Limits...
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.


Phylogentic informativeness profiles.The K2P model was used to estimate substitution rates in HyPhy as implemented in the software PhyDesign. Different evolutionary models produced similar results (data not shown). The dated phylogenetic tree was obtained using BEAST v1.8.2.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5036811&req=5

pone.0163529.g004: Phylogentic informativeness profiles.The K2P model was used to estimate substitution rates in HyPhy as implemented in the software PhyDesign. Different evolutionary models produced similar results (data not shown). The dated phylogenetic tree was obtained using BEAST v1.8.2.

Mentions: Phylogenetic informativeness (PI) profiles varied considerably between the selected markers, showing different degrees of signal across the more than 100 Ma of weevil evolutionary history (Fig 4). The net PI values showed a marked decline for all markers towards the Cretaceous era. Iap2 displayed the highest PI peak in recent times, followed by four other markers with lower PI profiles (TPI, Prp1 and Arr2, FEN1). The gene EF2 showed a diverse profile, having lower PI for recent times but relatively more PI than FEN1 and Arr2 at more ancient times. PABP1, which presented the highest homoplasy level among the selected genes (S3 Table), showed an intermediate PI profile, following the same trend of Hsp70, Cda4, CCNC and almost identical to UBA5. Cda4 and CCNC showed higher PI in recent times while Hsp70 maintained marginally higher PI for ancient times. The gene with the lowest PI value was SOD1. Four markers (HDAC Rpd3, ADA2, RCC1 and CTR9) were not included in the analysis due to missing data.


Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles
Phylogentic informativeness profiles.The K2P model was used to estimate substitution rates in HyPhy as implemented in the software PhyDesign. Different evolutionary models produced similar results (data not shown). The dated phylogenetic tree was obtained using BEAST v1.8.2.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163529.g004: Phylogentic informativeness profiles.The K2P model was used to estimate substitution rates in HyPhy as implemented in the software PhyDesign. Different evolutionary models produced similar results (data not shown). The dated phylogenetic tree was obtained using BEAST v1.8.2.
Mentions: Phylogenetic informativeness (PI) profiles varied considerably between the selected markers, showing different degrees of signal across the more than 100 Ma of weevil evolutionary history (Fig 4). The net PI values showed a marked decline for all markers towards the Cretaceous era. Iap2 displayed the highest PI peak in recent times, followed by four other markers with lower PI profiles (TPI, Prp1 and Arr2, FEN1). The gene EF2 showed a diverse profile, having lower PI for recent times but relatively more PI than FEN1 and Arr2 at more ancient times. PABP1, which presented the highest homoplasy level among the selected genes (S3 Table), showed an intermediate PI profile, following the same trend of Hsp70, Cda4, CCNC and almost identical to UBA5. Cda4 and CCNC showed higher PI in recent times while Hsp70 maintained marginally higher PI for ancient times. The gene with the lowest PI value was SOD1. Four markers (HDAC Rpd3, ADA2, RCC1 and CTR9) were not included in the analysis due to missing data.

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.