DOI: 10.5281/zenodo.18347967
title: Time-Calibrated Phylogenies of Hemiptera

description: Time-Calibrated Phylogenies of Hemiptera Using BEAST 2

This repository contains all input files and outputs used to infer time-calibrated phylogenetic trees based on mitochondrial and nuclear data using BEAST v2.6.3.

Contents:





BEAST_time_trees_zenodo.tar.gz: full BEAST analyses including XML input files, .log parameter traces, .trees outputs, consensus trees, and visualizations (PDF, SVG, PNG).



BEAST_time_trees/├── mitochondrial/│ ├── runs/ # Individual BEAST runs (XML, log, .trees)│ ├── concatenated/ # Consensus trees and common ancestor heights│ └── figures/ # PDF, SVG, PNG visualizations of trees│├── nuclear/│ ├── runs/ # Individual BEAST runs (XML, log, .trees)│ ├── concatenated/ # Consensus trees and common ancestor heights│ └── figures/ # PDF, SVG, PNG visualizations of trees





mito_sequences.fasta: aligned mitochondrial sequences used for BEAST analyses (41 species, 18,818 bp).




nucl_sequences.fasta: aligned nuclear sequences used for BEAST analyses (51 BUSCO genes, 36,639 bp, 44 species).



 

Datasets



Mitochondrial dataset: mitochondrial sequences from publicly available assemblies, supplemented with sequences from our own species.



41 species in total 

Alignment length: 18,818 bp 

23 outgroups from public databases  

18 Rhodnius species from Filée et al. 2022 and Merle et al. submitted  






Nuclear dataset: 51 BUSCO coding genes (36.3 kb) from publicly available genomes and our own assemblies 



44 species in total 

Alignment length: 36,639 bp 

24 from public databases including Rhodnius prolixus reference (Mesquita et al., 2015)  

20 Rhodnius species from Filée et al. 2022 and Merle et al. submitted  




Accession numbers of sequences used from public databases

The table below lists all sequences retrieved from public databases that were used as outgroups or references in the analyses.

 

  Taxa            Species                        mitochondrial ID    genome ID            |--------------|--------------------------------|-----------------|-----------------------|| Aleyrodoidea | Bemisia tabaci                 | MH714535.1      | GCF_001854935.1       || Aleyrodoidea | Trialeurodes vaporariorum      | AY521265.2      | GCA_011764245.1       || Aphididae    | Acyrthosiphon pisum            | NC_011594.1     | GCF_005508785.1       || Aphididae    | Aphis gossypii                 | MK994521.1      | GCF_004010815.1       || Aphididae    | Cinara cedri                   | -               | GCA_902439185.1       || Aphididae    | Therioaphis tenera             | MH643885.1      | -                     || Blattodea    | Blattella germanica            | EU854321.1      | GCA_003018175.1       || Blattodea    | Coptotermes formosanus         | NC_015800.1     | GCA_013340265.1       || Blattodea    | Cryptotermes secundus          | KP026283.1      | GCF_002891405.2       || Blattodea    | Periplaneta americana          | GU947663.1      | GCA_002939525.1       || Blattodea    | Zootermopsis nevadensis        | KJ958410.1      | GCF_000696155.1       || Cimicoidea   | Cimex lectularius              | JQ739180.1      | GCF_000648675.2       || Cimicoidea   | Orius laevigatus               | -               | GCA_018703685.1       || Cimicoidea   | Orius sauteri                  | KJ671626.1      | -                     || Cimicoidea   | Gorpis humeralis               | JF927830.1      | -                     || Miridae      | Apolygus lucorum               | KU234539.1      | GCA_009739505.2       || Miridae      | Cyrtorhinus lividipennis       | -               | GCA_019603395.1       || Miridae      | Nesidiocoris tenuis            | JQ806057.1      | GCA_902806785.1       || Miridae      | Pachypeltis micranthus         | -               | GCA_020466155.1       || Miridae      | Trigonotylus caelestialium     | KJ170899.1      | -                     || Miridae      | Adelphocoris lineolatus        | KJ020286.1      | -                     || Pentatomidae | Aelia acuminata                | OU426986.1      | GCA_911387785.1       || Pentatomidae | Euschistus heros               | MG253270.1      | GCA_003667255.1       || Pentatomidae | Halyomorpha halys              | FJ685650.1      | GCF_000696795.2       || Pentatomidae | Stiretrus anchorago            | -               | GCA_010014745.1       || Pentatomidae | Picromerus lewisi              | MW355499.1      | -                     || Triatomini   | Panstrongylus lignarius        | -               | PRJNA395235.fa        || Triatomini   | Panstrongylus rufotuberculatus | MF614953.1      | -                     || Triatomini   | Triatoma brasilliensis         | -               | -                     || Triatomini   | Triatoma infestans             | KY640305.1      | GCA_011037195.1       || Triatomini   | Triatoma rubrofasciata         | MH934953.1      | Triatoma_chr_assembly |

BEAST Analyses



Clock model: Lognormal relaxed clock  

Tree prior: Birth-Death Incomplete Sampling  

Calibration: 7 fossil calibration points (see Supplementary Table 3)  

Runs: 6 independent runs per dataset  

Generations: 10,000,000 per run, sampled every 1,000 generations  

Burn-in: 25%  

All other settings were default in BEAUti 2.6.3  


Each independent run includes the XML input file, the `.log` of parameter traces, and the `.trees` output. Consensus trees were generated from concatenated runs using TreeAnnotator.

Notes

- Only publicly available sequences and our own assemblies were used.  - HPC-specific scripts and temporary files have been removed. All necessary parameters are included in the XML files.  - This repository contains all files required to reproduce the BEAST analyses and the resulting trees.  

Citation

If you use these data, please cite the associated publication.