DOI: 10.5281/zenodo.14765277
title: Melting memories: Decoupled effects of ice and climate shaped genetic diversity in Andean Lady's Slippers during the Quaternary

description: Melting memories: Decoupled effects of ice and climate shaped genetic diversity in Andean Lady's Slippers during the Quaternary

Overview  This datataset contains the data, procedures, and code required to replicate analyses in "Melting memories: Decoupled effects of ice and climate shaped genetic diversity in Andean Lady's Slippers during the Quaternary"

Data Spatial Scope Andean Patagonian forests from Argentina and Chile.

Funding This work was supported by the National Ministry of Science and Technology  FONCYT-PICT-2018-0890, to A.N.S, and PICT‐2019‐1609, to M.C.B)  and by the National Council of Science and Technology (CONICET-PIBAA-28720210100101CO, to M.C.B.).

Sharing/AccessThis work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.

Data Sources

Genetic Data- Chloroplast DNA per species (intergenic spacers sequenced PsbA-trnH2, trnS-trnG, and trnL-trnF) for 75 sites and 230 individuals. See details of the amplificaction, sequencing and editing in the main text. + C. crenatiflora DNA matrix + C. filicaulis DNA matrix + C. tenella DNA matrix Occurrence data- Occurrence data: + own data obtained during the 2020-2023 field trips + GBIF (www.gbif.org) + iNaturalist (www.inaturalist.org/). 

Paleo-distribution models - Climate data + Current bioclimatic variables (~1979–2013): http://www.paleoclim.org/ + Last Glacial Maximum bioclimatic variables (21000 years ago): PaleoClim http://www.paleoclim.org/ + Bølling-Allerød period (14700–12000 years ago): PaleoClim http://www.paleoclim.org/ + Early Holocene (11 700–8 326 years): http://www.paleoclim.org/

Ice extension shapes + Last Glacial Maximum (~21 ka): https://www.antarcticglaciers.org/glacial-geology/patagonian-ice-sheet/patice/ + Bølling-Allerød (14700–12000 years ago):https://www.antarcticglaciers.org/glacial-geology/patagonian-ice-sheet/patice/ + Early-Holocene(11 700–8 326 years): https://www.antarcticglaciers.org/glacial-geology/patagonian-ice-sheet/patice/

Data sintesis- Haplotype and nucleotide diversity indices per sample sites- Distance to climatic favourabylity and ice mass

Description of the data and file structure. 

Occurrence datathree files corresponding to curated ocurrence data  for Calceolaria crenatiflora, Calceolaria filicaulis, and Calceolaria tenella (Occurrence data.xlsx)

Genetic Datathree .fasta files with the combined chloropalstidial DNA arrays for Calceolaria crenatiflora (01. Calceolaria crenatiflora.fas), Calceolaria filicaulis (01. Calceolaria filicaulis.fas), and  Calceolaria tenella (01. Calceolaria tenella.fas)After processing the matrices using Arlequin v3.5 (https://cmpg.unibe.ch/software/arlequin3/) and DnaSP v5.1 (https://www.ub.edu/dnasp/), we obtained the haplotype and nucleotide diversity values for each sampled site (Appendix 1).These values were then used for statistical analysis (see script 04_Relationship among genetic diversity, ice mass, and climate factors.R).

Bioclimatic variables .rar files corresponding  bioclimatic variables for Calceolaria crenatiflora (01.crenatiflora_current_tif, 02.crenatiflora_Holocene_tif, 03.crenatiflora_Bolling_Allenrod_tif,  04.crenatiflora_LGM_tif), Calceolaria filicaulis (01.filicaulis_current_tif, 02.filicaulis_Holocene_tif, 03.filicaulis_Bolling_Allenrod_tif,  04.filicaulis_LGM_tif), and  Calceolaria tenella (01.tenella_current_tif, 02.tenella_Holocene_tif, 03.tenella_Bolling_Allenrod_tif,  04.tenella_LGM_tif). These data frames are used for variable selection, and model calibracion and evaluation (see script 01_Paleo-distribution models-crenatiflora.R, 02_Paleo-distribution models-filicaulis.R, and 03_Paleo-distribution models-tenella.R)      Variables are the same in the all   Bioclimatic variables iles:   - Longitude- Latitude- BIO1. Annual Mean Temperature- BIO2. Mean Diurnal Range (Mean of monthly (max temp - min temp))- BIO3. Isothermality (BIO2/BIO7) (×100)- BIO4. Temperature Seasonality (standard deviation ×100)- BIO5. Max Temperature of Warmest Month- BIO6. Min Temperature of Coldest Month- BIO7. Temperature Annual Range (BIO5-BIO6)- BIO8. Mean Temperature of Wettest Quarter- BIO9. Mean Temperature of Driest Quarter- BIO10. Mean Temperature of Warmest Quarter- BIO11. Mean Temperature of Coldest Quarter- BIO12. Annual Precipitation- BIO13. Precipitation of Wettest Month- BIO14. Precipitation of Driest Month- BIO15. Precipitation Seasonality (Coefficient of Variation)- BIO16. Precipitation of Wettest Quarter- BIO17. Precipitation of Driest Quarter- BIO18. Precipitation of Warmest Quarter- BIO19. Precipitation of Coldest Quarter

Ice extension shapesone .rar file with three shapefiles with the ice mass limits during the three milestones analysed.

Data sintesis two .txt files that combine genetic information (Appendix 1) with data from paleodistribution models and the distances to ice masses at the sampled sites calculated in Qgis (https://qgis.org/; Appendix 5) for the 74 sites analyzed. These files are analyzed in the section Relationship between genetic diversity and climate and ice factors (see script 04_Relationship among genetic diversity, ice mass, and climate factors.R).

- Variables included are: + species  Categorical variable with three levels, corresponding to each of the analyzed species. + sitios Code representing each sampled site. + longitude Longitude of the sampled site. + latitude Latitude of the sampled site. + h Haplotype diversity calculated per site. + Pi Nucleotide diversity calculated per site. + refugio  Binary variable indicating whether the site was classified as a historical refugium (1) or not (0). + clima_21k_05  Distance to the climatically favorable area 21 000 years ago for each sampled site. + hielo_21k  Distance to the ice mass 21 000 years ago for each sampled site. + clima_15k_05  Distance to the climatically favorable area 15 000 years ago for each sampled site. + hielo_15k Distance to the ice mass 15 000 years ago for each sampled site. + clima_10k_05  Distance to the climatically favorable area 10 000 years ago for each sampled site. + hielo_10k Distance to the ice mass 10 000 years ago for each sampled site. + promedio_hielo Average distance to the ice mass during the last glacial cycle for each sampled site. + promedio_clima05 Average distance to the climatically favorable area during the last glacial cycle for each sampled site. Scripts - 01_Paleo-distribution models-crenatiflora.R  This script generates the M areas (historically accessible areas) for C.crenatiflora, selects bioclimatic variables, calibrates and evaluates the models, and projects them onto the three considered climatic milestones.- 02_Paleo-distribution models-filicaulis.R  This script generates the M areas (historically accessible areas) for C. filicaulis, selects bioclimatic variables, calibrates and evaluates the models, and projects them onto the three considered climatic milestones.- 03_Paleo-distribution models-tenella.R  This script generates the M areas (historically accessible areas) for C. tenella, selects bioclimatic variables, calibrates and evaluates the models, and projects them onto the three considered climatic milestones.- 04_Relationship among genetic diversity, ice mass, and climate factors.R  This script perform independent-effects analyses and generalized additive mixed models.