Genetic architecture of Pacific lamprey body forms
The genetic architecture underlying these traits related to body size and maturity is highly concentrated. However, this result is somewhat expected given the high degree of gene flow exhibited in Pacific lamprey (Spice et al . 2012). When natural selection is strongly acting on a particular trait in the face of high gene-flow, the genes involved in the trait tend to become highly concentrated and physically linked within the genome. Concentrated genetic architecture (i.e., few quantitative trait loci, QTL, of large effect) has been predicted to evolve under a set of conditions that include, among other factors, higher rates of gene flow between diverging populations compared to conditions leading to more diffuse genetic architecture (i.e., many QTL of small effect, Yeaman and Whitlock 2011). We have previously found that the adaptive genetic markers were statistically linked (i.e. exhibited linkage disequilibrium within populations) and that allowed categorization of these markers into four groups of linked loci (groups A, B, C, and D; Hess et al. 2013). Now we can confirm that groups previously characterized as A, B, C, and D loci (Hess et al. 2015; Parker et al. 2019) localize to chromosomes 02, 04, 22, and 01, respectively, out of a total of 83 chromosomes characterized. Further, we observed that several of these chromosomes have one or more inversion alleles that distinguish the species from a non-inverted state (based on sea lamprey), and appear polymorphic within the species (based on alignments between male and female Pacific lamprey genome assemblies). These inversions appear to coincide with the adaptive SNPs identified asF ST outliers, particularly for the cases of chromosome 01 and 04, which suggests that polymorphic inversions may play an important role in the adaptation of Pacific lamprey to local environments. Since recombination is highly reduced, the fitness conferred by these inverted haplotypes can help maintain them as a polymorphism in a population through both forces of balancing and divergent selection (Wellenreuther and Bernatchez 2018; Faria et al. 2019; Pearse et al. 2019).