Phylogenomics-based click-beetle classification tackles multiple origins of phenotypic modifications

Click beetles (Elateridae) have garnered scientific interest due to their diversity, bioluminescence, and ontogenetic modifications. However, their classification is still poorly resolved. Here, we explore the internal relationships by analyzing 46 tribes and ~4,200 orthologs. We classify elaterids into 17 subfamilies and 52 tribes. We propose new ranks for Protelaterinae stat. nov., Thylacosternini stat. nov. (Lissominae), Semiotina stat. nov. (Dendrometrini), and Aplastini stat. nov. (Elaterinae). We resurrect Drapetini stat. nov. (Lissominae), Pachyderini stat. nov. (Agrypninae), and Corymbitina stat. nov. (Dendrometrini). and synonymize Pomachiliini syn. nov., and Synaptini syn. nov. to Agriotini and Quasimusini syn. nov. to Negastriini. Hypnoidinae retains its subfamily rank, regardless of its documented affinities to Dendrometrinae. Our research provides a phylogenomic framework for unde..., For references, see the final manuscript!
Material and Methods
Data Collection, Assembly, and Processing
Whole genome sequencing (WGS) and transcriptomic (TSA) data were explicitly generated for this study to enhance the coverage of principal lineages (42% of taxa). Some genomic data were sourced from previous large-scale phylogenies and other genomic studies (4% of taxa; (Amaral et al., 2019; Fallon et al., 2018; McKenna et al., 2019). This was supplemented by newly assembled data from primary anchored hybrid enrichment (AHE) reads published by Douglas et al. (Douglas et al., 2021) (Table 1, S1). The AHE data were newly processed following the methods of Kusy et al. (2019, 2021). Raw reads were trimmed using fastp (parameters: -q 15 -u 40 -n 5 -l 50) and assembled using IDBA-UD (parameters: --step 5 --maxk 120). This approach substantially increased the volume of information compared to the earlier published dataset. Six polyphagan outgroup taxa were selected to root the tree (Table S1..., # Phylogenomics-based click-beetle classification tackles multiple origins of phenotypic modifications

Dataset DOI: [10.5061/dryad.xksn02vts](10.5061/dryad.xksn02vts)

## Description of the data and file structure

Data description

Format of the data

XX_YY.ZZZZ

X - data type AA or NT

Y - genes tested by SymTest; SG - genes not rejected or SB genes rejected by SymTest

Z - file type: .PART for partition file or .FAS for matrix

### Files and variables

#### File: NT_SB.part

Description:  Partition file for SymTest refused genes at nucleotide level.

#### File: NT_SG.part

Description: Partition file for SymTest valid genes at nucleotide level.

#### File: NT_SB.fasta

Description: Fasta with with SymTest refused genes at nucleotide level.

#### File: AA_SB.part

Description: Partition file for SymTest refused genes at amino acid level.

#### File: AA_SB.fasta

Description:  Fasta with with SymTest refused genes at amino acid level.

#### File: AA_SG.part

Description: Partition fil...,