Phylogenomic insights into the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha)

Planthoppers (Hemiptera: Fulgoromorpha) are a species-rich and globally distributed insect clade with high economic, ecological, and evolutionary importance. However, the relationships among planthopper lineages and families remain unclear. Previous efforts based on inconsistent morphological traits, a few genes, or limited sampling often resulted in conflicting tree topologies. Here, we used genome-level data to assemble 1164 nuclear single-copy genes and 13 mitochondrial protein-coding genes for 149 planthopper species representing 19 out of 21 extant families. Additional markers were added from published mitogenomes, expanding our sampling to 285 species. These markers were used for Maximum Likelihood-based tree inference and dating analyses. The newly inferred phylogenies validated well-accepted relationships and recovered novel placements for several taxa, including the family Achilixiidae and species from the tribe Lyncidini and genus Madagascaritia in Dictyopharidae and Fulgorida..., Sample processing and metagenomic sequencing
Individuals of 151 planthopper species from 19 families were sampled ethically following all applicable international and local permitting requirements from their natural habitats around the world (Table S1). The remaining two established families, Gengidae and Hypochthonellidae, known only from limited specimens collected in southern Africa and, to our knowledge, with no molecular data published, are not included due to sampling difficulties. For all individuals, we extracted DNA from either the abdomen or bacteriome – an organ hosting symbiotic bacteria, using various DNA extraction kits (Table S1). Metagenomic libraries of each individual were prepared with NEBNext Ultra II DNA Library Prep Kit (BioLabs, New England) and sequenced on Illumina HiSeq 2500 in a Rapid Run mode (2x250bp), HiSeq X, or NovaSeq 6000 S4 (2x150bp reads) (Table S1). 
Single-copy nuclear gene assembly and multiple sequence alignment
We prepared the multiple sequence a..., , # Phylogenomic insights into the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha)

[https://doi.org/10.5061/dryad.3ffbg79sc](https://doi.org/10.5061/dryad.3ffbg79sc)

This data repository contains gene alignments and outputs from all phylogenomic analyses (tree inference and divergence time analysis) in Deng et al. (2024)

## Description of the data and file structure

### Supporting Information\_Data File S1. iqtree outputs from mitogenomes of 149 species

Files with the prefix **mtfulgo_149sp_wo3rd** are outputs based on DNA models. The gene alignments and partitions used for this run are **mtfulgo_nucl_149sp_final_wo3rd.phy** and **mtfulgo_nucl_149sp_final_wo3rd.nex**

Files with the prefix **mtfulgo_aa_149sp** are outputs based on protein models. The gene alignments and partitions used for this run are **mtfulgo_aa_149sp_final.phy** and **mtfulgo_aa_149sp_final.nex**

The gene alignments **WITH** the 3rd codon position are **mtfulgo_nucl_...