DOI: 10.5061/dryad.c2fqz61d9
title: Data from: Fluctuation of ecological niches and geographic range shifts along chile pepper's domestication gradient

description: Domestication is an ongoing well-described process. However, while many
 have stud- ied the changes domestication causes in plant genetics, few
 have explored its impact on the portion of the geographic landscape in
 which the plants exist. Therefore, the goal of this study was to
 understand how the process of domestication changed the geographic space
 suitable for chile pepper (Capsicum annuum) in its center of origin
 (domestication). C. annuum is a major crop species globally whose center
 of domes- tication, Mexico, has been well-studied. It provides a unique
 opportunity to explore the degree to which ranges of different
 domestication classes diverged and how these ranges might be altered by
 climate change. To this end, we created ecological niche models for four
 domestication classes (wild, semiwild, landrace, modern cultivar) based on
 present climate and future climate scenarios for 2050, 2070, and 2090.
 Considering present environment, we found substantial overlap in the
 geographic niches of all the domestication classes. Yet, environmental and
 geographic aspects of the current ranges did vary among classes. Wild and
 commercial varieties could grow in desert conditions, while landraces
 could not. With projections into the future, habitat was lost
 asymmetrically, with wild, semiwild, and landraces at greater risk of
 territorial declines than modern cultivars. Further, we identified areas
 where future suitability overlap between landraces and wilds is expected
 to be lost. While range expansion is widely associated with domestication,
 we found little support of a con- stant niche expansion (either in
 environmental or geographical space) throughout the domestication gradient
 in chile peppers in Mexico. Instead, particular domestication transitions
 resulted in loss, followed by capturing or recapturing environmental or
 geographic space. The differences in environmental characterization among
 domes- tication gradient classes and their future potential range shifts
 increase the need for conservation efforts to preserve landraces and
 semiwild genotypes
description: # Data collection # Field trips by team
 members Biblliographic data point occurences
 Publicly available databases # Data processing
 # Principal Components Analyses
 Ecological Niche Modelling in Maxent
 Projection of ENM for future climate change
description: maxent.jar Maximum Entropy
 Modeling of Species Geographic Distributions version
 3.4.0 R version 4.0.2
 (2020-06-22)   Main R packages: 
 "sp" version 1.4-4
 "rgdal" Geospatial Data Abstraction Library version: 1.5-19
 "raster" version 3.4-5 
 "FactoMineR" version 2.3
 "corrplot" version 0.84
 "factoInvestigate" version 1.7
 "spThin" version 0.2.0
 "ENMeval" Automated runs and
 evaluations of ecological niche models version 0.3.1
 "dismo" Species distribution modeling version:
 1.3-3 "ENMTools" version 1.0.5
 "spatstat" version 1.64-1
 "rgeos" version 0.5-5
description: **Input *Capsicum annuum* occurence points in Mexico and scripts used to
 run analyzes in paper** **"Fluctuation of ecological niches and
 geographic range shifts along chile pepper's domestication
 gradient."** --- \#################################################
 **Description of the data and file structure**
 \################################################# These are the input
 files of chile pepper (C. annuum) occurence points. They are run with
 extractPoints.html to get the environmental information associated for all
 domestication categories (wild, semiwild "arvense", landrace,
 commercial) **Complete Chile Collection_Diversity_and_distributions.csv**
 * Coordinates from field trips throughout Mexico (2013-2015 and 2018-2019)
 on behalf of Mercer Lab (Ohio State University - OSU) and Jardón Lab
 (National Autonomous University of Mexico - UNAM). **WILDS**
 **KraftSupp_ThirdPage.csv** * You will need to download the third page of
 the supplementary dataset S3 from: Kraft, K. H., Brown, C. H., Nabhan, G.
 P., Luedeling, E., Luna Ruiz, J. de J., Coppens d’Eeckenbrugge, G.,
 Hijmans, R. J., & Gepts, P. (2014). Multiple lines of evidence for the
 origin of domesticated chili pepper, Capsicum annuum, in Mexico.
 *Proceedings of the National Academy of Sciences*, *111*(17), 6165–6170.
