Abstract
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our 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.
Highlights
Phylogenomic datasets comprising hundreds to thousands of genome segments produced through high throughput sequencing technology have shown promise to resolve difficult phylogenetic problems (e.g., Faircloth et al, 2013; Faircloth et al, 2012; Gilbert et al, 2015; Harrington et al, 2016; Lemmon & Lemmon, 2013)
Following orthology assessment and filtering for loci not present in 31 of 34 Operational Taxonomic Units (OTUs), the dataset is composed of a total of 53 UCE loci, 17,957 characters, 9,576 distinct alignment patterns and 22.11% gaps or missing data
The two approaches implemented in this study indicate large areas of congruence in topology resolving several relationships within early-branching euteleost relationships
Summary
Phylogenomic datasets comprising hundreds to thousands of genome segments produced through high throughput sequencing technology have shown promise to resolve difficult phylogenetic problems (e.g., Faircloth et al, 2013; Faircloth et al, 2012; Gilbert et al, 2015; Harrington et al, 2016; Lemmon & Lemmon, 2013). Novel and refined inference tools including implementations of the multispecies coalescent model to address incomplete lineage sorting (ILS) through Gene Trees-to-Species Tree (GT-ST) methods (Knowles & Kubatko, 2011) continue to extend the power and complexity of phylogenetic research. Despite these advances in genomic-scale dataset production and phylogenetic inference, difficult areas of the tree of life remain unresolved (Delsuc, Brinkmann & Philippe, 2005; Pyron, 2015; Rokas & Carroll, 2006). Subsequent phylogenetic studies of mitochondrial (e.g., López, Chen & Ortí, 2004; Lavoué et al, 2008) and nuclear DNA (e.g., Betancur-R et al, 2013; Near et al, 2012) supported a monophyletic Euteleostei including esocoids but excluding Ostariophysi and the Alepocephaliformes (previously classified in Argentiniformes nested in the Euteleostei)
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