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Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera)

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Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera) https://t.co/zCBuQqPus2
PJpreprint: Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera) https://t.co/EDrL4FuxIY
Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera) https://t.co/nFoFfIoxS1
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Supplemental Information

Voucher specimen information

Data regarding voucher specimen collection dates and localities and repositories.

DOI: 10.7287/peerj.preprints.27329v1/supp-1

Data file used in final phylogeny and divergence time estimation analyses

Nexus file of alined sequences used for analyses.

DOI: 10.7287/peerj.preprints.27329v1/supp-2

Table S1. Taxonomic and Genetic Sampling

Taxonomic and Genetic Sampling. Exemplars used from Deans et al. (2006) are listed with the reference from that paper (Deans ID) beside the internal voucher number (Extract ID). Included genes for each taxon are marked with an x. Gene codes: 28S for 28S rDNA; AM2 for alpha-mannosidase II; CAD1 and CAD2 for carbamoyl-phosphate sythetase-asparate transcarbamoylase-dihydroorotase (CAD) (for amplicon regions for each segment, see Figure 1); RPS23 for Ribosomal Protein S23; COI for cytochrome oxidase I; and 16S for 16S rDNA

DOI: 10.7287/peerj.preprints.27329v1/supp-3

Primers and PCR protocols used in this study

For protein-coding genes, the Primer Name is based off the amino acid position in the Apis mellifera CDS for that gene. An Alternate Primer Name is given if a different name was used in a previously published study or in-house.

DOI: 10.7287/peerj.preprints.27329v1/supp-4

Average nucleotide composition (%) across genes

Highlighted genes indicate that the test for base composition homogeneity across taxa was falsified. Statistics are provided below the table.

DOI: 10.7287/peerj.preprints.27329v1/supp-5

Recovered clades across individual genes and concatenated analyses (All genes)

Monophyletic clades are marked with an x, which is shaded grey if the posterior probability was 0.95 or greater. N/A indicates that there was a missing taxon so the clade could not be recovered. A “C” preceding a taxon name in a cell indicates that a congruent clade was recovered even though the indicated taxon was missing. Taxon Abbreviations are as follows: Mic (Micrevania); Bra (Brachygaster); Pro (Prosevania); Tri (Trissevania); Eva (Evania); Zeu (Zeuxevania); Par (Parevania); CEv (Evaniscus); Dec (Decevania); Sem (Semaeomyia); Hyp (Hyptia); Alo (Alobevania); LEv (Evaniella); Sze (Szepligetella); Aca (Acanthinevania).

DOI: 10.7287/peerj.preprints.27329v1/supp-6

Individual gene trees

Bayesian analysis of each gene individually for Evaniidae. Posterior probabilities are listed beside each node

DOI: 10.7287/peerj.preprints.27329v1/supp-7

Sequence motifs

Figures that illustrate the unique sequence motifs (RPS23 and 28S rDNA) for certain lineages of Evaniidae

DOI: 10.7287/peerj.preprints.27329v1/supp-8

Estimated divergence times for Evaniidae under a normal distribution

Posterior probabilities are listed beside the relevant node. The 95% HDP for all clades is listed in Table 2. The scale is in millions of years.

DOI: 10.7287/peerj.preprints.27329v1/supp-9

Figure Maximum Likelihood results

Maximum Likelihood analyses of the concatenated dataset. Bootstrap values are listed beside each node.

DOI: 10.7287/peerj.preprints.27329v1/supp-10

Fossil calibration points and references

Fossil calibration points and references for the divergence time estimation analyses.

DOI: 10.7287/peerj.preprints.27329v1/supp-11

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Barbara J Sharanowski conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Leanne Peixoto analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper.

Anamaria Dal Molin analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper.

Andrew R Deans conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Sequences described here are accessible via GenBank accession numbers KY082187 to KY082565.

Data Deposition

The following information was supplied regarding data availability:

Relevant input files for all analyses are available through Penn State's ScholarSphere repository (https://scholarsphere.psu.edu): https://doi.org/10.18113/S1D06H (collection of alignment and other input files)

Funding

This material is based on work supported by the U.S. National Science Foundation (grant numbers DBI-0850223, DEB-0842289, DEB-0956049, and EF0905606). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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