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

Eytan RI, Evans BR, Dornburg A, Lemmon AR, Lemmon EM, Wainwright PC, Near TJ - BMC Evol. Biol. (2015)

Bottom Line: 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.Although 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA. eytanr@tamug.edu.

ABSTRACT

Background: The 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.

Results: After 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.

Conclusions: Although 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.

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Concatenated phylogeny inferred using the CAT Bayesian mixture model, implemented in PhyloBayes. Shapes and colored circles represent the posterior probability for a given node. Higher-level named clades are noted. Note that Pseudochromidae is a clade, with good support
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Fig5: Concatenated phylogeny inferred using the CAT Bayesian mixture model, implemented in PhyloBayes. Shapes and colored circles represent the posterior probability for a given node. Higher-level named clades are noted. Note that Pseudochromidae is a clade, with good support

Mentions: Partitioning by codon had a much lower AIC score than partitioning by gene (Δ AIC = 38907). The average bootstrap support for the concatenated analyses differed among the partitioning schemes, ranging between 83 % and 76 % (Table 4). Partitioning by gene had the highest average bootstrap support, while phylogenetic analysis of the amino acid translation was lowest. The MP-EST analysis had an average bootstrap support of 69 %. The trees inferred from the full datasets, as well as the species tree, had poor support for the backbone of the phylogeny, with most bootstrap values being less than or close to 50 % (Figs. 2, 3, 4 and 6, Additional file 3: Table S3, Additional file 4: Figure S1, and Additional file 5: Figure S2). However, there were sets of clades that were consistently resolved with high support in all the trees including Ovalentaria, monophyly of cichlids and Pholidichthys, the Atherinomorpha, the bleniimorphs, the Blenniiformes, and the Pomacentridae (damselfishes). How these clades relate to one another, or to the other taxa in the analysis was not resolved, as there was very low bootstrap support for nearly all of the other nodes in the tree (Figs. 2, 3, 4 and 6; Additional file 3: Table S3, Additional file 4: Figure S1, and Additional file 5: Figure S2). This included the Pseudochromidae (dottybacks), which did not form a clade when using the full matrix datasets or the species tree analysis, but was resolved as monophyletic in the phylogenies inferred from the dataset with the 3rd codon positions removed and in the tree resulting from analysis of the amino acid matrices, albeit all with poor support (Figs. 3 and 4, and Additional file 5: Figure S2). However, the tree inferred using PhyloBayes provided strong support for this clade (Fig. 5).Table 4


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

Eytan RI, Evans BR, Dornburg A, Lemmon AR, Lemmon EM, Wainwright PC, Near TJ - BMC Evol. Biol. (2015)

Concatenated phylogeny inferred using the CAT Bayesian mixture model, implemented in PhyloBayes. Shapes and colored circles represent the posterior probability for a given node. Higher-level named clades are noted. Note that Pseudochromidae is a clade, with good support
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4465735&req=5

Fig5: Concatenated phylogeny inferred using the CAT Bayesian mixture model, implemented in PhyloBayes. Shapes and colored circles represent the posterior probability for a given node. Higher-level named clades are noted. Note that Pseudochromidae is a clade, with good support
Mentions: Partitioning by codon had a much lower AIC score than partitioning by gene (Δ AIC = 38907). The average bootstrap support for the concatenated analyses differed among the partitioning schemes, ranging between 83 % and 76 % (Table 4). Partitioning by gene had the highest average bootstrap support, while phylogenetic analysis of the amino acid translation was lowest. The MP-EST analysis had an average bootstrap support of 69 %. The trees inferred from the full datasets, as well as the species tree, had poor support for the backbone of the phylogeny, with most bootstrap values being less than or close to 50 % (Figs. 2, 3, 4 and 6, Additional file 3: Table S3, Additional file 4: Figure S1, and Additional file 5: Figure S2). However, there were sets of clades that were consistently resolved with high support in all the trees including Ovalentaria, monophyly of cichlids and Pholidichthys, the Atherinomorpha, the bleniimorphs, the Blenniiformes, and the Pomacentridae (damselfishes). How these clades relate to one another, or to the other taxa in the analysis was not resolved, as there was very low bootstrap support for nearly all of the other nodes in the tree (Figs. 2, 3, 4 and 6; Additional file 3: Table S3, Additional file 4: Figure S1, and Additional file 5: Figure S2). This included the Pseudochromidae (dottybacks), which did not form a clade when using the full matrix datasets or the species tree analysis, but was resolved as monophyletic in the phylogenies inferred from the dataset with the 3rd codon positions removed and in the tree resulting from analysis of the amino acid matrices, albeit all with poor support (Figs. 3 and 4, and Additional file 5: Figure S2). However, the tree inferred using PhyloBayes provided strong support for this clade (Fig. 5).Table 4

Bottom Line: 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.Although 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA. eytanr@tamug.edu.

ABSTRACT

Background: The 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.

Results: After 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.

Conclusions: Although 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.

Show MeSH