DOI: 10.5281/zenodo.17932004
title: Supplementary Data: Evolutionary rates provide genomic insights into convergent and lineage-specific evolution in carnivorous plants

description: # Supplementary Data for cp-erc-analysis

This Zenodo record contains processed data and summary outputs used in theevolutionary rate and evolutionary rate covariation (ERC) analyses, networkanalyses, gene ontology enrichment, and HyPhy-based selection tests (aBSREL andRELAX) for carnivorous and non-carnivorous angiosperms.

All tabular files are tab-delimited text (`*.tsv`) unless otherwise noted.

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## Directory Overview

- `ERC_Network_Assortativity/`- `ERC_Network_Outputs_and_Comparison/`- `GO_Enrichment_Results_By_Species_Rate_Category/`- `GO_Enrichment_Results_By_Species_SubCellular_Localization/`- `GO_Term_Freqeuncy_Heat_Maps_by_Species/`- `HOG_Annotation_Tables/`- `HOG_BL_and_Zscore_Matrices/`- `HYPHY_aBSREL_Omega_CompareRateCategories/`- `HYPHY_aBSREL_Omega_CompareSubCell/`- `HYPHY_RELAX/`- `InferredERCNetwork/`

Below, each directory is described in more detail.

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## 1. ERC_Network_Assortativity

Outputs related to assortativity and permutation tests on ERC-derived networks.

- `calculate_assortativity.py`    Script used to calculate network assortativity statistics.

- `AssortRef.tsv`    Reference table summarizing assortativity coefficients for focal node/edge  categories (e.g. rate categories, subcellular localization).

- `HOG_GO_Table.tsv`    Mapping of HOGs to GO terms used to annotate nodes in the ERC networks and  to link network structure with functional categories.

- `overlapping_interactions.tsv`    List of edges shared across networks or conditions (e.g. overlapping ERC  interactions between different datasets).

- `Permutation_3Categories/`    Results of permutation tests for networks with three node categories (e.g.  rate-defined groups). Contains permuted assortativity values and summary  statistics.

- `Permutation_4Categories/`    As above, but for networks with four node categories.

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## 2. ERC_Network_Outputs_and_Comparison

Filtered ERC networks and comparisons between networks built from differentbranch-length transformations.

- `01_Notes.txt`    Short description of how these network files were generated and compared.

- `ERC_Edges_Norm_filtered.tsv`    Filtered ERC edge list derived from normalized branch-length data.

- `ERC_Edges_LogNorm_filtered.tsv`    Filtered ERC edge list derived from log-normalized branch-length data.

- `unique_to_ERC_Edges_Norm_filtered.tsv`    Edges present only in the normalized-branch ERC network.

- `unique_to_ERC_Edges_LogNorm_filtered.tsv`    Edges present only in the log-normalized ERC network.

- `overlapping_interactions.tsv`    ERC edges shared between the normalized and log-normalized networks.

- `shared_nodes.tsv`    List of nodes (genes/HOGs) common to networks being compared.

- `venn_diagram_interactions.png`    Venn diagram summarizing overlap of ERC edges between networks.

- `venn_diagram_nodes.png`    Venn diagram summarizing overlap of nodes between networks.

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## 3. GO_Enrichment_Results_By_Species_Rate_Category

GO enrichment analyses for gene sets stratified by **rate category** (e.g.accelerated vs conserved) for each carnivorous plant lineage.

Files follow the pattern:

- `<Species>_ACC_INTERSECT_GO_Full_table.tsv`- `<Species>_ACC_INTERSECT_GO_Filtered_table.tsv`- `<Species>_ACC_INTERSECT_go_enrichment_log.txt`- `<Species>_CON_INTERSECT_GO_Full_table.tsv`- `<Species>_CON_INTERSECT_GO_Filtered_table.tsv`- `<Species>_CON_INTERSECT_go_enrichment_log.txt`

where:

- `ACC_INTERSECT` = gene set(s) intersecting accelerated categories  - `CON_INTERSECT` = gene set(s) intersecting conserved categories  - `GO_Full_table.tsv` = complete enrichment output from the GO tool  - `GO_Filtered_table.tsv` = subset of enriched GO terms after applying  filtering (e.g. FDR threshold, minimum term size)  - `go_enrichment_log.txt` = log of the enrichment run (parameters, counts)

Species include (as subfile prefixes): `Aldrovanda`, `Byblis`, `Cephalotus`,`Dionaea`, `Drosera`, `Genlisea`, `Heliamphora`, `Nepenthes`, `Pinguicula`,`Sarracenia`, `Utricularia`.

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## 4. GO_Enrichment_Results_By_Species_SubCellular_Localization

GO enrichment analyses for gene sets stratified by **subcellular localization**(e.g. plastid-targeted vs non-plastid) within species.

Files are numbered (e.g. `1_`, `2_`, …, `47_`) to represent distinctspecies/localization combinations. For each number `N`:

- `N_GO_Full_table.tsv`  - `N_GO_Filtered_table.tsv`  - `N_go_enrichment_log.txt`

with the same meanings as above (full vs filtered GO tables, plus run log).The mapping from index numbers to species/localization categories is describedin the associated Methods / supplementary documentation.

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## 5. GO_Term_Freqeuncy_Heat_Maps_by_Species

PNG heatmaps summarizing frequencies or significance patterns of enriched GOterms across lineages and categories.

