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

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.


Schematic tree showing well supported relationships between tribes within the subfamily Scolytinae and other weevil families and subfamilies considered in this study.
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pone.0163529.g001: Schematic tree showing well supported relationships between tribes within the subfamily Scolytinae and other weevil families and subfamilies considered in this study.

Mentions: An indirect measure of the phylogenetic signal in each marker was assessed through topological congruence with previously well documented clades [5–7, 10, 11, 68] which were used to derive a scheme of the current classification of Curculionoidea (Fig 1). These clades belong to six tribes of Scolytinae (A = Dryocoetini including Xyleborini, B = Ipini, C = Hylurgini + Hylesinini, D = Scolytini) and the subfamily Platypodinae (E). Rooting of the trees was dependent on the sequences available, and used in the following order: 1) Brentidae, 2) Platypodinae, 3) Cossoninae, Molytinae and Lixinae, 4) Scolytini [5, 6].


Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles
Schematic tree showing well supported relationships between tribes within the subfamily Scolytinae and other weevil families and subfamilies considered in this study.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163529.g001: Schematic tree showing well supported relationships between tribes within the subfamily Scolytinae and other weevil families and subfamilies considered in this study.
Mentions: An indirect measure of the phylogenetic signal in each marker was assessed through topological congruence with previously well documented clades [5–7, 10, 11, 68] which were used to derive a scheme of the current classification of Curculionoidea (Fig 1). These clades belong to six tribes of Scolytinae (A = Dryocoetini including Xyleborini, B = Ipini, C = Hylurgini + Hylesinini, D = Scolytini) and the subfamily Platypodinae (E). Rooting of the trees was dependent on the sequences available, and used in the following order: 1) Brentidae, 2) Platypodinae, 3) Cossoninae, Molytinae and Lixinae, 4) Scolytini [5, 6].

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.