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

Domestication is considered a model of adaptation that can be used to draw
conclusions about the modus operandi 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 Pisum
sativum (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 P. sativum revealed
five distinct groups with a notable geographic pattern. Pisum abyssinicum
clustered unequivocally within the P. sativum complex, without any
indication of hybrid origin. We detected 32 genomic regions putatively
subjected to selection: 29 in P. sativum ssp. sativum and three in
P. abyssinicum. The two domesticated groups did not share regions under
selection and did not display similar haplotype patterns within those
regions. Wild P. sativum is structured into well-diverged subgroups.
Although Pisum sativum ssp. humile is not supported as a taxonomic entity,
the so-called 'southern humile' 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.