Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

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.

Resolving Cypriniformes relationships using an anchored enrichment approach

“…Although the Anchored Hybrid Enrichment kit developed for vertebrates by Lemmon et al [36] contains a fish reference ( Danio ) and has been utilized in teleosts with moderate success [41], we desired an enrichment tool more efficient and appropriate for phylogenomics in teleosts. Because of the complex nature of teleost genome evolution, which involved multiple whole-genome duplications and lineage-specific gene losses [42], it is impractical to identify a set of loci that are truly single-copy across all of Teleostei.…”

“…Multilocus sequence data were collected at the Center for Anchored Phylogenomics at Florida State University (www.anchoredphylogeny.com) following Lemmon et al [41] with some adjustments. Each genomic DNA sample was sonicated to a fragment size of ~175–300 bp using a Covaris E220 Focused-ultrasonicator with Covaris microTUBES.…”

Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

“…Bi et al, 2012;Kawahara & Breinholt, 2014;Misof et al, 2014;Kjer et al, 2015;Lei & Dong, 2016) or target enrichment (e.g. Faircloth et al, 2012;Lemmon et al, 2012;Smith et al, 2014;Brandley et al, 2015;Eytan et al, 2015;Prum et al, 2015;Hamilton et al, 2016;Young et al, 2016;Breinholt et al, 2017), to generate large-scale phylogenomic datasets for use in phylogeny reconstruction, particularly in groups for which relationships have been difficult to resolve using smaller samples of molecular data (see Lemmon & Lemmon, 2013 for a review of alternative approaches). WGS produces the most data, but is the most expensive of these approaches and also carries a high bioinformatic and computational burden.…”

“…Anchored Hybrid Enrichment (AHE) is a relatively recent approach for hybrid enrichment that is now being used rather widely in phylogenomic studies of vertebrates (e.g. Brandley et al, 2015;Eytan et al, 2015;Prum et al, 2015) and most recently invertebrates (Diptera: Young et al, 2016;Arachnida: Hamilton et al, 2016;Lepidoptera: Breinholt et al, 2017). It is a fast and cost-efficient method for enriching hundreds of a priori targeted loci for use in phylogeny reconstruction.…”

Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish: Proof of concept for key components of the insulin-like growth factor axis

“…In this respect, a particularly effective approach has been to capture extremely-conserved regions within the genome (e.g. Lemmon et al, 2012;Faircloth et al, 2012;Eytan et al, 2015;Prum et al, 2015). Moreover, with modifications to the stringency of hybridization, sequence capture can be used to obtain even highlydistant homologous sequences of interest (e.g.…”