The diverse superfamily Oestroidea with more than 15 000 known species includes among others blow flies, flesh flies, bot flies and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome, making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10 and 550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent‐based analyses produced well‐resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.
Next‐generation sequencing technologies (NGS) allow systematists to amass a wealth of genomic data from non‐model species for phylogenetic resolution at various temporal scales. However, phylogenetic inference for many lineages dominated by non‐model species has not yet benefited from NGS, which can complement Sanger sequencing studies. One such lineage, whose phylogenetic relationships remain uncertain, is the diverse, agriculturally important and charismatic Coreoidea (Hemiptera: Heteroptera). Given the lack of consensus on higher‐level relationships and the importance of a robust phylogeny for evolutionary hypothesis testing, we use a large data set comprised of hundreds of ultraconserved element (UCE) loci to infer the phylogeny of Coreoidea (excluding Stenocephalidae and Hyocephalidae), with emphasis on the families Coreidae and Alydidae. We generated three data sets by including alignments that contained loci sampled for at least 50%, 60%, or 70% of the total taxa, and inferred phylogeny using maximum likelihood and summary coalescent methods. Twenty‐six external morphological features used in relatively comprehensive phylogenetic analyses of coreoids were also re‐evaluated within our molecular phylogenetic framework. We recovered 439–970 loci per species (16%–36% of loci targeted) and combined this with previously generated UCE data for 12 taxa. All data sets, regardless of analytical approach, yielded topologically similar and strongly supported trees, with the exception of outgroup relationships and the position of Hydarinae. We recovered a monophyletic Coreoidea, with Rhopalidae highly supported as the sister group to Alydidae + Coreidae. Neither Alydidae nor Coreidae were monophyletic; the coreid subfamilies Hydarinae and Pseudophloeinae were recovered as more closely related to Alydidae than to other coreid subfamilies. Coreinae were paraphyletic with respect to Meropachyinae. Most morphological traits were homoplastic with several clades defined by few, if any, synapomorphies. Our results demonstrate the utility of phylogenomic approaches in generating robust hypotheses for taxa with long‐standing phylogenetic problems and highlight that novel insights may come from such approaches.
more » « less- NSF-PAR ID:
- 10461139
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Zoologica Scripta
- Volume:
- 48
- Issue:
- 4
- ISSN:
- 0300-3256
- Page Range / eLocation ID:
- p. 520-534
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The phytophagous insect superfamily Coreoidea (Heteroptera) is a diverse group of ~3100 species in five extant families, with many of agricultural importance and model organisms in behavioural studies. Most species (~2800 species) are classified in the family Coreidae (four subfamilies, 37 tribes). While previous phylogenetic studies have primarily focused on the larger and more diverse subfamilies and tribes of Coreidae, several smaller tribes remain poorly studied in a phylogenetic context. Here, we investigated the phylogenetic positions of three less diverse tribes using ultraconserved elements: Agriopocorini, Amorbini, and Manocoreini. Our study is the first to test phylogenetic hypotheses for the Agriopocorini and Amorbini in a cladistic analysis. All three tribes were recovered within the subfamily Coreinae with robust support. The monophyletic Agriopocorini were supported as the sister-group of Colpurini, the monophyletic Amorbini as sister to Mictini, and the monogeneric Manocoreini as sister to Dasynini + Homoeocerini. We briefly discuss the evolution of wing development in Coreidae, putative synapomorphies for clades of interest, and taxonomic considerations. Our study emphasizes the importance of including smaller, less diverse groups in phylogenetic analyses. By doing so, we gain valuable insights into evolutionary relationships, identify future investigations of trait evolution, and resolve systematic controversies.
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