Details on the covariates and ways in which loci were used taking population structure and relatedness into account in the GLM and MLM tests:
Equations for the GLM and MLM are described in the TASSEL manual (Bradbury et al. 2007). A kinship matrix using the ‘scaled IBS’ method (Endelman et al. 2012) based on 76 vetted neutral SNPs (the neutral SNPs that overlap the 85 neutral SNPs characterized by Hesset al. 2015) was generated in TASSEL to represent cryptic familial relationships. The MLM was implemented using default options, i.e. ‘P3D’ (Zhang et al. 2010) parameter option and the ‘optimum compression’ option. The GLM effectively represents a ‘maximum compression’ option, and thus provides contrast to the MLM. Permutation tests (1000) were used to calculate P -values to determine significant associations of SNPs with traits. The association tests using a GLM were performed with covariates of population structure. For population structure, the first 3 Principal Coordinate (PC) axes of the 76 neutral SNPs were used. Datasets were also analyzed using an MLM, and the kinship matrix was included as an additional covariate. In all datasets except for GAR, the GLM was a better fit to the data based on the fact that most of the neutral loci aligned closer to the 1:1 line on the Q-Q plot; therefore, reported P-values were generated exclusively from the GLM.
Phenotypic traits measured for association testing
  1. Willamette (“WFA”) Falls 2016 adult Pacific lamprey were split into separate analyses for a group of males (N=136) and females (N=133) collected as part of the tribal harvest. The following six traits were measured: ordinal “day” of arrival, girth, total “length”, weight, “gonad” weight, and distance between dorsal fins (“dorsal”). Willamette Falls is 205.6 Rkm upstream from the Columbia River mouth.
  2. Total (“T_BON”) sample of Bonneville Dam adult Pacific lamprey in 2014 was measured with six traits: Ordinal day, length, weight, dorsal, girth, and upstream migration distant (“Rkm”) (N=883). Bonneville Dam is 235.1 Rkm upstream of the Columbia River mouth.
  3. Swimming (“S_BON”) trials of Bonneville Dam adult Pacific lamprey were a subset (N=295) of the fish included in the T_BON sample, and included 3 swimming behavioral trait categories, in addition to the 6 traits: Ordinal day, length, weight, dorsal, girth, and upstream migration distant (“Rkm”). Swimming trial traits were measured from previous work (Kirk et al. 2016), and included 3 swimming behavioral trait categories: approached experiment (“approached”), passed challenge (“pass”), and passed challenge without fallback (“passrep”). The “approached” category refers to those that approached vs . did not approach the flume, which was a possible indicator of motivation. The “passed” category refers to those that approached and passed the swimming challenge compared to those that approached and did not pass the challenge, which was the major descriptor of performance and success (Kirk et al. 2016). Finally, the “passrep” category refers to a subset of fish that approached and passed the challenge, and unlike others that passed the challenge, they did not fall back downstream of the challenge. In summary, “approach” indicates motivation, “pass” indicates motivation + performance and “passreq” indicates motivation, performance and perseverance.
  4. Sample of John Day Dam (“JDD”) adult Pacific lamprey with 6 traits: Ordinal day, length, weight, dorsal, girth, and upstream migration distant (“Rkm”) (N=656). Year and Translocation status were used as covariates. John Day Dam is 346.9 Rkm upstream of the Columbia River mouth. Most of the fish were translocated upstream to Ice Harbor Dam (N = 571, 537.7 Rkm) in both years (2014, 2015), and a portion (N=85) were released at John Day Dam in 2014.
  5. Common garden experiment using artificial propagation of larval Pacific lamprey with early larval growth (“GAR”) rate data (N=334). Traits of growth rate were calculated as: (length / time), and a corrected growth rate (“growth rate_b”) was calculated as: [(length - 4mm) / time] to correct for length at hatch (~4 mm). The MLM that used a kinship matrix as a covariate was a better fit to the data as compared to the GLM, and so the P-values generated by the MLM were used for all downstream analysis.