Assessment of barriers to gene flow in S. hesperis
The northern and southern S. hesperis lineages identified in this
study are largely parapatric in their distributions. It is therefore
possible that genetic drift resulting from barriers to dispersal (i.e.,
vicariance and speciation without selection or mutation-order
speciation), rather than ecologically-based divergent selection (i.e.,
ecological speciation), has been the dominant evolutionary process
underlying diversification and reinforcement of the identified lineages
(sensu Nosil, 2012). To test for this possibility, we assessed
whether there are present-day barriers to dispersal between the northern
and southern S. hesperis lineages related to arrangements of
suitable habitat. This was accomplished using resistance surfaces
parameterized as the inverse of predicted habitat suitability (McRae &
Beier 2007; Wang et al. 2008; Storfer et al. 2010; Wang et al. 2012;
MacDonald et al. 2020). This approach assumes that organisms are more
likely to disperse within suitable habitat and experience high
resistance when moving through unsuitable habitat; large stretches of
unsuitable habitat thereby pose significant barriers to dispersal (Coyne
& Orr 2004; Crispo et al. 2006; McRae 2006; McRae & Beier 2007; Thorpe
et al. 2008, 2010; Sánchez-Ramírez et al. 2018). We averaged resistance
surfaces of the northern and southern S. hesperis lineages to
generate a single resistance surface reflecting the probability that
dispersing individuals of the two lineages will come into contact that
could result in reciprocal gene flow. Using this single resistance
surface, we then calculated pairwise resistance distances between all
individuals using the R package gdistance (van Etten 2017) and organized
them into a pairwise matrix. These resistance distances are analogous to
circuit distances (McRae & Beier 2007), measuring expected random-walk
commute time between nodes (i.e., localities of sequenced individuals)
in a graph (i.e., resistance surface) (Chandra et al. 1996). We also
generated a pairwise matrix of Euclidean distances between all
individuals using the R package sp (Pebesma & Bivand 2005). A third
pairwise matrix (“lineage distance”) indicated whether individuals
belonged to the same lineage (value = 0) or to different lineages (value
= 1).
We used a partial mantel test to evaluate whether resistance distances
between individuals of different lineages were significantly greater
than those between individuals of the same lineage after controlling for
Euclidean distance. This analysis effectively evaluates whether
significant barriers to dispersal exist between the northern and
southern S. hesperis lineages. A significant correlation between
resistance distance and lineage distance after partialling out Euclidean
distance would suggest that reduced gene flow resulting from barriers to
dispersal (vicariance) cannot be ruled out as a principal mechanism
reinforcing the genomic integrity of the northern and southern S.
hesperis lineages. Alternatively, the absence of a significant
correlation between resistance distance and lineage distance after
partialling out Euclidean distance would suggest that ecologically-based
divergent selection likely contributes to reinforcement of the northern
and southern S. hesperis lineages.