Incorporating evolutionary and threat processes into crop wild relatives conservation

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