Data from: A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies.

Background: Previous molecular studies on the phylogeny and classification
of clupeocephalan fishes revealed numerous new taxonomic entities. For
re-analysing these taxa on a phylogenomic scale, we perform target gene
capturing and subsequent next generation sequencing of putative ortholog
exons of major clupeocephalan lineages. Sequence information for the RNA
bait design was derived from publicly available genomes of bony fishes.
Newly acquired sequence data comprising >800 exon sequences was
subsequently used for phylogenetic reconstructions. Results: Our results
support monophyletic Otomorpha comprising Alepocephaliformes. Within
Ostariophysi, Gonorynchiformes are sister to a clade comprising
Cypriniformes, Characiformes, Siluriformes and Gymnotiformes, where the
interrelationships of Characiformes, Siluriformes and Gymnotiformes remain
enigmatic. Euteleosts comprise four major clades: Lepidogalaxiiformes,
Protacanthopterygii, Stomiatii, and Galaxiiformes plus Neoteleostei. The
monotypic Lepidogalaxiiformes form the sister-group to all remaining
euteleosts. Protacanthopterygii, comprising Argentini-, Esoci- and
Salmoniformes, is sister to Stomiatii (Osmeriformes and Stomiatiformes)
and Galaxiiformes plus Neoteleostei. Conclusions: Several proposed
monophyla defined by morphological apomorphies within the Clupeocephalan
phylogeny are confirmed by the phylogenetic estimates presented herein.
However, other morphologically described groups cannot be reconciled with
molecular phylogenies. Thus, numerous morphological apomoprhies of
supposed monophyla are called into question. The interpretation of
suggested morphological synapomorphies of otomorph fishes is strongly
affected by the inclusion of deep-sea inhabiting, and to that effect
morphologically adapted Alepocephaliformes. Our revision of these
potential synapomorphies, in the context that Alepocephaliformes are
otomorph fishes, reveal that only a single character of the total nine
characters proposed as synapomorphic for the group is clearly valid for
all otomorphs. Two further characters associated to the swim bladder
remain possible apomorphies, as their status could not be evaluated, since
Alepocephaliformes do not have this structure. Further, our analysis
places Galaxiiformes as sister group to neoteleosts, which contradicts
some previous molecular phylogenetic studies. This needs further
investigation from a morphological perspective, as suggested synapomophies
for several euteleostean lineages are challenged or still lacking. For the
verification of results presented herein, a denser phylogenomic-level
taxon sampling should be applied.