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Dryad

Incorporating evolutionary and threat processes into crop wild relatives conservation

Cite this dataset

Tobón-Niedfeldt, Wolke et al. (2022). Incorporating evolutionary and threat processes into crop wild relatives conservation [Dataset]. Dryad. https://doi.org/10.5061/dryad.7m0cfxpxm

Abstract

Crop wild relatives (CWR) intra- and interspecific diversity is essential for crop breeding and food security. However, intraspecific genetic diversity, which is central given the idiosyncratic threats to species in landscapes, is usually not considered in planning frameworks. Here, we introduce an approach to develop proxies of genetic differentiation to identify conservation areas, applying systematic conservation planning tools that produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa-specific tolerance to human-modified habitats, and their extinction risk status. Our results support the development of national strategies for the conservation and use of CWR in Mexico and inform public policy to mitigate threat processes to CWR. Although we focus on Mesoamerican CWR within Mexico, our methodology offers opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.

Methods

We applied a modified version of a planning framework for CWR conservation including CWR checklist, CWR inventory, taxa extinction risk assessment and a systematic conservation planning assessment. The first three steps are thoroughly described in Goettsch et al. (https://doi.org/10.1002/ppp3.10225). Here, we focus on the systematic conservation planning assessment, introducing an approach in order to identify conservation areas for CWR that account for genetic differentiation in a spatially explicit way, through the use of proxies of genetic differentiation.

The data presented here includes Zonation input and output files, habitat rasters, Table with IUCN category per taxa, metadata, and genetic data used for the conservation planning assessment and figures. The genetic data used to validate our findings belongs to a maize wild relative, the teosinte Zea mays subsp. parviglumis. Raw genetic data was produced by a different study (Ph.D. thesis Rivera-Rodríguez, D. M. Estudio de la Diversidad y Estructura Genómica del Teocintle. Doctoral Thesis, Advisor: Sánchez, J.J., Universidad de Guadalajara, 2018) and it is available elsewhere (Rivera-Rodríguez under review). Here, the admixture and plink files used for the analyses of this paper are provided.

Code used to process and analyse the data is available at https://github.com/CONABIO/analisisUniCons_proxiGen

Usage notes

The data set includes raster files (.tiff), text files (.csv, .txt), Admixture output files (.Q) and plink files (.fam, .bed, .bim) that are meant to be used with Zonation, R, and GIS software such as ArcMap or QGis.

In this data repository, related files used together for analyses are compressed in a .zip or .tar.gz file (for larger files that needed more compression).

Code used to process and analyse the data is available at https://github.com/CONABIO/analisisUniCons_proxiGen. Release: Mastretta-Yanes, Alicia, Tobón-Niedfeldt, Wolke, & Cuervo-Robayo, Angela P. (2022). CONABIO/analisisUniCons_proxiGen: v.1.0.0. In Nature Communications (v.1.0). Zenodo. https://doi.org/10.5281/zenodo.7015703

See README for details on full list of content within compressed files, variable names of .csv and .txt files, and how the data should be organized in order for scripts to run.

Check Zonation documentation for details on Zonation's input/output data. https://conservationcorridor.org/corridor-toolbox/programs-and-tools/zonation/

MAIN FILES:



Comparing_output_txt.zip
========================

Uncompressed directory name: `comparations_output`

Contains txt output of the script `spatial_analyses_zonationVSproxiesdivgen_all_ms.R`, which compares the performance of five preliminary systematic conservation planning scenarios (SDM, SDM+LZ, SDM+PGD, SDM*PGD, SDM*PGD, SDM and PGD as ADMU) considering the Zonation solution for 20% of the country considering only taxa distribution models (no habitat, etc).


genetic.tar.gz
==============

Uncompressed directory name: `genetic`

Genetic data and metadata including Admixture output, plink files, passport data and geographic-PGD data for each sampling point:


IUCN_threat_category.csv
=========================

Table with IUCN category per taxa. For scripts to run it should be saved in: `/data/spatial/Zonation_final_solutions/IUCN_threat_category.csv`.


Life_zones_rasters.tar.gz
=========================

Uncompressed files should be sabed in a directory named: `zv27`

Rasters (.tif) of Holdrige life zones.


PGD_rasters.tar.gz
===================

Uncompressed files should be sabed in a directory named: `areasProxyDivGen`

Rasters (.tif) with proxies of genetic differentiation (PDG). Rasters file names are as follow: each of the Holdrige life zones (`zv_[1:27]`) are subdivided with a `_[letter].tif` for each of the PGD for that life zone. For example: `zv_1a.tif`, `zv_1b.tif`, `zv_1c.tif`.


PGD_croptoSDM_rasters.tar.gz
=============================

Uncompressed directory name: `crop_to_sp`

Contains the raster output of the script `spatial_analyses_zonationVSproxiesdivgen_all_ms.R`, which is the crop (subdivision) of each taxon SDM into the proxies of genetic differentiation (PGDs) it covers.


SDM_rasters.tar.gz
==================

Uncompressed files should be sabed in a directory named: `modelos_darwin_all_final`

Rasters (.tif) of species distribution models for each of the cwr taxon used for Zonation analyses. Raster names are `[taxon_name].tif`.


Zonation_input_conservationfeatures.tar.gz
==========================================

Uncompressed directory name: `MDP_PDG`

Zonation Conservation Features input data, i.e: Biodiversity rasters result of the combination of species distribution models (SDM, MDP in Spanish) and proxies of genetic diversity (PDG, PGD in Spanish).


Zonation_input_habitat.tar.gz
=============================

Uncompressed directory name: `condition_habitat2_final`

Zonation "Habitat layers" input data.


Zonation_input_points.zip
==============================

Uncompressed directory name: `puntos`

Zonation "Species of Special Interest files" input files, i.e. records for taxa without potential distribution model.


Zonation_output_final.tar.gz  
=============================
 
Uncompressed directory name: `Zonation_final_solutions`

Contains Zonation output curves and rasters within the scenario considering potential species distribution models subdivided by PGD (5,004 layers); taxon-specific habitat preferences considering land-use and land-cover information; occurrence records for taxa without SDM; and taxa weights according to their IUCN threat category


Zonation_scenarios_rasters.tar.gz
=================================
 
Uncompressed directory name: `Zonation_output`

Contains the rasters of Zonation output solutions for the different scenarios tested.

Funding

Darwin Initiative, Award: 23-007