Phylogeny and disparate selection signatures suggest two genetically independent domestication events of pea (Pisum L.)

<p>Domestication is considered a model of adaptation that can be used to draw conclusions about the <em>modus operandi</em> of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 <em>Pisum sativum</em> (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild <em>P. sativum</em> revealed five distinct groups with a notable geographic pattern. <em>Pisum abyssinicum</em> clustered unequivocally within the <em>P. sativum</em> complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in <em>P. sativum</em> ssp. <em>sativum</em> and three in <em>P. abyssinicum</em>. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild <em>P. sativum</em> is structured into well-diverged subgroups. Although <em>Pisum sativum</em> ssp<em>. humile</em> is not supported as a taxonomic entity, the so-called 'southern <em>humile</em>' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.</p>