Ethnobotanical and genetic assessments of Central American avocado landraces reveal novel sources of biodiversity and ancient migration patterns

Societal Impact Statement Avocados are a multibillion‐dollar global commodity, but their growing export market pressures local farmers to abandon local fruit tree diversity in favor of commercial cultivar production. Interviews with rural avocado farmers and households from the Southern Mexican Highlands, Pacific Coastal Honduras, and Western Nicaragua, as well as the genetic analysis of their cultivars, highlight the importance of native avocado conservation in sustainable breeding programs. Local Central American avocados serve as hearty rootstocks well‐adapted to their specific climate and grow in symbiosis alongside commercial trees. Landraces are also substantially genetically separated from commercial cultivars, representing a source of genetic diversity in the face of threats to global production such as climate change and pathogens. Summary The genomes of landrace cultivars offer a unique view into a plant's history of human usage and a fuller understanding of the genetic diversity available for sustainable production. The avocado tree ( Persea americana Mill., family Lauraceae), native to Central and South America, has a complicated history of traditional and commercial production revealed through previous genetic research. We sequenced 50 low‐coverage genomes from avocado landraces grown in home gardens and local farms from Honduras, Nicaragua, and on roadsides in Chiapas, Mexico. We also interviewed local cultivators to document traditional perspectives on native Central American avocado management and biodiversity. Samples collected from Chiapas show evidence for recent hybridization both within and between native and commercial cultivars. In contrast, lowland Nicaraguan and Honduran landraces were substantially differentiated from commercial genomes. Lowland genomes show evidence for ancient episodes of migration from South American avocados detectable only in noncommercial germplasm. Differences in relatedness to commercial avocados between regions are explained by the region's historical involvement in exports to large consumer markets throughout time. Chiapas landraces are closer genetically to commercial avocados than those in lowland Honduras and Nicaragua, as the highlands of Southern Mexico offer a better growth environment for more exportable varieties. Since the humid lowlands are largely unaffected by commercial production, we are able to detect ancient signals of pre‐colonial migration from South America.