DOI: 10.5061/dryad.nk98sf876
title: Phylogenomics of Anthomyiidae and a revised classification of Scathophagidae (Diptera: Calyptratae)

description: The Anthomyiidae have been recovered as paraphyletic with regard to the
 Scathophagidae in several recent molecular analyses and need resolution.
 We address this issue by producing a robust phylogeny of the family
 Anthomyiidae, based on a broad sampling of anthomyiid genera and over 300
 single-copy orthologous loci captured using anchored hybrid enrichment
 (AHE). Most notably, the phylogenomic analyses provide strong support that
 family rank for Scathophagidae renders Anthomyiidae paraphyletic. We
 propose a revised classification with a basal Coenosopsiinae Bailey
 & Michelsen (subfam. nov.), including the Neotropical Phaonantho
 Albuquerque and the Neotropical and southern Nearctic Coenosopsia Malloch,
 which emerge as sister taxa and together comprise one of the two earliest
 diverging clades; a Hyporitinae (stat. rev.) including Hyporites Pokorny
 and the predatory genus Alliopsis Schnabl & Dziedzicki; and a
 Scathophaginae (stat. rev.) relegated to subfamily rank within
 Anthomyiidae which includes the former subfamilies Scathophaginae and
 Delininae as tribes Scathophagini (stat. rev.) and Delinini (stat. rev.).
description: # Phylogenomics of Anthomyiidae and a revised classification of
 Scathophagidae (Diptera: Calyptratae) Dataset DOI:
 [10.5061/dryad.nk98sf876](https://doi.org/10.5061/dryad.nk98sf876) ##
 Description of the data and file structure This repository includes
 assemblies of genomic data, individual models for all loci, and final
 treefiles. ### Files and variables #### File:
 anthofinal.raxml_partition.aa.txt.best_scheme **Description:** Individual
 models for all loci in amino acid dataset. #### File:
 anthofinal.raxml_partition.dna.txt.best_scheme **Description:** Individual
 models for all loci in nucleotide dataset. #### File:
 Anthomyiidae_AA.newick **Description:** Final treefile in amino acid
 dataset. #### File: Anthomyiidae_DNA.newick **Description:** Final
 treefile in nucleotide dataset. #### Sequence Files: | Sequence File Name
 | Species Name | | :----------------- | :--------------------------- | |
 aalbi | *Alliopsis billbergi* | | aalsiRG | *Alliopsis silvestris* | |
 aanli | *Botanophila discreta* | | aanmo | *Anthomyia monilis* | | aanpr |
 *Anthomyia procellaris* | | aboap | *Botanophila apiceta* | | abobi |
 *Botanophila biciliaris* | | abobr | *Botanophila brunneilinea* | | abodi
 | *Botanophila discreta* | | abola | *Botanophila laterella* | | abost |
 *Botanophila striolata* | | achab | *Chirosia aberrans* | | achal |
 *Chirosia albitarsis* | | achci | *Chirosia cinerosa* | | achdeRG |
 *Chiastocheta dentifera* | | achfl | *Chirosia flavipennis* | | achse |
 *Chiastocheta setifera* | | achtr | *Chiastocheta trollii* | | acoesp |
 *Coenosopsia* sp. | | adefl | *Delia florilega* | | adefr | *Delia
 frontella* | | adeli | *Delia linearis* | | aegci | *Egle ciliata* | |
 aegrh | *Egle rhinotmeta* | | aemgr2 | *Emmesomyia grissea* | | aeuhil |
 *Eustalomyia hilaris* | | aeupi2 | *Eutrichota pilimana* | | afute2 |
 *Fucellia tergina* | | ahenoRG | *Heterostylodes nominabilis* | | ahyla |
 *Hydrophoria lancifer* | | ahyliRG | *Hydrophoria linogrisea* | | ahypa |
 *Hylemyza partita* | | ahyru | *Hydrophoria ruralis* | | ahysi |
 *Hydrophoria silvicola* | | ahyur | *Hylemya urbica* | | ahyvag | *Hylemya
 vagans* | | alapi | *Lasiomma picipes* | | aleobRG | *Leucophora obtusa* |
 | alepe | *Leucophora personata* | | apaau | *Paregle audacula* | | apeae
 | *Pegoplata aestiva* | | apefl | *Pegomyia flavifrons* | | apein |
 *Pegoplata infirma* | | apeni | *Pegoplata nigroscutellata* | | apevi |
 *Pegomya vittigera* | | aphbe | *Phaonantho benevola* | | aphcu | *Phorbia
 curvicauda* | | aphfu | *Phorbia fumigata* | | aphge | *Phorbia genitalis*
 | | aphme | *Phorbia fumigata* | | azaamRG | *Zaphne ambigua* | | azaca |
 *Zaphne caudata* | | azadi | *Zaphne divisa* | | KEIB\_00835 | *Stomoxys
 calcitrans* | | KEIB\_00978 | *Neomyia cornicina* | | KEIB\_00982 |
 *Mesembrina meridiana* | | KEIB\_01132 | *Muscina stabulans* | | Sc1 |
 *Peratomyia vittata* | | Sc2 | *Cordilura* sp. 1 | | Sc3RG | *Nanna* sp. |
 | Sc5RG | *Orthacheta* sp. 1 | | Sc7 | *Orthacheta* sp. 2 | | sc4 |
 *Scathophaga stercoraria* | ## Code/software All workflow to assemble
 sequences, select models per loci, and reconstruct phylogenetic trees as
 is described in Beza‐Beza, Cristian F., et al. "Phylogenomics and the
 evolution of larval feeding habits in the blow flies (Diptera:
 Calliphoridae)." Systematic Entomology (2025)