Phylogeny and tribal classification of Australian Prioninae (Coleoptera: Cerambycidae)
Data files
Sep 28, 2023 version files 4.18 MB
Abstract
We applied whole genome shotgun sequencing to museum specimens of longhorn beetles and reconstructed the phylogenetic relationships of Australian Prioninae using mitochondrial protein-coding genes. Based on the molecular phylogeny and morphological characters, we suggest downgrading the subfamily Parandrinae Blanchard to the tribe Parandrini in the Prioninae Latreille and synonymise Erichsoniini Thomson with Parandrini Blanchard. Australian Prioninae are classified in seven tribes: Catypnini Lacordaire stat. rev., Mocrotomini Thomson, Osphryonini trib. nov., Parandrini Blanchard, Rhipidocerini trib. nov., Sceleocanthini Lacordaire stat. rev., and Tereticini Lameere. Tribal compositions and generic relationships are tested, and the subtribal divisions within the large tribe Macrotomini are briefly discussed.
README: Phylogeny and tribal classification of Australian Prioninae (Coleoptera: Cerambycidae)
https://doi.org/10.5061/dryad.3bk3j9kr6
Description of the data and file structure
This data package contains the sequence alignments and phylogenetic trees from Jin et al., Phylogeny and tribal classification of Australian Prioninae (Coleoptera: Cerambycidae), Annales zoologici, (Warsaw), 2023, 73(3), 499-512.
Corresponding author: Mengjie Jin; jinmengj@mail2.sysu.edu.cn; mengjie.jin@csiro.au (CSIRO)
All files including:
- Samples been sequenced in this study: AppendixS1_sample info.xlsx;
- Alignment files of 13 mitochondrial protein-coding genes(used to generate phylogenies): AppendixS4_NTalignment.nex (concatenated alignment of nucleotides);
- Maximum likelihood phylogenies from IQ-TREE2 v2.0.3 (http://www.iqtree.org/): AppendixS2_treefile.Prioninae.aa.bs200.tre (Newick-format tree from amino acid dataset, partitioned by gene position);
- AppendixS3_treefile.Prioninae.nt.bs200.tre (Newick-format tree from nucleotide dataset, partitioned by gene position).
All files edited for Dryad were initially uploaded on 17 Aug 2023, README_file.txt was uploaded on 17 Aug 2023 and updated on 28 Sep 2023. AppendixS1_sample info.xlsx was edited on 28 Sep 2023 for adding on GenBank Accession IDs.
Sharing/Access information
NCBI GenBank Accession IDs for all sequences that are used for phylogenetic reconstructions are provided in AppendixS1 and can be retrieved from https://www.ncbi.nlm.nih.gov/genbank/ accordingly.
Methods
A total of 174 pinned specumens (57 from Australia and 117 from outside Australia) were sampled for this study. DNA was extracted from leg tissue using the DNeasy 96 Blood and Tissue Kit protocol (Qiagen) and measured with a Qubit fluorometer (Thermo Fisher). Libraries were prepared following the QIAseq FX DNA Library Kit protocol (Qiagen) with one-thrid reaction volumes. The sample DNA was fragmented with the FX Enhancer for 15 minutes, and a right-side size selection was performed at the adaptor ligation cleanup stage. Samples were triple-indexed using custom adapters based on standard Illumina TruSeq UDI adaptors. Individual libraries were pooled equally and sequenced on a NovaSeq6000 S1 with 150 bp PE at the Biomolecular Resource Facility, Australian National University.
Sequencing raw reads were trimmed by Trimmomatic v.0.36 and de novo assembled using Spades v.3.11.1. Putative mitochondrial (mt) contigs were recognized using BLAST and a reference dataset containing 25 complete mt-genomes of Australian prionines, then blasted against NCBI GenBank and against each other to remove contaminants. mt-PCGs were annotated based on references and extracted accordingly, aligned at the translated amino acid level using Muscle and concatenated to a final supermatrix. Final nucleotide sequence (NT) and amino acid sequence (AA) alignments were partitioned by gene positions and analysed in ModelFinder with +MERGE option. Phylogenetic relationships were inferred under Maximum Likelihood criterion in IQTREE2 v.2.0.3. We performed 20 independent tree searches for AA and NT datasets, respectively, and selected the tree with the best likelihood score. Nodal support values were estimated using the slow standard nonparametric bootstrap in IQ-TREE2 with 200 replicates.