The Andean highlands are a hotspot of domestication, yet our understanding of the origins of early Andean agriculture remains fragmentary. Key questions of where, when, how many times and from what progenitors many Andean crops were domesticated remain unanswered. The Andean crop lupin, tarwi, Lupinus mutabilis, is a regionally important pulse crop with exceptionally high seed protein and oil content and is the focus of modern breeding efforts, but its origins remain obscure. A large genome-wide DNA polymorphism dataset was generated using nextRADseq to infer relationships among more than 200 accessions of Andean Lupinus species, including 24 accessions of L. mutabilis and close relatives. Phylogenetic and demographic analyses were used to identify the likely progenitor of tarwi, and elucidate the area and timing of domestication in combination with archaeological evidence.
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