Phylogenomics reveals the history of host use in mosquitoes

Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: 188–250 MYA]), considerably older than previous estimates. Moreover, we utilize an extensive database of host associations for mosquitoes to show that mosquitoes have shifted to feeding upon the blood of mammals numerous times, and that mosquito diversification and host-use patterns within major lineages appear to coincide in earth history both with major continental drift events and with the diversification of vertebrate classes. © 2023, Springer Nature Limited

Single-copy nuclear genes resolve the phylogeny of the holometabolous insects

Background: Evolutionary relationships among the 11 extant orders of insects that undergo complete metamorphosis, called Holometabola, remain either unresolved or contentious, but are extremely important as a context for accurate comparative biology of insect model organisms. The most phylogenetically enigmatic holometabolan insects are Strepsiptera or twisted wing parasites, whose evolutionary relationship to any other insect order is unconfirmed. They have been controversially proposed as the closest relatives of the flies, based on rDNA, and a possible homeotic transformation in the common ancestor of both groups that would make the reduced forewings of Strepsiptera homologous to the reduced hindwings of Diptera. Here we present evidence from nucleotide sequences of six single-copy nuclear protein coding genes used to reconstruct phylogenetic relationships and estimate evolutionary divergence times for all holometabolan orders. Results: Our results strongly support Hymenoptera as the earliest branching holometabolan lineage, the monophyly of the extant orders, including the fleas, and traditionally recognized groupings of Neuropteroidea and Mecopterida. Most significantly, we find strong support for a close relationship between Coleoptera (beetles) and Strepsiptera, a previously proposed, but analytically controversial relationship. Exploratory analyses reveal that this relationship cannot be explained by long-branch attraction or other systematic biases. Bayesian divergence times analysis, with reference to specific fossil constraints, places the origin of Holometabola in the Carboniferous (355 Ma), a date significantly older than previous paleontological and morphological phylogenetic reconstructions. The origin and diversification of most extant insect orders began in the Triassic, but flourished in the Jurassic, with multiple adaptive radiations producing the astounding diversity of insect species for which these groups are so well known. Conclusion: These findings provide the most complete evolutionary framework for future comparative studies on holometabolous model organisms and contribute strong evidence for the resolution of the 'Strepsiptera problem', a long-standing and hotly debated issue in insect phylogenetics

Anchored phylogenomics and revised classification of the Miltogramminae (Diptera: Sarcophagidae)

The Miltogramminae (Diptera: Sarcophagidae) includes ~600 species across \u3e40 genera, which constitute ~20% of global Sarcophagidae. While molecular phylogenetic hypotheses have been produced for this group, critical problems persist, including the presence of paraphyletic genera, uncertain relationships between genera, a bias of sampling towards Palaearctic taxa, and low support for many branches. The present study remedies these issues through the application of Anchored Hybrid Enrichment (AHE) to a sample including ~60% of the currently recognised genera (16% of known species) representing all biogeographic regions except the Neotropical. An alignment of 1,281 concatenated loci was analysed with maximum likelihood (RAxML, IQ-TREE), Bayesian inference (ExaBayes) and coalescent-based approaches (ASTRAL, SVDquartets), which resulted in highly supported and concordant topologies, providing unprecedented insight into the relationships of this subfamily of flesh flies, allowing a major update to miltogrammine classification. The AHE phylogenetic hypothesis supports the monophyly of a large proportion of genera. The monophyly of Metopia Meigen is restored by synonymy with Aenigmetopia Malloch, syn.n. To achieve monophyly of Miltogramma Meigen, eight species are transferred from Pterella Robineau-Desvoidy. The genus Pterella is shown to be paraphyletic in its current circumscription, and to restore generic monophyly Pterella is restricted to contain only Pt. grisea (Meigen). Erioprocta Enderlein, stat.rev., is resurrected. The genus Senotainia Macquart is reconstructed as paraphyletic. The monotypic genus Metopodia Brauer & Bergenstamm is synonymised with Taxigramma Macquart, syn.n. In light of our phylogenetic hypotheses, a new Miltogramminae tribal classification is proposed, composed of six tribes

Towards a new classification of Muscidae (Diptera): a comparison of hypotheses based on multiple molecular phylogenetic approaches

Muscidae are a megadiverse dipteran family that exhibits extraordinary diversity in morphology and life history as both immatures and adults. The classification of Muscidae has been long debated, and most higher-level relationships remain unknown. In this study, we used multilocus Sanger sequencing (mS-seq), anchored hybrid enrichment (AHE) and restriction-site associated DNA sequencing (RAD-seq) approaches to examine relationships within Muscidae. The results from AHE and RAD-seq largely correspond to those obtained from mS-seq in terms of overall topology, yet phylogenomic approaches received much higher nodal support. The results from all molecular approaches contradict the traditional classification based predominantly on adult morphology, but provide an opportunity to re-interpret the morphology of immature stages. Rearrangements in Muscidae classification are proposed as follows: (i) Mesembrina Meigen and Polietes Rondani are transferred from Muscinae to Azeliinae; (ii) Reinwardtiinae stat. rev. is resurrected as a subfamily distinct from Azeliinae; (iii) Eginia Robineau-Desvoidy, Neohelina Malloch, Syngamoptera Schnabl and Xenotachina Malloch are transferred to Reinwardtiinae stat. rev

ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair

The findings that amyotrophic lateral sclerosis (ALS) patients almost universally display pathological mislocalization of the RNA-binding protein TDP-43 and that mutations in its gene cause familial ALS have nominated altered RNA metabolism as a disease mechanism. However, the RNAs regulated by TDP-43 in motor neurons and their connection to neuropathy remain to be identified. Here we report transcripts whose abundances in human motor neurons are sensitive to TDP-43 depletion. Notably, expression of STMN2, which encodes a microtubule regulator, declined after TDP-43 knockdown and TDP-43 mislocalization as well as in patient-specific motor neurons and postmortem patient spinal cord. STMN2 loss upon reduced TDP-43 function was due to altered splicing, which is functionally important, as we show STMN2 is necessary for normal axonal outgrowth and regeneration. Notably, post-translational stabilization of STMN2 rescued neurite outgrowth and axon regeneration deficits induced by TDP-43 depletion. We propose that restoring STMN2 expression warrants examination as a therapeutic strategy for ALS

Nad6-alnFLYTREE

Alignment of dipteran mitochondrial NADH6 gene sequences from the FLYTREE project in fasta format