Between forest and homegarden, geographic patterns of genetic variation in the Mesoamerican Soncoya (Annona purpurea)

Methods

Summary

This project combines field biology, genomics, morphology, ethnobotany, and ecological modeling to investigate the effects of domestication on Annona purpurea across its distribution in Mexico. We will sample wild and managed populations spanning different management systems, including natural forests, agricultural landscapes, and traditional homegardens. Fieldwork will be complemented with ethnobotanical interviews to document traditional uses and management practices.

Genomic data will be generated using target enrichment of hundreds of nuclear genes, providing thousands of genome-wide markers to evaluate genetic diversity, population structure, gene flow, and demographic history. We will compare patterns of genetic variation among management categories to determine whether domestication has altered connectivity, diversity, or population size through time.

In parallel, fruit morphology will be quantified using traits associated with human selection, allowing us to assess whether managed populations show signs of phenotypic divergence. Finally, ecological niche models and genomic offset analyses will integrate genomic and environmental data to evaluate the adaptive potential of populations under future climate change scenarios. Together, these approaches provide a comprehensive framework for understanding the evolutionary consequences of domestication and informing conservation strategies for this culturally important Mesoamerican fruit tree.

Challenges

One challenge is ensuring adequate sampling across the full geographic, environmental, and management range of Annona purpurea, as population density and fruit availability may vary among regions and seasons. To address this, we will conduct extensive field surveys and prioritize broad geographic coverage to maximize representation of both wild and managed populations.

Another challenge is disentangling the effects of domestication from those of historical biogeographic processes and environmental variation. We will address this by combining genomic, morphological, ethnobotanical, and ecological data, allowing us to explicitly evaluate the relative contributions of human management, geographic isolation, and local adaptation to observed patterns of variation.

The project also relies on the generation of high-quality genomic data from diverse populations. This risk is minimized through the use of a target-capture system specifically developed for Annonaceae, which has been successfully applied to recover hundreds of nuclear loci across the family

Pre Analysis Plan

Our central hypothesis is that domestication and human management have shaped patterns of genetic and morphological variation in Annona purpurea, but that the magnitude of these effects varies geographically according to management intensity and connectivity with surrounding wild populations.

We predict that managed populations, particularly those maintained in homegardens and agricultural systems, will differ from wild populations in fruit morphology and may exhibit reduced genetic diversity as a consequence of founder effects, genetic drift, or selective propagation. However, because domestication is likely incipient and heterogeneous, we also predict that some managed populations will retain substantial genetic diversity due to ongoing gene flow with nearby forest populations.

Genomic data will be used to quantify genetic diversity, identify population structure, estimate levels of admixture and connectivity among populations, and evaluate the distribution of genetic variation across management categories and biogeographic regions. Morphological traits will be compared among management systems to determine whether human use and cultivation are associated with phenotypic divergence.

To distinguish the effects of domestication from those of geography and historical processes, analyses will explicitly compare alternative sources of variation, including management category, genetic cluster membership, geographic distance, and biogeographic region. Historical demographic analyses will evaluate whether managed populations show evidence of population bottlenecks or demographic shifts associated with human management.

Finally, ecological niche models and genomic offset analyses will be used to assess the relationship between genetic variation and environmental conditions, and to identify populations that may be particularly vulnerable or resilient under future climate change scenarios. Together, these analyses will provide multiple independent lines of evidence for evaluating the evolutionary consequences of domestication in this culturally important Mesoamerican fruit tree.