Abstract
BackgroundThe past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be.ResultsAfter using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree.ConclusionsAlthough it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0415-0) contains supplementary material, which is available to authorized users.
Highlights
The past decade has witnessed remarkable progress towards resolution of the Tree of Life
The phylogenetic analyses of more than 100 loci to infer the relationships of the acanthomorph teleost clade Ovalentaria demonstrates that some, but not all, lineages connected by short internodes may avoid resolution under certain analytical conditions
After accounting for paralogous gene copies and attempting to minimize missing data, we had substantially fewer loci than the 512 that were targeted. This was not unexpected given the long divergence time between Ovalentaria and the model teleost used in this first version of the anchored hybrid enrichment method (AHE) capture kit, as well as the teleost-specific whole genome duplication event
Summary
The past decade has witnessed remarkable progress towards resolution of the Tree of Life. Most phylogenetic studies with comprehensive taxon sampling that use large DNA sequence datasets continue to exhibit several shallow and deep nodes in the phylogeny that remain poorly resolved [9,10,11]. Phylogenomic datasets provide resolution to both shallow [16] and deep [23] phylogenetic relationships by employing different classes of markers, dependent on the time scale of divergence among the lineages in a particular study (see [24] for a review). This flexibility in phylogenomic data sampling strategies allows investigators to collect DNA sequence data that facilitates the simultaneous resolution of both shallow and deep phylogenetic divergences
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
