CoChat
Sign Up
Cited by 2Diptera species taxonomy and behaviorDevelopmental Biology and Gene RegulationGenomics and Phylogenetic Studies

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies

Open access
Mulhair, Peter O., Pennati, Alessandro, Herrera-Ubeda, Carlos, Holland, Peter W.H.·2025·Current Biology
DOI 10.1016/j.cub.2025.09.051

Published version of a preprint

Open this paper in CoChat — free account

Abstract

The specification of the anterior-posterior axis in the embryo is a crucial step in early insect development. Despite its importance, the underlying genetic and regulatory architecture controlling this process varies significantly between species. In cyclorrhaphan flies, such as Drosophila melanogaster, anterior determination is controlled by the transcription factor bicoid, which emerged through duplication of the ancestral Hox3 gene (called zen in insects). With new, high-quality genomic data, we mine the genomes of 186 dipteran species and find the presence of bicoid in non-cyclorrhaphan flies, including bee flies (family Bombyliidae) and stiletto flies (Therevidae). We confirm maternal expression and localization of the non-cyclorrhaphan bicoid mRNA to the anterior region of the unfertilized oocyte in the dark-edged bee fly, Bombylius major. To determine the timing and origin of bicoid, we address uncertainty in the dipteran phylogeny, uncovering a ladder-like topology in the branching orders of the early Brachycera lineages. This new species phylogeny suggests that bicoid emerged in the common ancestor of Bombyliidae, Asiloidea, and Eremoneura (collectively Heterodactyla) and was subsequently lost at least 16 times. These findings expand our understanding of early developmental processes in flies and provide new insights into the backbone phylogeny of Diptera and the evolution of bicoid.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.cub.2025.09.051

