Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome

Abstract Understanding how environmental variation influences population
genetic structure can help predict how environmental change influences
population connectivity, genetic diversity, and evolutionary potential. We
used riverscape genomics modelling to investigate how climatic and habitat
variables relate to patterns of genetic variation in two stonefly species,
one from mainstem river habitats (Sweltsa coloradensis) and one from
tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We
produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp,
BUSCO > 95% using “insecta_ob9” reference genes). We genotyped
1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153
individuals for S. fidelis. We found higher genetic diversity for S.
coloradensis compared to S. fidelis, but nearly identical genetic
differentiation among sites within each species (both had global loci
median FST = 0.000), despite differences in stream network location. For
landscape genomics and testing for selection, we produced a less
stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and
S. fidelis, respectively). Environmental variables (mean summer
precipitation, slope, aspect, mean June stream temperature, land cover
type) were correlated with 19 putative adaptive loci for S. coloradensis.
but there was only one putative adaptive locus for S. fidelis (correlated
with aspect). Interestingly, we also detected potential hybridization
between multiple Sweltsa species which has never been previously detected.
Studies like ours, that test for adaptive variation in multiple related
species are needed to help assess landscape connectivity and the
vulnerability of populations and communities to environmental change.