Museum genomics of reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of genetic diversity through time offer a window into
evolutionary processes that maintain diversity. Over time, lineages may
expand or contract their distribution, causing turnover in population
genetic composition. At individual loci, drift, environmental changes, and
purifying selection may affect allele frequencies. Museum specimens of
widely distributed species offer a unique window into genetic composition
of understudied populations and changes over time. Here, we sequenced
genomes of 130 herbarium specimens and 91 new field collections of
Arabidopsis thaliana and combined these with published genomes. We sought
a broader view of genomic diversity across the species, and to test if
population genomic composition is changing through time. Using herbarium
specimen sequences, we documented extensive and previously uncharacterized
diversity in a range of populations in Africa, populations that are under
threat from anthropogenic climate change. Through time, we did not find
dramatic changes in population genomic composition of populations.
Instead, we found a pattern of genetic change every 100 years of the same
magnitude seen when comparing Eurasian populations that are 185 km apart,
potentially due to a combination of drift and changing selection. However,
we found only mixed signals of polygenic adaptation at phenology and
physiology QTL. We did find that genes conserved across eudicots show
altered levels of directional allele frequency change, potentially due to
variable purifying and background selection. Our study highlights how
museum specimens can reveal new dimensions of population diversity and
show how wild populations are evolving in recent history.