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 79

  1. Berleth, 1988, The role of localization of bicoid RNA in organizing the anterior pattern of the Drosophila embryo, EMBO J., 7, 1749, 10.1002/j.1460-2075.1988.tb03004.x · DOI
  2. Rivera-Pomar, 1996, RNA binding and translational suppression by bicoid, Nature, 379, 746, 10.1038/379746a0 · DOI
  3. McGregor, 2005, How to get ahead: the origin, evolution and function of bicoid, BioEssays, 27, 904, 10.1002/bies.20285 · DOI
  4. Porcher, 2010, The bicoid morphogen system, Curr. Biol., 20, R249, 10.1016/j.cub.2010.01.026 · DOI
  5. Huang, 2017, Decoding temporal interpretation of the morphogen Bicoid in the early Drosophila embryo, eLife, 6, 10.7554/eLife.26258 · DOI
  6. Holland, 2017, New genes from old: asymmetric divergence of gene duplicates and the evolution of development, Philos. Trans. R. Soc. Lond. B Biol. Sci., 372, 10.1098/rstb.2015.0480 · DOI
  7. Onal, 2021, Suboptimal intermediates underlie evolution of the Bicoid homeodomain, Mol. Biol. Evol., 38, 2179, 10.1093/molbev/msab051 · DOI
  8. Klomp, 2015, Embryo development. A cysteine-clamp gene drives embryo polarity in the midge Chironomus, Science, 348, 1040, 10.1126/science.aaa7105 · DOI
  9. Yoon, 2019, Embryo polarity in moth flies and mosquitoes relies on distinct old genes with localized transcript isoforms, eLife, 8, 10.7554/eLife.46711 · DOI
  10. Sommer, 1991, Segmentation gene expression in the housefly Musca domestica, Development, 113, 419, 10.1242/dev.113.2.419 · DOI
  11. Schröder, 1993, A comparison of transplantable bicoid activity and partial bicoid homeobox sequences in several Drosophila and blowfly species (Calliphoridae), Rouxs Arch. Dev. Biol., 203, 34, 10.1007/BF00539888 · DOI
  12. Stauber, 2002, A single Hox3 gene with composite bicoid and zerknüllt expression characteristics in non-Cyclorrhaphan flies, Proc. Natl. Acad. Sci. USA, 99, 274, 10.1073/pnas.012292899 · DOI
  13. Trovisco, 2016, bicoid mRNA localises to the Drosophila oocyte anterior by random Dynein-mediated transport and anchoring, eLife, 5, 10.7554/eLife.17537 · DOI
  14. Driever, 1988, A gradient of bicoid protein in Drosophila embryos, Cell, 54, 83, 10.1016/0092-8674(88)90182-1 · DOI
  15. Driever, 1989, Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen, Nature, 340, 363, 10.1038/340363a0 · DOI
  16. Struhl, 1989, The gradient morphogen bicoid is a concentration-dependent transcriptional activator, Cell, 57, 1259, 10.1016/0092-8674(89)90062-7 · DOI
  17. Chen, 2012, A system of repressor gradients spatially organizes the boundaries of Bicoid-dependent target genes, Cell, 149, 618, 10.1016/j.cell.2012.03.018 · DOI
  18. Frohnhöfer, 1986, Organization of anterior pattern in the Drosophila embryo by the maternal gene bicoid, Nature, 324, 120, 10.1038/324120a0 · DOI
  19. Stauber, 1999, The anterior determinant bicoid of Drosophila is a derived Hox class 3 gene, Proc. Natl. Acad. Sci. USA, 96, 3786, 10.1073/pnas.96.7.3786 · DOI
  20. Rafiqi, 2008, Evolutionary origin of the amnioserosa in cyclorrhaphan flies correlates with spatial and temporal expression changes of zen, Proc. Natl. Acad. Sci. USA, 105, 234, 10.1073/pnas.0709145105 · DOI
  21. Schmidt-Ott, 2022, How two extraembryonic epithelia became one: serosa and amnion features and functions of Drosophila’s amnioserosa, Philos. Trans. R. Soc. Lond. B Biol. Sci., 377, 10.1098/rstb.2021.0265 · DOI
  22. Panfilio, 2008, Extraembryonic development in insects and the acrobatics of blastokinesis, Dev. Biol., 313, 471, 10.1016/j.ydbio.2007.11.004 · DOI
  23. Lipshitz, 2000, Mechanisms of RNA localization and translational regulation, Curr. Opin. Genet. Dev., 10, 476, 10.1016/S0959-437X(00)00116-7 · DOI
  24. Niessing, 2000, Homeodomain position 54 specifies transcriptional versus translational control by Bicoid, Mol. Cell, 5, 395, 10.1016/S1097-2765(00)80434-7 · DOI
  25. Niessing, 2002, Bicoid associates with the 5′-cap-bound complex of caudal mRNA and represses translation, Genes Dev., 16, 2576, 10.1101/gad.240002 · DOI
  26. Liu, 2018, Ancient mechanisms for the evolution of the bicoid homeodomain’s function in fly development, eLife, 7, 10.7554/eLife.34594 · DOI
  27. Wiegmann, 2011, Episodic radiations in the fly tree of life, Proc. Natl. Acad. Sci. USA, 108, 5690, 10.1073/pnas.1012675108 · DOI · Paper page
