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

  title={A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies},
  author={Nicolas Straube and Chenhong Li and Matthias Mertzen and Hao Yuan and Timo Moritz},
  journal={BMC Evolutionary Biology},
BackgroundPrevious molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, 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… 
Anatomical revision of the Australian teleosts Cavenderichthys talbragarensis and Waldmanichthys koonwarri impacting on previous phylogenetic interpretations of teleostean relationships
  • L. Bean, G. Arratia
  • Environmental Science
    Alcheringa: An Australasian Journal of Palaeontology
  • 2019
The new results suggest that the three Gondwanan genera are stem taxa to the Osteoglossocephala (osteoglosomorphs plus more advanced teleosts), and their combination of morphological characters has a major effect on the interpretation of basal euteleosts, questioning some previous interpretations.
Musculotendinous system of mesopelagic fishes: Stomiiformes (Teleostei)
The posterior most myosepta of the dragonfishes are equipped for a multisegmental force transmission towards the caudal fin, which indicates that this unique anatomical condition might be essential for steady swimming during diel vertical migrations, when prey is rarely available.
Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal
High-throughput DNA sequencing techniques are used to generate mitochondrial genomes of P. oxyrhynchus, and a temporal phylogenetic analysis suggests a single marine dispersal event between New Zealand and Australia, though the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance.
An Oligocene Tubeshoulder (Teleostei, Alepocephaliformes) from the Central Paratethys (Czech Republic): The First Skeletal Record for the Family Platytroctidae
The morphological analysis of the specimen reveals a series of features that unambiguously support its recognition as a new member of the alepocephaliform family Platytroctidae.
Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics
It is shown that loci with known paralogs are at risk of assembling duplicated sequences with target-capture, but it is also shown that useful orthologous sequences can be assembled from raw reads to alignments for downstream analysis.
Unexpected diversity of median caudal cartilages in teleosts
It seems that median caudal cartilages seem to have evolved at the base of clupeocephalans and occur in many taxa up to about aulopiforms, as well as single beryciforms and may have re-evolved in some taxa.
Exon capture - principle and applications to phylogenomics and population genomics of fishes
The advancement of shifting from single-gene method to genomic approach and the benefit of applying exon capture method comparing to alternative genomic techniques are shown and detailed recommendations for applying this method are provided.
The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
The analysis reveals the value of model validation and comparison in phylogenomic data analysis, as well as the need for further improvements of multilocus models and computational tools for phylogenetic inference.
The accessory neural arch: development, morphology, and systematic distribution
Although the accessory neural arch cannot be homologous between several teleostean taxa, the concept of parallelism may explain the presence of such a similar character in a variety of non-acanthomorph teleostorean taxa.


The phylogenetic position of an undescribed paedomorphic clupeiform taxon: mitogenomic evidence
The complete mitogenome of a remarkable undescribed marine paedomorphic clupeiform fish was sequenced to gain insight into its phylogenetic position and resulted in a strong placement within the order Clupeiformes, suborder Clupeoidei, and the family Clupeidae.
Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation
The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans.
Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences
The results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.
The origin and early diversification of this clade is reexamine based on a comprehensive time‐calibrated, molecular‐based phylogenetic analysis and event‐based approaches for ancestral range inference of lineages, which demonstrate Siluriformes is never sister to Gymnotiformes and Characiformes are most likely nonmonophyletic.
The varasichthyid and other crossognathiform fishes, and the Break-up of Pangaea
Abstract Crossognathiforms have been traditionally considered typical marine Cretaceous forms widely represented in the Northern Hemisphere and by a few members in Brazil. During the last 30 years
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
A practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny is presented and is an improvement over traditional approaches because it uses genomic information and automates the process to identify large numbers of candidate makers.