Figure S8: Calculate_C_tro_dxy_10kb_geo.sh →
Plot_dxy_geo_change_in_dxy_per_km.R

Figure S9. Pairwise fixation index (F_st) among C. tropicalis from different geographic regions

Figure S9: Calculate_C_tro_fst_geo.sh →
Plot_fst_geo.R

Figure S10. LD decay for all autosomes

Figure S10: Calculate_LD_per_Mb_all.sh + Calculate_LD_per_Mb_geo.sh →
Plot_LD_geo_all_chromosome.R

Figure S11. Species wide (D_xy) of C. tropicalis

Figure S11: Calculate_C_tro_dxy_10kb_chunk_I_to_X.sh + Calculate_C_tro_dxy_10kb_chunk_V_1.sh + Calculate_C_tro_dxy_10kb_chunk_V_2.sh →
Calculate_C_tro_dxy_10kb_stat.sh →
Plot_dxy_species_wide.R

Figure S12-S16. Relatedness of 518 C. tropicalis isotype reference strains at five different maternal effect regions

Figure S12-S16: Plot_TAs_vcf2tree.R

Table S4. Diversity statistic (π, θ, Tajima's D) for all isotype reference strains and for each geographic region

Table S4: Calculate_vcf_to_zarr_geo.sh →
Calculate_zarr_to_pi_theta_d_geo.sh →
Table_geo_p_theta.R

Table S5. Effective population size (N_e) for all isotype reference strains and for each geographic region except for the two under-sampled regions, Africa and Australia.

Table S5: Calculate_vcf_to_zarr_geo.sh →
Calculate_zarr_to_pi_theta_d_geo.sh + Calculate_LD_per_Mb_all.sh + Calculate_LD_per_Mb_geo.sh →
Table_isotypes_Ne_Outcrossing rate.R

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README.md

README.md

Ct_pop_gen_project

How to use the scripts in this repository to plot figures and generate tables in the manuscript

Main Figures & Tables

Figure 1. Global distribution of 518 C. tropicalis isotype reference strains

Figure 2. The ML tree of 518 C. tropicalis isotype reference strains generated from variants pruned with LD r² values less than or equal to 0.9

Figure 3. Diversity statistic calculated across global C. tropicalis isotypes

Figure 4. LD decay for all C. tropicalis isotype reference strains across all autosomes

Figure 5. Hyper-variable regions (HVRs) in C. tropicalis

Figure 6. Relatedness and frequency of 518 C. tropicalis isotype reference strains at the Medea regions

Figure 7. Human Impact Index of nematode sampling sites

Table 1. Effective population size (N_e) for Caenorhabditis spp. samples from different studies

Table 2. Outcrossing rate of isotype reference strains from different sampling sites

Supplemental Figures & Tables

Figure S1. Global distribution of 690 C. tropicalis strains

Figure S2. Geographical distance between strains within an isotype

Figure S3-S5. The ML trees of 518 C. tropicalis isotype reference strains generated from LD-pruned variants with r² values less than or equal to 0.7-0.9

Figure S6. Unrooted maximum likelihood trees of 518 C. tropicalis isotype reference strains generated from LD-pruned variants

Figure S7. Scatter plot shows significant positive correlation between geographic distance and phylogenetic distance

Figure S8. Genetic distance (D_xy) correlation with geographic distance and regional variation

Figure S9. Pairwise fixation index (F_st) among C. tropicalis from different geographic regions

Figure S10. LD decay for all autosomes

Figure S11. Species wide (D_xy) of C. tropicalis

Figure S12-S16. Relatedness of 518 C. tropicalis isotype reference strains at five different maternal effect regions

Table S4. Diversity statistic (π, θ, Tajima's D) for all isotype reference strains and for each geographic region

Table S5. Effective population size (N_e) for all isotype reference strains and for each geographic region except for the two under-sampled regions, Africa and Australia.

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README.md

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Ct_pop_gen_project

How to use the scripts in this repository to plot figures and generate tables in the manuscript

Main Figures & Tables

Figure 1. Global distribution of 518 C. tropicalis isotype reference strains

Figure 2. The ML tree of 518 C. tropicalis isotype reference strains generated from variants pruned with LD r2 values less than or equal to 0.9

Figure 3. Diversity statistic calculated across global C. tropicalis isotypes

Figure 4. LD decay for all C. tropicalis isotype reference strains across all autosomes

Figure 5. Hyper-variable regions (HVRs) in C. tropicalis

Figure 6. Relatedness and frequency of 518 C. tropicalis isotype reference strains at the Medea regions

Figure 7. Human Impact Index of nematode sampling sites

Table 1. Effective population size (Ne) for Caenorhabditis spp. samples from different studies

Table 2. Outcrossing rate of isotype reference strains from different sampling sites

Supplemental Figures & Tables

Figure S1. Global distribution of 690 C. tropicalis strains

Figure S2. Geographical distance between strains within an isotype

Figure S3-S5. The ML trees of 518 C. tropicalis isotype reference strains generated from LD-pruned variants with r2 values less than or equal to 0.7-0.9

Figure S6. Unrooted maximum likelihood trees of 518 C. tropicalis isotype reference strains generated from LD-pruned variants

Figure S7. Scatter plot shows significant positive correlation between geographic distance and phylogenetic distance

Figure S8. Genetic distance (Dxy) correlation with geographic distance and regional variation

Figure S9. Pairwise fixation index (Fst) among C. tropicalis from different geographic regions

Figure S10. LD decay for all autosomes

Figure S11. Species wide (Dxy) of C. tropicalis

Figure S12-S16. Relatedness of 518 C. tropicalis isotype reference strains at five different maternal effect regions

Table S4. Diversity statistic (π, θ, Tajima's D) for all isotype reference strains and for each geographic region

Table S5. Effective population size (Ne) for all isotype reference strains and for each geographic region except for the two under-sampled regions, Africa and Australia.

Figure 2. The ML tree of 518 C. tropicalis isotype reference strains generated from variants pruned with LD r² values less than or equal to 0.9

Table 1. Effective population size (N_e) for Caenorhabditis spp. samples from different studies

Figure S3-S5. The ML trees of 518 C. tropicalis isotype reference strains generated from LD-pruned variants with r² values less than or equal to 0.7-0.9

Figure S8. Genetic distance (D_xy) correlation with geographic distance and regional variation

Figure S9. Pairwise fixation index (F_st) among C. tropicalis from different geographic regions

Figure S11. Species wide (D_xy) of C. tropicalis

Table S5. Effective population size (N_e) for all isotype reference strains and for each geographic region except for the two under-sampled regions, Africa and Australia.