Future-Proofing Agrobiodiversity: Effective Population Size as a Tool to Conserve Wild–Domesticated Lineages

The conservation of genetic diversity in species forming wild–domesticated complexes requires robust indicators that account for their differentiated evolutionary histories. These complexes have been shaped by varying divergence times, spatial patterns, and human processes such as ongoing domestication in indigenous communities, traditional management practices, and intensive cultivation systems. For genetic indicators to be effective, it is essential to identify each component of the wild–domesticated continuum and ensure monitoring captures the evolutionary and biocultural dynamics maintaining diversity. This approach is critical not only for conserving wild areas but also for safeguarding cultural diversity and the stability of local and regional food systems. However, these components are often analysed in isolation, without integration into broader assessment frameworks or consideration of sociocultural factors. This study proposes explicitly incorporating wild–domesticated complexes into genetic diversity indicators to strengthen monitoring and ensure effective conservation outcomes.

We present an integrated analysis based on empirical data from wild–domesticated complexes within Mexico’s agrobiodiversity. Using examples from cotton, agaves, maize, chayotes, and their wild relatives, and employing genetic estimates of effective population size (Ne) alongside Ne derived from census size (Nc), we show that evaluating each component enhances the precision and reliability of decision-making at local and regional levels. Understanding species-specific threats is essential, as the traits that make these species valuable also render them vulnerable. For example, gene flow from cultivated plants can introduce domestication-selected traits into wild populations; rapid turnover of commercially attractive varieties can lead to the loss of multiple varieties and costly recovery processes; and intellectual property regulations may disrupt traditional seed management and the intra- and inter-varietal genetic diversity conserved in centers of origin, domestication, or within broader crop genetic diversity.

Integrating evolutionary and biocultural perspectives provides a framework for conserving the processes that generate and maintain genetic diversity. This approach contributes directly to safeguarding local agrobiodiversity, especially in regions where biocultural diversity is prominent, supports food sovereignty, promotes equitable futures, and ensures that diversity continues to provide adaptive potential across diverse environmental conditions, securing the capacity to nourish future generations.