@article{hickner_sim_luecke_bailey_saelao_yusseff-vanegas_corpuz_bodine_bendele_quintero_et al._2026, title={Haplotype-resolved genome assemblies for the New World screwworm, <i>Cochliomyia hominivorax</i> (Diptera: Calliphoridae), using the trio binning approach}, volume={2}, DOI={10.1093/g3journal/jkag053}, abstractNote={The New World screwworm, Cochliomyia hominivorax, is an obligate parasite of warm-blooded animals and a major pest of livestock and wildlife in the Americas. The first genome assembly for C. hominivorax enabled substantial progress in key areas including gene expression related to fly behavior and physiology and gene editing technologies. However, the first genome was sequenced prior to several technological advances that result in fewer errors and better genome annotations. Here, we used the trio-binning approach to produce haplotype-resolved genome assemblies of C. hominivorax. A single male progeny from the cross of a Panama line male with a production strain female was sequenced using PacBio HiFi and scaffolded using Hi-C chromatin conformation, while Illumina NextSeq 2000 was used for short read sequencing of both parents to facilitate trio-binning. We produced a linear haploid reference assembly by transferring a copy of the X chromosome and mitochondrial genome to the paternal haplotype. This assembly is comprised of five autosomes, two sex chromosomes, the mitogenome, and 75 unplaced scaffolds spanning 455.6 Mb, which is closer to the predicted size based on flow cytometry (443.8 Mb) than the previous assembly of 534.4 Mb. NCBI's external Eukaryotic Genome Annotation Pipeline (EGAPx) was used to annotate the protein coding and non-coding genes in the linear haploid reference and the maternal haplotype assemblies. Due to the better resolution of the sex chromosomes and updated genome annotations, these improved assemblies will advance future experiments aimed at understanding sex determination, gene expression, and the evolution of parasitism in the Calliphoridae.}, journal={G3 Genes Genomes Genetics}, author={Hickner, Paul V and Sim, Sheina B and Luecke, David and Bailey, Ezra and Saelao, Perot and Yusseff-Vanegas, Sohath Z and Corpuz, Renee L and Bodine, Deanna and Bendele, Kylie G and Quintero, Gladys and et al.}, year={2026}, month={Feb} }
 @article{bailey_michelsen_cassel_szpila_bayless_grzywacz_powell_pape_wiegmann_2026, title={Phylogenomics of Anthomyiidae and a revised classification of Scathophagidae (Diptera: Calyptratae)}, volume={1}, DOI={10.5061/dryad.nk98sf876}, abstractNote={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.).}, journal={DRYAD}, author={Bailey, Ezra and Michelsen, Verner and Cassel, Brian and Szpila, Krzysztof and Bayless, Keith and Grzywacz, Andrzej and Powell, Gareth and Pape, Thomas and Wiegmann, Brian}, year={2026}, month={Jan} }
 @article{beza‐beza_soghigian_bailey_johnston_cassel_bayless_wells_yeates_wallman_yan_et al._2025, title={Phylogenomics and the evolution of larval feeding habits in the blow flies (Diptera: Calliphoridae)}, DOI={10.1111/syen.70018}, abstractNote={Abstract Blow flies (Diptera: Calliphoridae) occur worldwide and exhibit a wide range of larval feeding habits, including saprophagy, coprophagy, parasitism and predation. Understanding their biology is critical for medical and veterinary science and ecology. Calliphorids thrive across a range of habitats and exhibit complex life histories, with larvae developing immersed in their food substrate, while adults are free‐living and have diverse feeding strategies. Some species have evolved specialized parasitic associations with vertebrate or invertebrate hosts, which are behaviors with important implications for agriculture and for understanding evolutionary transitions between saprophagy and parasitism. This study presents a comprehensive phylogenetic analysis of the Calliphoridae, utilizing 711 of 736 analysed nuclear genes, using anchored hybrid enrichment, from a global collection of blow flies and their relatives. Our results provide a robust and novel reconstruction of the evolutionary history of this group, pinpointing major transitions in larval feeding habits. We argue that saprophagy evolved independently multiple times from invertebrate parasitic ancestors, with vertebrate parasitism emerging from a number of different feeding strategies. These findings challenge prior hypotheses and offer new insights into the adaptive traits driving trophic specialization and diversification in this group.}, journal={Systematic Entomology}, author={Beza‐Beza, Cristian F. and Soghigian, John and Bailey, Ezra and Johnston, Nikolas P. and Cassel, Brian K. and Bayless, Keith M. and Wells, Jeffrey D. and Yeates, David K. and Wallman, James F. and Yan, Liping and et al.}, year={2025}, month={Dec} }