Description
Time-Calibrated Phylogenies of Hemiptera Using BEAST 2This 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.Scripts are available at: https://github.com/marieblackbird/phylo_busco_concat 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 treesmito_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). DatasetsMitochondrial 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 databasesThe 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 AnalysesClock 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. CitationIf you use these data, please cite the associated publication.