Domestication has had a strong impact on the development of modern societies. We sequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first time to our knowledge that a single population, the Criollo population, underwent strong domestication ~3600 years ago (95% CI: 2481–13,806 years ago). We also show that during the process of domestication, there was strong selection for genes involved in the metabolism of the colored protectants anthocyanins and the stimulant theobromine, as well as disease resistance genes. Our analyses show that domesticated populations of T. cacao (Criollo) maintain a higher proportion of high-frequency deleterious mutations. We also show for the first time the negative consequences of the increased accumulation of deleterious mutations during domestication on the fitness of individuals (significant reduction in kilograms of beans per hectare per year as Criollo ancestry increases, as estimated from a GLM, P = 0.000425).
Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid
Capsella bursa-pastoris
in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse
Capsella grandiflora
(
Cbp
Cg
) and the other one from the selfing and genetically depauperate
Capsella orientalis
(
Cbp
Co
). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (
N
e
), signatures of positive and negative selection, and gene expression patterns. In all three regions,
N
e
of the two subgenomes decreased gradually over time and the
Cbp
Co
subgenome accumulated more deleterious changes than
Cbp
Cg
. There were signs of widespread admixture between
C. bursa-pastoris
and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of
C. bursa-pastoris
. Selective sweeps were more common on the
Cbp
Cg
subgenome in Europe and the Middle East, and on the
Cbp
Co
subgenome in Asia. In contrast, differences in expression were limited with the
Cbp
Cg
subgenome slightly more expressed than
Cbp
Co
in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of
C. bursa-pastoris
still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.