Comparative Genomics and Positive selection analyses
To identify genes associated with adaptation to a pelagic lifestyle in
the Procellariiformes, we performed a positive selection analysis across
12 species including eight Procellariiformes species applying the HyPhy
aBSREL model. We identified the hallmark of positive selection in 20
(out of the 6,172 single-copy orthologs genes), after correcting for
multiple testing (Table S5). The enriched GO analysis uncovered terms
related with striated muscle cell differentiation, nutrient reservoir
activity, response to starvation, visual learning, positive regulation
of neural retina development, olfactory receptor activity or natriuresis
(Table S6). We also performed an analysis to assess the global impact of
natural selection in Procellariformes (both positive and negative
selection), which uncovered a total of 310 genes (Table S7). The GO
terms enriched in these genes include wound healing, response to
wounding, inflammatory response, sensory perception of sound, smell and
chemical stimulus, neurological system process, defense response,
response to stress, camera-type eye development, renal system and
chloride transport among others (Table S8).
Using OrthoFinder 2.3.8, we identified 182,487 N:N orthogroups across
all genes identified in the 12 analysed genomes. This data, together
with the estimated ultrametric tree, was used to estimate gene gains,
losses, and number of genes in the ancestral nodes using BadiRate; for
the analysis we selected the Free Rates (FR) model, since it was the
best fitted branch model. The analysis was conducted including all
orthogroups, and the minimum number of gains and losses per branch is
represented in Figure 3. Our analysis showed a tendency to gain genes in
Procellariiformes (+442/-34), while the branch leading to albatrosses
(Diomedeidae) showed an opposite effect, with a noticeable loss of genes
(+464/-3258); the branch leading to the rest of the Procellariiformes
(+379/-15) is in the line of the general behavior of the tubenoses
(Table S9). Within the order, families Oceanitidae and Hydrobatidae
present the same trend, with the branch leading to H. thethyspresenting a stronger gene loss balance (+325/-966) than the branch
leading to the ancestor of Oceanitidae (O. oceanicus and F.
grallaria (+182/-414)).
We identified three gene families significantly expanded in the branch
leading to the Procellariiformes (Table S9). These families encode zinc
finger proteins (OG0000000), olfactory receptors (OG0000084) and avian
histones (OG0000224).