  28. Shin, 2018, Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera), Syst. Entomol., 43, 277, 10.1111/syen.12275 · DOI
  29. Mulhair, 2023, Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera, Genome Res., 33, 32, 10.1101/gr.277118.122 · DOI
  30. Mulhair, 2024, Evolution of the insect Hox gene cluster: Comparative analysis across 243 species, Semin. Cell Dev. Biol., 152–153, 4, 10.1016/j.semcdb.2022.11.010 · DOI
  31. Wiegmann, 2003, Time flies, a new molecular time-scale for brachyceran fly evolution without a clock, Syst. Biol., 52, 745, 10.1080/10635150390250965 · DOI
  32. Yeates, 1999, Congruence and controversy: toward a higher-level phylogeny of Diptera, Annu. Rev. Entomol., 44, 397, 10.1146/annurev.ento.44.1.397 · DOI
  33. Yeates, 2002, Relationships of extant lower Brachycera (Diptera): a quantitative synthesis of morphological characters, Zool. Scr., 31, 105, 10.1046/j.0300-3256.2001.00077.x · DOI
  34. Lambkin, 2013, The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence, Syst. Entomol., 38, 164, 10.1111/j.1365-3113.2012.00652.x · DOI
  35. Simão, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351 · DOI · Paper page
  36. Mongiardino Koch, 2021, Phylogenomic subsampling and the search for phylogenetically reliable loci, Mol. Biol. Evol., 38, 4025, 10.1093/molbev/msab151 · DOI
  37. Mulhair, 2022, Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life, Curr. Biol., 32, 5180, 10.1016/j.cub.2022.10.036 · DOI
  38. Susko, 2021, Long Branch attraction biases in phylogenetics, Syst. Biol., 70, 838, 10.1093/sysbio/syab001 · DOI
  39. Steenwyk, 2023, Incongruence in the phylogenomics era, Nat. Rev. Genet., 24, 834, 10.1038/s41576-023-00620-x · DOI
  40. Trautwein, 2010, A multigene phylogeny of the fly superfamily Asiloidea (Insecta): Taxon sampling and additional genes reveal the sister-group to all higher flies (Cyclorrhapha), Mol. Phylogenet. Evol., 56, 918, 10.1016/j.ympev.2010.04.017 · DOI
  41. Ferguson, 2014, Ancient expansion of the hox cluster in lepidoptera generated four homeobox genes implicated in extra-embryonic tissue formation, PLoS Genet., 10, 10.1371/journal.pgen.1004698 · DOI
  42. Shen, 2020, An investigation of irreproducibility in maximum likelihood phylogenetic inference, Nat. Commun., 11, 10.1038/s41467-020-20005-6 · DOI
  43. Degnan, 2009, Gene tree discordance, phylogenetic inference and the multispecies coalescent, Trends Ecol. Evol., 24, 332, 10.1016/j.tree.2009.01.009 · DOI
  44. Lanfear, 2024, The meaning and measure of concordance factors in phylogenomics, Mol. Biol. Evol., 41, 10.1093/molbev/msae214 · DOI
  45. Kubatko, 2007, Inconsistency of phylogenetic estimates from concatenated data under coalescence, Syst. Biol., 56, 17, 10.1080/10635150601146041 · DOI
  46. Mendes, 2018, Why concatenation fails near the anomaly zone, Syst. Biol., 67, 158, 10.1093/sysbio/syx063 · DOI
  47. Wang, 2022, Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies, Zool. J. Linn. Soc., 194, 938, 10.1093/zoolinnean/zlab042 · DOI
  48. Song, 2022, Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences, Zool. J. Linn. Soc., 196, 720, 10.1093/zoolinnean/zlab125 · DOI
  49. Tihelka, 2021, The evolution of insect biodiversity, Curr. Biol., 31, R1299, 10.1016/j.cub.2021.08.057 · DOI
  50. Di Franco, 2022, Lower statistical support with larger data sets: Insights from the Ochrophyta radiation, Mol. Biol. Evol., 39, 10.1093/molbev/msab300 · DOI
  51. Narayanan Kutty, 2019, Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera, Cladistics, 35, 605, 10.1111/cla.12375 · DOI
  52. Bayless, 2021, Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics, BMC Biol., 19, 10.1186/s12915-020-00944-8 · DOI
  53. Soghigian, 2023, Phylogenomics reveals the history of host use in mosquitoes, Nat. Commun., 14, 10.1038/s41467-023-41764-y · DOI
  54. Kim, 2024, Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life, PLoS Biol., 22, 10.1371/journal.pbio.3002697 · DOI
  55. Trautwein, 2012, Advances in insect phylogeny at the dawn of the postgenomic era, Annu. Rev. Entomol., 57, 449, 10.1146/annurev-ento-120710-100538 · DOI
  56. O’Leary, 2024, Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets, Sci. Data, 11, 10.1038/s41597-024-03571-y · DOI
