Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

Abstract

Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a population genomic data set which shows that M. nasutus budded from a central Californian M. guttatus population within the last 200 to 500 thousand years. In this time, the M. nasutus genome has accrued genomic signatures of the transition to predominant selfing, including an elevated proportion of nonsynonymous variants, an accumulation of premature stop codons, and extended levels of linkage disequilibrium. Despite clear biological differentiation, we document genomic signatures of ongoing, bidirectional introgression. We observe a negative relationship between the recombination rate and divergence between M. nasutus and sympatric M. guttatus samples, suggesting that selection acts against M. nasutus ancestry in M. guttatus.

Involvement of Interleukin-1 Receptor–Associated Kinase-1 in Vascular Smooth Muscle Cell Proliferation and Neointimal Formation After Rat Carotid Injury

“…Together with earlier indications in other species (18)(19)(20), our findings show the distribution of minor parent ancestry to be at least in part predictable from genomic features. Knowledge of local recombination should therefore provide a guide to where in the genome minor parent ancestry is expected to be highest.…”

“…S1) (6,11). Previous studies have reported patterns consistent with these expectations (18)(19)(20) but without investigating ancestry patterns and their relationship to local recombination rates, distinguishing among selection in the parental or hybrid lineages, or determining the major sources of selection in hybrid populations.…”

Natural selection interacts with recombination to shape the evolution of hybrid genomes

“…S1). Previous studies have reported patterns consistent with these expectations (18–20), but without investigating ancestry patterns and their relationship to local recombination rates, or distinguishing among sources of selection.…”

Population-level genetic variation and climate change in a biodiversity hotspot

“…Understanding the distribution of genetic variation on the landscape and the life history or ecological parameters that influence this variation will be important in identifying the taxa most vulnerable to anthropogenic change (Peter and Slatkin, 2013;Brandvain et al, 2014). High levels of heterozygosity have been repeatedly shown to confer resistance to environmental change (Hanski et al, 2006;Willi et al, 2006;Bonin et al, 2007).…”

“…Even where phenotypic variation is present, measuring genetic variability due to recent divergence can be a problem, particularly in places like California, where speciation and evolutionary diversification have occurred recently (Boykin et al, 2005;Burge et al, 2011). Detection of patterns of recent genetic divergence now can be achieved, however, through the use of markers more suitable for measuring population-level variation, such as microsatellites, restriction site-associated DNA markers (RADseq) (Davey and Blaxter 2010) and whole-genome sequences (Brandvain et al, 2014).…”