Potential gene-interaction effects
To identify potential gene-gene interactions across the four primary
adaptive chromosomes related to body size and maturity we conducted
Generalized Multifactor Dimensionality Reduction (GMDR). Analyses were
conducted for maturity using adult females from the WFA♀ (N=133) data
set and for total length using the WFA♀ and T_BON (N=883) data sets. We
used the software GMDR version 0.9 (Lou et al. 2007; Chen 2011) to
conduct an exhaustive search for all possible one to four locus models.
The best model was defined as the model with the maximal
cross-validation consistency. For additional details on GMDR and
analysis methods see Parker et al. (2019).
Results
The gene-interaction analysis using GMDR for egg mass in the WFA♀
collection identified Etr_464 (chromosome 1) as the best single-locus
model (Table S10). However, this model was only identified in 6 of the
10 training data sets, indicating limited support. Additionally,
cross-validation accuracy for higher order models (two-locus 4/10;
three-locus 3/10; four-locus 2/10) indicated the lack of support for
gene combinations associated with egg mass. This result contrasts with
Parker et al. (2019) who found evidence for a two-locus interaction
model including chromosomes 1 and 4 for egg mass in Klamath River
collections of Pacific lamprey. The discrepancy may be explained by the
differences in collections of Pacific lamprey that have recently
initiated their freshwater migration (Parker et al. 2019) versus
collection of individuals further upstream (herein). The latter data set
likely contains a mixture of current year and hold-over individuals
whereas the former contained only current year migrants.
For total length, the GMDR produced different results depending upon the
data set (Table S10). The gene-interaction analysis for WFA♀ collection
produced support for a single-locus model including Etr_1806
(Chromosome 4) with cross-validation accuracy (10/10) and testing
balance accuracy (77%). Higher order models with more loci were not
supported. In contrast, for T_BON the model with maximal
cross-validation accuracy (10/10) and highest testing balance accuracy
(73%) was a three-locus interaction model (Table S10). The testing
balance accuracy for the one-locus model (Etr_5317/Chromosome 2) was
67%. A 5% increase in testing balanced accuracy was realized in a
two-locus interaction model (72%) that included Etr_5317/Chromosome 2
and Etr_1806/Chromosome 4. However, only a 1% increase was observed in
the three-locus interaction model (73%), which included
Etr_5317/Chromosome 2, Etr_1806/Chromosome 4, and Etr_4281/Chromosome
22. Models involving four loci had considerably lower cross validation
accuracy (3/10) indicating lack of support. Under the best three-locus
model, if Etr_5317 = AA and Etr_1806 = AA and Etr_4281 = AA, or if
Etr_5317 = AA and Etr_1806 = AA and Etr_4281 = AT then individuals
are classified as large body size whereas all other genotype
combinations are classified as small body size. Classifying T_BON
individuals using these methods produces a mean total length for large
body size of 681 mm and for small body size of 632 mm. The analysis of
Parker et al. (2019) also suggested support for a two-locus interaction
model for total length involving chromosomes 2 and 4.
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