- `BP_GO_Comparisons_Heatmap_TopTerms_p1.png` … `BP_GO_Comparisons_Heatmap_TopTerms_p8.png`    Heatmaps for **Biological Process (BP)** GO terms.

- `CC_GO_Comparisons_Heatmap_TopTerms_p1.png` … `CC_GO_Comparisons_Heatmap_TopTerms_p2.png`    Heatmaps for **Cellular Component (CC)** GO terms.

- `MF_GO_Comparisons_Heatmap_TopTerms_p1.png` … `MF_GO_Comparisons_Heatmap_TopTerms_p3.png`    Heatmaps for **Molecular Function (MF)** GO terms.

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## 6. HOG_Annotation_Tables

Annotation tables linking hierarchical orthogroups (HOGs) to functional andsequence metadata.

- `HOG_Arabidopsis _GO_Annotation_Table.tsv`    Mapping between HOG IDs and Arabidopsis gene IDs/GO annotations used to  transfer functional information to orthogroups.

- `HOG_with_Corresponding_Sequence_Name.tsv`    Table linking HOG IDs to species-specific sequence names (gene IDs) used in  the phylogenomic and ERC analyses.

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## 7. HOG_BL_and_Zscore_Matrices

Branch-length estimates and transformed matrices used as input for ERC andnetwork analyses.

Subdirectories:

- `Raw_BL_Estimates_5_ERCnet_Replicates/`    Raw branch-length estimates from ERCnet across five ERCnet replicates.

- `BL_Consensus_and_Summaries/`    Consensus branch-length matrices and summary statistics aggregated across  replicates for each HOG/branch.

- `BL_Transformation_and_Normalization/`    Normalized and log-transformed branch-length matrices used to control for  lineage-specific rate variation and heteroskedasticity.

- `Z_Scores/`    Z-score matrices derived from normalized/log-transformed branch lengths,  used as input for ERC calculations and network/community analyses.

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## 8. HYPHY_aBSREL_Omega_CompareRateCategories

HyPhy aBSREL-based summaries and plots of selection (ω) across rate-definedgene categories and species.

- `aBSREL_Master_Summary.tsv`    Master summary table combining aBSREL results across genes and branches,  with annotations for rate categories.

- `Overall_By_Rate_Categories/`    Aggregated results and summary statistics for ω distributions across rate  categories pooled across species.

- `<Species>/` (e.g. `Aldrovanda`, `Byblis`, `Cephalotus`, `Dionaea`,  `Drosera`, `Genlisea`, `Heliamphora`, `Nepenthes`, `Sarracenia`,  `Utricularia`)    Species-specific summaries and plots of ω by rate category.

- `plot_all_species.py`    Script to generate multi-species ω comparison plots.

- `plot_and_test_omega_violin.py`    Script to generate violin plots and perform statistical tests on ω across  rate categories.

- `plot_and_test_omega_scatter.py`    Script to generate scatter plots and related tests for ω vs rate metrics.

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## 9. HYPHY_aBSREL_Omega_CompareSubCell

HyPhy aBSREL-based summaries and tests contrasting ω across subcellularlocalization categories.

- `aBSREL_Master_Summary.tsv`    Master summary table for aBSREL ω estimates annotated by subcellular  localization.

- `AssortRef.tsv`    Reference table linking localization categories to network/assortativity  analyses (if applicable).

- `SubCel_Test_Res/`    Results of statistical tests comparing ω across localization categories.

- `SubCel_Summary.numbers`    Summary table saved in Apple Numbers format (macOS spreadsheet).

- `Test_SubCell_Omega.py`    Script used to perform tests and summarise subcellular ω comparisons.

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## 10. HYPHY_RELAX

RELAX output summaries and intermediate files for tests of selectionintensity (K) across focal lineages/groups.

Subdirectories correspond to different lineage contrasts:

- `AurUtr_ACCCON/`  - `DioAld_RELAX_ACCCON/`  - `Sarraceniaceae_RELAX_ACCCON/`  

Each folder contains RELAX result files and summaries for accelerated vsconserved (ACCCON) gene sets within the indicated clades/lineages. See themain Methods for detailed definitions of these comparisons.

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## 11. InferredERCNetwork

Inferred ERC network in Cytoscape format.

- `NetworkAUG25.cys`    Cytoscape session file containing the ERC network (nodes, edges, and  associated attributes such as rate category, localization, and GO  annotations). This file can be opened directly in Cytoscape to reproduce  network visualizations and to explore node/edge attributes used in the  manuscript.

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## 12. ERC_Network_Community_Normalized_BLs

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## 13. ERC_Network_Community_Plot_Z_Scores

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## File Formats and Conventions

- **TSV (`*.tsv`)** – tab-delimited text; can be opened in R, Python, or  spreadsheet software (Excel, LibreOffice, etc.).- **TXT (`*.txt`)** – plain-text logs describing parameters, run metadata,  or notes.- **PNG (`*.png`)** – raster images used in figures or exploratory plots.- **CYS (`*.cys`)** – Cytoscape session file.- **NUMBERS (`*.numbers`)** – Apple Numbers spreadsheet (macOS).

For detailed descriptions of how these files were generated and used, pleaserefer to the Methods section and figure legends of the associated manuscript.