Focal Populations
The goal of this study was to compare the P matrices of allopatric generalist pupfish populations to sympatric populations of pupfish containing both generalist and specialist species, and to estimate the P-matrices of F2 hybrid pupfish to make inferences about the underlying mechanisms of craniofacial traits on SSI. To that end, we measured and compared craniofacial traits of fish from: five Caribbean populations of pupfish that contained only generalist species (Lake Cunningham (New Providence Island, Bahamas), Flamingo Pond (Acklins, Bahamas), Lake George (Rum Cay Island, Bahamas), Etang Saumatre (Dominican Republic), and Laguna Oviedo (Dominican Republic)); six SSI populations that do not contain the full radiation of pupfishes, and instead contain only or mostly generalist species (Wild Dilly Pond, Reckley Field Pond, Pain Pond, Moon Rock Pond, Six Pack Pond, and Mermaid Pond); and three SSI populations of pupfish that contained the full radiation of pupfishes in sympatry (Crescent Pond, Little Lake, and Oyster Pond), although only generalist and scale-eater specimens were available for measurement from Oyster Pond (Table 1; Figure 1). A portion of the specimens from the above ponds were initially collected, measured, and analyzed in a previously published article (Martin, 2016), and complete collection details can be found there. Additional justification and information about the use and categorization of these populations can be found in appendix A. For simplicity, we collectively refer to the five Caribbean populations of pupfish as the ‘Caribbean’ group/population (N = 61), the six populations that do not contain the full pupfish radiation as the ‘generalist-only’ group/population (N=85), and the three populations containing all three pupfish species in sympatry as the ‘radiating’ group/population (N=42).
To make inferences about the potential mechanisms underlying craniofacial traits on SSI, we measured traits of F2 scale-eater X snail-eater hybrid offspring and estimated phenotypic variation and covariation of these traits. We produced F2 hybrids by first crossing a single male snail-eater with a single female scale-eater to produce F1 offspring. We repeated this process independently for the Crescent Pond and Little Lake populations. At least four F1 offspring from each population were then allowed to interbreed to produce F2 hybrids. In total we produced and measured 301 F2 hybrids from Crescent Pond and 194 hybrids from Little Lake (Table 1). These measurements were used for separate QTL mapping study of these crosses (St. John et al. 2021).
When comparing F2 hybrid phenotypes and P matrices we assume a simple additive model of inheritance (Falconer 1996; Roff 1997). The assumptions of this model include: 1) that there are two alleles per locus, 2) that mendelian laws of segregation are adhered to, 3) that loci across the genome are in linkage equilibrium, and 4) that there are only additive genetic effects (i.e., no dominance or epistatic effects). With these assumptions we expect that the distribution of phenotypic traits in the F2 generation should follow a 1:2:1 ratio, where intermediate phenotypes are most common and phenotypes aligning with either parental phenotype are less common and equally distributed, and we expect covariation between traits to correspond to recombination events, which for the sake of simplicity we assume to uniformly distributed across the genome. To investigate deviations from these assumptions we estimate expectations of additivity by calculating the average of parental traits from the F0 generation and calculate expectations of variation within traits using the parental trait values and hybrid population sample sizes (Appendix E: Tables E1, E2, & E3).