  57. Steinegger, 2017, MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets, Nat. Biotechnol., 35, 1026, 10.1038/nbt.3988 · DOI · Paper page
  58. Madeira, 2019, The EMBL-EBI search and sequence analysis tools APIs in 2019, Nucleic Acids Res., 47, W636, 10.1093/nar/gkz268 · DOI · Paper page
  59. Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010 · DOI · Paper page
  60. Capella-Gutiérrez, 2009, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, 25, 1972, 10.1093/bioinformatics/btp348 · DOI
  61. Minh, 2020, IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era, Mol. Biol. Evol., 37, 1530, 10.1093/molbev/msaa015 · DOI · Paper page
  62. Zhou, 2022, Ggmsa: A visual exploration tool for multiple sequence alignment and associated data, Brief. Bioinform., 23, 10.1093/bib/bbac222 · DOI
  63. Yu, 2017, Ggtree: An r package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods Ecol. Evol., 8, 28, 10.1111/2041-210X.12628 · DOI
  64. Lopez-deLisle, 2021, pyGenomeTracks: reproducible plots for multivariate genomic datasets, Bioinformatics, 37, 422, 10.1093/bioinformatics/btaa692 · DOI
  65. Pohl, 2014, bwtool: a tool for bigWig files, Bioinformatics, 30, 1618, 10.1093/bioinformatics/btu056 · DOI
  66. Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 · DOI · Paper page
  67. Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 · DOI · Paper page
  68. Steenwyk, 2020, ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference, PLoS Biol., 18, 10.1371/journal.pbio.3001007 · DOI
  69. Steenwyk, 2021, PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data, Bioinformatics, 37, 2325, 10.1093/bioinformatics/btab096 · DOI
  70. Mirarab, 2014, ASTRAL: genome-scale coalescent-based species tree estimation, Bioinformatics, 30, i541, 10.1093/bioinformatics/btu462 · DOI
  71. Eaton, 2020, Toytree: A minimalist tree visualization and manipulation library for Python, Methods Ecol. Evol., 11, 187, 10.1111/2041-210X.13313 · DOI
  72. Yang, 2007, PAML 4: phylogenetic analysis by maximum likelihood, Mol. Biol. Evol., 24, 1586, 10.1093/molbev/msm088 · DOI · Paper page
  73. Luebbert, 2023, Efficient querying of genomic reference databases with gget, Bioinformatics, 39, 10.1093/bioinformatics/btac836 · DOI
  74. 2022, Sequence locally, think globally: The Darwin Tree of Life Project, Proc. Natl. Acad. Sci. USA, 119
  75. Zhong, 2008, HomeoDB: a database of homeobox gene diversity, Evol. Dev., 10, 516, 10.1111/j.1525-142X.2008.00266.x · DOI
  76. Zhong, 2011, HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology, Evol. Dev., 13, 567, 10.1111/j.1525-142X.2011.00513.x · DOI
  77. Kalyaanamoorthy, 2017, ModelFinder: fast model selection for accurate phylogenetic estimates, Nat. Methods, 14, 587, 10.1038/nmeth.4285 · DOI · Paper page
  78. Zimmerman, 2013, Optimized RNA ISH, RNA FISH and protein-RNA double labeling (IF/FISH) in Drosophila ovaries, Nat. Protoc., 8, 2158, 10.1038/nprot.2013.136 · DOI
  79. Mirarab, 2015, ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes, Bioinformatics, 31, i44, 10.1093/bioinformatics/btv234 · DOI

Metadata

Authors
Mulhair, P. O., Pennati, A., Herrera-Ubeda, C., & Holland, P. W. H.
Affiliations
  • University of Liverpool (GB)
  • University of Oxford (GB)
Corresponding author
Mulhair, Peter O.
ORCID
Venue
Current Biology
Publisher
Elsevier BV
Published
2025-11
Volume
35
Issue
21
Pages
5308-5319.e3
ISSN
0960-9822 (ISSN-L)
DOI
10.1016/j.cub.2025.09.051
OpenAlex
W4415295435
Cited by
2
References
1
Citations by year
2026: 2
FWCI
1.90
Type
journal article
Language
en
Open access
Licence
Locations
  • Current Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Wellcome Trust (218328, 226458)
  • Biotechnology and Biological Sciences Research Council (UKRI893)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Diptera species taxonomy and behavior
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
Bicoid, Brachycera, Diptera phylogeny, Zen Buddhism, Bombyliidae, maternal gene expression, gene loss, insect embryonic development
MeSH terms
Animals, Diptera, Biological Evolution, Phylogeny, Trans-Activators, Homeodomain Proteins, Evolution, Molecular, Insect Proteins

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review