DOI: 10.5061/dryad.7d7wm3864
title: Data from: A new phylogeny of <em>Anastrepha</em> (Diptera: Tephritidae) based on nuclear loci obtained by phylogenomic methods

description: Phylogenetic alignments, datasets, and tree files from anchored hybrid
 enrichment (AHE) from Norrbom et al. for Anastrepha true fruit flies
 (Diptera: Tephritidae). The data sets include sequences from 293
 (DS1) and 1110 (DS2) aligned orthologous loci sampled for 735
 sampled specimens, with 728 identified as representatives of 237
 species. Multiple sequence alignments were inferred using the
 program MAFFT. Phylogenetic data sets are formatted for use in IQTree2 and
 were used to reconstruct phylogenetic trees depicted in Figures 1 and 2,
 S1, S2 ,and S3 in the manuscript. This study presents a comprehensive
 phylogenetic analysis of the genus Anastrepha, utilizing anchored hybrid
 enrichment to sample hundreds of nuclear genes from a global collection of
 their diversity. Our results provide a robust and novel reconstruction of
 the evolutionary history of this group, allowing a better resolution of
 their lineages and a revised classification in species groups.
description: # Data from: A new phylogeny of *Anastrepha* (Diptera: Tephritidae) based
 on nuclear loci obtained by phylogenomic methods Dataset DOI:
 [10.5061/dryad.7d7wm3864](10.5061/dryad.7d7wm3864) \[article doi pending
 acceptance in *Systematic Entomology*] ## Description of the data and file
 structure: 1. The zip file “Indiviual_Locus_Alignments.zip“ contains
 multiple sequence alignments (MSAs) for all of the orthologous gene loci
 used in the study. Subfiles included here: “DS1_loci” includes the
 individual locus alignments used to construct concatenated phylogenetic
 data set 1 (DS1); “DS2_loci” includes the individual locus alignments used
 to construct concatenated phylogenetic data set 2. 2.
 AnastrephaNames_LabCodes_2025_08_02.csv: The CSV file containing lab codes
 and their associated taxonomic names, collection localities, and specimen
 data used in the multiple sequence alignments (MSAs) and phylogenetic data
 sets. Each row in the data set includes the specimen labcode (used in
 alignments and trees as taxon identifier codes) and its associated
 metadata descriptor in the form of
 SpeciesGroupIdentifier_speciesNameIdentifier_localityCode_SpecimenIdentificationCode. 3. DS1_Anastrepha_dipkit90424_final.dna.phy: The concatenated alignment referred to as data set 1 (DS1) that was used for the phylogenetic reconstruction depicted in Figures 1 and 2. 4. DS1_Anastrepha_dipkit9042.partition.dna.txt.best_scheme.nex: The gene locus partitions and associated models corresponding to positions in the concatenated data set 1(DS1) used for phylogenetic analysis and model testing in IQTree2. 5. DS2_Anastrepha_AllLoci50pct_90424_final.dna.phy: The concatenated alignment referred to as data set 2 (DS2) that was used for the phylogenetic reconstruction depicted in Figures S1. 6. DS2_final.raxml_partition.dna.txt: This text file contains a list of the gene locus partitions corresponding to nucleotide positions in the concatenated data set 2 (DS2) used for phylogenetic analysis and model testing in IQTree2. Each line of the file is in the form "DNA, GeneLocusIdentifier nucleotide = nt position range in DS2". Example, DNA, sco_38052at7203 = 1-402. 7. AnastrephaDipKit90pruneApr24.tree: Maximum likelihood topology tree file and branch lengths from IQTree2 in Newick format depicted in Figures 1 and 2 and Figure S1. 8. Anastrepha_PrunedDipKit90april24_AstralNT_species.tre: Astral tree topology tree file and support values in Newick format depicted in Figure S2. 9. “AnastrephaAllLoci50pctJul24.tree”: Maximum likelihood topology tree file and branch lengths from IQTree2 in Newick format depicted in Figure S3 10. “Anastrepha_GeneTrees_for_DS1_Loci.zip”: The zip file includes all individual locus tree files calculated in RaXml-NG used in the coalescent-based Astral tree of figure S2.