Phylogenetic relationships
OrthoFinder analysis estimated 6,172 single copy (1:1) ortholog genes
across the 12 genomes surveyed. With this data we generated three
supermatrices: 1) CDS supermatrix of 10,534,506 bp long to extract the
4D sites, 2) 4D supermatrix with 1,512,677 4-fold degenerate sites, and
3) the amino acid supermatrix including 3,466,564 sites. Phylogenetic
analyses using the 4D and the amino acid supermatrices recovered the
same topology with full support at all nodes (ultrafast bootstrap = 100;
Figures S2 and S3).
The analysis performed to explicitly account for incomplete lineage
sorting (ILS) with ASTRAL using either the individual gene sequences
(CDS gene trees) or the individual amino acid sequences (amino acid gene
trees), produced species trees with the same topology as those obtained
by ML using 4D or amino acid supermatrices (Figures S4 and Figure S5).
The normalized quartet score (proportion of input gene tree quartet
trees in agreement with the species tree) was 0.78 for CDS gene trees
and 0.64 for amino acid gene trees.
The ultrametric tree (Figure 3) obtained using r8s from the 4D
supermatrix ML tree summarizes the recovered topology. In this topology,
the Atlantic yellow-nosed albatross (T. chlororhynchos ,
Diomedeidae) is the sister group to all the other Procellariiformes. We
also find that storm petrels (Hydrobatidae and Oceanitidae) do not
constitute a monophyletic group. In addition, diving petrels
(Pelecanoides ) are included within Procellariidae.