Data from: Ecotypic differentiation under farmers’ selection: molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes

Understanding the distribution of crop genetic diversity in relation to
environmental factors can give insights into the eco-evolutionary
processes involved in plant domestication. Yam beans (Pachyrhizus Rich. ex
DC.) are leguminous crops native to South and Central America that are
grown for their tuberous roots but are seed-propagated. Using a landscape
genetic approach, we examined correlations between environmental factors
and phylogeographic patterns of genetic diversity in Pachyrhizus landrace
populations. Molecular analyses based on chloroplast DNA sequencing and a
new set of nuclear microsatellite markers revealed two distinct lineages,
with strong genetic differentiation between Andean landraces (lineage A)
and Amazonian landraces (lineage B). The comparison of different
evolutionary scenarios for the diversification history of yam beans in the
Andes using Approximate Bayesian Computation (ABC) suggests that P. ahipa
and P. tuberosus share a progenitor-derivative relationship, with
environmental factors playing an important role in driving selection for
divergent ecotypes. The new molecular data call for a revision of the
taxonomy of Pachyrhizus but are congruent with palaeoclimatic and
archaeological evidence, and suggest that selection for determinate growth
was part of ecophysiological adaptations associated with the
diversification of the P. tuberosus–P. ahipa complex during the
Mid-Holocene.