Bean Genome Diversity Reveals the Genomic Consequences of Speciation, Adaptation, and Domestication

Abstract

Here we review whether genomic islands of speciation are repeatedly more prone to harbor within-species differentiation due to genomic features, such as suppressed recombination, smaller effective population size, and increased drift, across repeated hierarchically nested levels of divergence. Our discussion focuses on two species of Phaseolus beans with strong genepool and population substructure and multiple independent domestications each. We overview regions of species-associated divergence, as well as divergence recovered in withinspecies between-genepool comparisons and in within-genepool wild-cultivated comparisons. We discuss whether regions with overall high relative differentiation coincide with sections of low SNP density and with between-species pericentric inversions, since these convergences would suggest that shared variants are being recurrently fixed at replicated comparisons, and in a similar manner across different hierarchically nested levels of divergence, likely as the result of genomic features that make certain regions more prone to accumulate islands of speciation as well as within-species divergence. We conclude that neighboring signatures of speciation, adaptation, and domestication in Phaseolus beans seem to be influenced by ubiquitous genomic constrains, which may continue shaping, fortuitously, genomic differentiation at various other scales of divergence. This pattern also suggests that genomic regions important for adaptation may frequently be sheltered from recombination.

Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

“…The concept of separate gene pools for the south American region that includes the Andes Mountains compared to the Mesoamerican region of Central America and Mexico, which is less mountainous, is well established for wild versus cultivated and semi-domesticated chenopods (genus Chenopodium ) including Chenopodium quinoa , or cultivated kinwa/quinoa from the Andes and Chenopodium nuttalliae from Mexico ( Heiser and Nelson, 1974 ). Several New World legumes also have this pattern of Andean/Mesoamerican divergences, namely, Phaseolus lunatus (lima bean) and Phaseolus vulgaris (common bean) ( Blair et al., 2009 ; Cortés et al., 2018 ).…”