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
- 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.
- 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.
- 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.
- 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.
- 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.