 *
 (These are all Global Biodiversity Information Facility coordinates, save without title row as "KraftSupp_ThirdPage.csv") **Khoury2020_suppFirstPage.csv** * You will need to download the appendix S1: Khoury, C. K., Carver, D., Barchenger, D. W., Barboza, G. E., van Zonneveld, M., Jarret, R., Bohs, L., Kantar, M., Uchanski, M., Mercer, K., Nabhan, G. P., Bosland, P. W., & Greene, S. L. (2020). Modelled distributions and conservation status of the wild relatives of chile peppers (Capsicum L.). *Diversity and Distributions*, *26*(2), 209–225. * (Keep columns: taxon, latitude, longitude, db and country from the first tab '1_Occurence data', and save as: "Khoury2020_suppFirstPage.csv") **SilvestresCapsicum2014.csv** * CONABIO (National Commission for the Knowledge and Use of Biodiversity) through SNIB-REMIB (National Information System on Biodiversity-World Network of Information on Biodiversity) up to 2014 **Guerrero_Michoacan.csv** * Additional vouchers from MEXU (UNAM) herbarium accessions **Capsicum_annuum_glabriusculum.csv** * You will need to download the supporting dataset S2: Goettsch, B., Urquiza-Haas, T., Koleff, P., Acevedo Gasman, F., Aguilar-Meléndez, A., Alavez, V., Alejandre-Iturbide, G., Aragón Cuevas, F., Azurdia Pérez, C., Carr, J. A., Castellanos-Morales, G., Cerén, G., Contreras-Toledo, A. R., Correa-Cano, M. E., De la Cruz Larios, L., Debouck, D. G., Delgado-Salinas, A., Gómez-Ruiz, E. P., González-Ledesma, M., … Jenkins, R. K. B. (2021). Extinction risk of Mesoamerican crop wild relatives. *Plants People Planet*, *3*(6), 775–795. * (Filter only *Capsicum annuum* in Binomial column and save as: "Capsicum_annuum_glabriusculum.csv") **SEMIWILDS "ARVENSE"** **GonzalezJara_ManyAraceli.csv** * You will need to obtain the coordinates from the Table1 in González-Jara, P., Moreno-Letelier, A., Fraile, A., Piñero, D., & García-Arenal, F. (2011). Impact of human management on the genetic variation of wild pepper, Capsicum annuum var. glabriusculum. *PLoS ONE*, *6*(12). (Filter only Field popualtions, columns as : Species, Population, State, Latitude, Longitude, Habitat, Code and Type. Then save as "GonzalezJara_ManyAraceli.csv" --downstream we will keep only Let-standing samples, that is *live fence* or *pasture* 'habitat'.) * Add to "GonzalezJara_ManyAraceli.csv" the rows listed in the file "ManyAraceli.csv", we deduced these coordinates from the Localities reported in Table1 as semiwild in Aguilar-Meléndez, A., Morrell, P. L., Roose, M. L., & Kim, S. C. (2009). Genetic diversity and structure in semiwild and domesticated chiles ( Capsicum Annuum ; Solanaceae) from Mexico. *American Journal of Botany*, *96*(6), 1190–1202. **LANDRACES** **seasonal_points.csv** * proxies of occurrence points were estimated taking information from municipalities reported by (SAGARPA, 2018) to produce chile pepper through non-irrigated cultivation **COMMERCIALS** **irrigation_points.csv** * proxies of occurrence points were estimated taking information from municipalities reported by (SAGARPA, 2018) to produce chile pepper through irrigated cultivation **seasonal_points.csv** * proxies of occurrence points were estimated taking information from municipalities reported by (SAGARPA, 2018) to produce chile pepper through non-irrigated cultivation **CannuumCultivatedConabio2014.csv** * CONABIO (National Commission for the Knowledge and Use of Biodiversity) through SNIB-REMIB (National Information System on Biodiversity-World Network of Information on Biodiversity) up to 2014 **Final_Thinned_BIOS_soil_.csv** * Final thinned *C.annuum* referenced dataset with their bioclim and soil variables’ values. **The data structure can be replicated with "make_dirs.R" script running on "PresentDirs.txt", "futureDirs.txt" and "MapDirs.txt" files** \################################ **Sharing/Access information** \################################\ The following papers were used to extract the data coordinates as explained above and hold these licences. ·       Khoury etal 2020 (Open Access: CC-BY 4.0)\ * González-Jara etal 2011 (Open Access: Copyright: ß 2011 González-Jara et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited)\ * Kraft etal 2014 (Free Access, however data points used are from GBIF)\ * Aguilar-Melndez etal 2009 (Free Access, however we deduced our coordinates from the name of their locations)\ * Goettsch etal 2021 (Open Access: CC BY-NC-ND 4.0) Open Research, their Data Avaliability statement indicates "The data that supports the findings of this study are published in the supplementary material and The IUCN Red List . \ The following platform/institutions are public and were used to extract the reminder of the data as explained above. * Sistema Nacional de Información sobre la Biodiversidad (SNIB-REMIB)\ * Secretaría de Agricultura, Ganadería, Desarrollo Rural, Pesca y Alimentación (SAGARPA)\ * Herbario Nacional UNAM (MEXU)\ \################### **Code/Software** \###################\ "Script_index.html" script indexes the scripts used throughout this paper and the order in which they should be run. They are all R markdown html scripts.   ---