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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: 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.

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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Number of nodes out of the total nodes in the maximum likelihood-inferred phylogenies supported with different bootstrap proportions as more data was added to the analyses
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Fig9: Number of nodes out of the total nodes in the maximum likelihood-inferred phylogenies supported with different bootstrap proportions as more data was added to the analyses

Mentions: When looking at the rarefaction curves, the average global bootstrap support value started at 64 % and slowly increased as more loci were added, plateauing at 78–80 % once 35 loci were included (Fig. 7). Bootstrap support for monophyly of cichlids, atherinomorphs, and Blenniimorpha was over 90 % with the inclusion of five loci and reached 100 % when ten loci were sampled. Bootstrap support for the clade containing Pholidicthys and cichlids and monophyly of Blenniiformes increased as loci were added and both nodes were supported with 100 % bootstrap scores once 55 loci were included (Fig. 7). Support for a monophyletic Pseudochromidae was low when few loci were included and decreased to zero once 30 loci were added. Similarly, support for a clade containing gobiesocids and tripterygiids (triplefin blennies) quickly went to zero as more loci were included. The rarefaction curve that tracked number of nodes with bootstrap values appeared to reach a plateau, although the number of nodes with greater than 50 % bootstrap support was not stable (Fig. 8). The number of nodes with greater than 70 % and 90 % bootstrap support plateaued with the inclusion of 30 loci, although there was a slight uptick in the 70 % and 90 % nodes when all 107 loci were included (Fig. 9).Fig. 7


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)

Number of nodes out of the total nodes in the maximum likelihood-inferred phylogenies supported with different bootstrap proportions as more data was added to the analyses
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig9: Number of nodes out of the total nodes in the maximum likelihood-inferred phylogenies supported with different bootstrap proportions as more data was added to the analyses
Mentions: When looking at the rarefaction curves, the average global bootstrap support value started at 64 % and slowly increased as more loci were added, plateauing at 78–80 % once 35 loci were included (Fig. 7). Bootstrap support for monophyly of cichlids, atherinomorphs, and Blenniimorpha was over 90 % with the inclusion of five loci and reached 100 % when ten loci were sampled. Bootstrap support for the clade containing Pholidicthys and cichlids and monophyly of Blenniiformes increased as loci were added and both nodes were supported with 100 % bootstrap scores once 55 loci were included (Fig. 7). Support for a monophyletic Pseudochromidae was low when few loci were included and decreased to zero once 30 loci were added. Similarly, support for a clade containing gobiesocids and tripterygiids (triplefin blennies) quickly went to zero as more loci were included. The rarefaction curve that tracked number of nodes with bootstrap values appeared to reach a plateau, although the number of nodes with greater than 50 % bootstrap support was not stable (Fig. 8). The number of nodes with greater than 70 % and 90 % bootstrap support plateaued with the inclusion of 30 loci, although there was a slight uptick in the 70 % and 90 % nodes when all 107 loci were included (Fig. 9).Fig. 7

Bottom Line: 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.

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
Related in: MedlinePlus