Appendix A: Population groupings
For comparisons, we formed three focal groups: SSI generalist-only, SSI
radiating, and the Caribbean. The PCA (Figure A1) indicates that
generalists, snail-eaters, and scale-eaters on SSI form distinct
clusters based on their genetic variation. The PCA visualization also
suggests that: 1) Oyster Pond scale-eaters and generalists fall well
within the 95% confidence intervals for their species designations,
justifying their inclusion in the SSI radiating population analyses and
2) Mermaid Pond “scale-eaters” (designated as such based on their
morphological traits) do not fall within the 95% confidence interval
for genetically clustering scale-eaters, and are instead closer to the
centroid of generalists. Although previous studies suggest that Mermaid
Pond contains scale-eating individuals (Martin and Wainwright. 2013),
more recent work suggests that these individuals are distinct from
scale-eaters (Richards et al. 2021. Richards and Martin. 2022).
Furthermore, there are no published sightings of snail-eating pupfish in
Mermaid Pond. For these reasons, we included Mermaid Pond in the
generalist-only population calculations as opposed to the SSI radiating
populations. Finally, snail-eaters have previously been documented in
Moon Rock and Wild Dilly Pond, but scale-eating specialists have never
been found in these locations (Martin 2014). Considering that we did not
have access to any of the snail-eater specimens from these locations,
and that these populations have never contained the full radiation of
pupfish,
we included Moon Rock and Wild Dilly Pond in the generalist-only
population calculations as opposed to the SSI radiating populations.