Parallelism in DE gene identity and expression direction between
lineages
To ask whether parallel phenotypic changes across independent lineages
rely on shared gene expression changes, we evaluated overlap in DE
transcript identity and expression direction between the Aripo and Quare
lineage datasets. We used chi-square tests of independence to test for
greater than chance overlap between drainages in those gene sets
differentially expressed based on rearing environment or population of
origin within drainages, as well as to test for biases in
concordant versus non-concordant expression between drainages. We
performed two additional comparisons to address potential bias in our
conclusions due to high false negative rates in gene expression data
(Rice, Schork, & Rao, 2008). First, we performed the same analysis as
before at two less stringent p-value cut-offs (p=0.1 and 0.2). Second,
for comparisons of expression direction, we made an additional, more
conservative comparison by including not only those genes differentially
expressed in both drainages (i.e. the intersection of DE gene
lists), but also those differentially expressed in eitherdrainage (i.e. the union of DE gene lists) in the analysis. We again
used log-fold expression differences to call gene expression as being in
the same/concordant or opposite/non-concordant direction between
drainages.
We also performed one addition comparison to assess parallelism in a
subset of the population DE genes likely to arise from selection rather
than other evolutionary processes, such as drift. We identified to those
genes mostly likely to have diverged by selection, rather than by drift,
by calculating PST (a measure of phenotypic divergence
between populations) from phenotypic variance components and comparing
it to published estimates of FST (a measure of neutral
genetic divergence between populations) for the focal populations, using
the method of Leinonen, Cano, Mäkinen, & Merilä (2006). For these
calculations, we made the conservative assumption that heritability
(h2 ) of transcript abundance = 0.5 as we have
done previously (Ghalambor et al., 2015), and obtained estimates of
within and between population variance from general linear mixed models
(see Supplemental Methods). We then restricted DE gene sets in both
lineages to those in which PST >
FST and compared the number of overlapping genes and
their relative expression direction using chi-square tests as above. We
used FST estimates for our focal populations (Aripo =
0.225; Quare = 0.340) reported by Willing et al. (2010).