DOI: 10.5061/dryad.7b19f33
title: Data from: A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies.

description: 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 &gt;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.
description: Straube_et_al_829_DNA_loci_19092018.tar829 Single DNA loci used for phylogenetic reconstructions.Straube_et_al_PartitionFinder_results.tarBest partitioning schemes from PartitionFider and PartitionFinderProtein analyses.Straube_et_al_MARE_output.tarSvg graphical output and list of phylogentically most informative loci based on results of MARE.Straube_et_al_Script_collection_analysis_pipeline.tarPerl script collection for target capture NGS data analyses.