title: Lost crops of the Incas: Origins of domestication of the Andean pulse crop tarwi, Lupinus mutabilis.
abstract: 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 lupine crop 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 data set 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.
  
  
  
  We infer that tarwi was domesticated once in northern Peru, most likely in the Cajamarca region within, or adjacent to the extant distribution of L. piurensis, which is the most likely wild progenitor. Demographic analyses suggest that tarwi split from L. piurensis around 2600 BP and suffered a classical domestication bottleneck. The earliest unequivocal archaeological evidence of domesticated tarwi seeds is from the Mantaro Valley, central Peru ca. 1800 BP.
  
  
  
  A single origin of tarwi from L. piurensis in northern Peru provides a robust working hypothesis for the domestication of this regionally important crop and is one of the first clear-cut examples of a crop originating in the highlands of northern Peru.
authors.affiliation: Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland guy.atchison@systbot.uzh.ch.
authors.forename: Guy W
authors.initials: GW
authors.lastname: Atchison
authors.affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
authors.forename: Bruno
authors.initials: B
authors.lastname: Nevado
authors.affiliation: Millennium Seed Bank, Royal Botanic Gardens, Ardingly, RH17 6TN, UK.
authors.forename: Ruth J
authors.initials: RJ
authors.lastname: Eastwood
authors.affiliation: Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Apartado Aéreo 4976, Bogotá, Colombia.
authors.forename: Natalia
authors.initials: N
authors.lastname: Contreras-Ortiz
authors.affiliation: Departamento de Manejo Forestal, Facultad de Ciencias Forestales, Universidad Nacional Agraria La Molina, Apartado 456, La Molina, Lima, Peru.
authors.forename: Carlos
authors.initials: C
authors.lastname: Reynel
authors.affiliation: Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Apartado Aéreo 4976, Bogotá, Colombia.
authors.forename: Santiago
authors.initials: S
authors.lastname: Madriñán
authors.affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Filatov
authors.affiliation: Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
authors.forename: Colin E
authors.initials: CE
authors.lastname: Hughes
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D000071278:Domestication; D031297:Lupinus / Q000235:genetics*; D010568:Peru; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: Andes; Leguminosae; Lupinus mutabilis; domestication; nextRAD; tarwi