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Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles

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ABSTRACT

Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

No MeSH data available.


Phylogenetic trees based on Bayesian analyses of 16 selected genes.Trees were rooted with the most distant outgroup available for each marker. Posterior probabilities are given to the left of the nodes. Sequences of D. ponderosae (ToDen00) were obtained from GenBank.
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pone.0163529.g003: Phylogenetic trees based on Bayesian analyses of 16 selected genes.Trees were rooted with the most distant outgroup available for each marker. Posterior probabilities are given to the left of the nodes. Sequences of D. ponderosae (ToDen00) were obtained from GenBank.

Mentions: Single gene analyses resulted in partially resolved phylogenies, mainly recovering a monophyletic Scolytinae, the majority of the predefined subgroups of Scolytinae (A-B-C-D), and the subfamily Platypodinae (Fig 3). All selected genes enabled the correct reconstruction of the most recent clade (A), with 3 genes obtaining the correct sister group (B). None of the selected genes showed high degree of incongruence that received high node support. Overall mean divergence in nucleotide sequences was reported for each codon position for each gene (S3 Fig).


Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles
Phylogenetic trees based on Bayesian analyses of 16 selected genes.Trees were rooted with the most distant outgroup available for each marker. Posterior probabilities are given to the left of the nodes. Sequences of D. ponderosae (ToDen00) were obtained from GenBank.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036811&req=5

pone.0163529.g003: Phylogenetic trees based on Bayesian analyses of 16 selected genes.Trees were rooted with the most distant outgroup available for each marker. Posterior probabilities are given to the left of the nodes. Sequences of D. ponderosae (ToDen00) were obtained from GenBank.
Mentions: Single gene analyses resulted in partially resolved phylogenies, mainly recovering a monophyletic Scolytinae, the majority of the predefined subgroups of Scolytinae (A-B-C-D), and the subfamily Platypodinae (Fig 3). All selected genes enabled the correct reconstruction of the most recent clade (A), with 3 genes obtaining the correct sister group (B). None of the selected genes showed high degree of incongruence that received high node support. Overall mean divergence in nucleotide sequences was reported for each codon position for each gene (S3 Fig).

View Article: PubMed Central - PubMed

ABSTRACT

Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

No MeSH data available.