Comparative Analysis of the Mitochondrial Genomes of Chloropidae and Their Implications for the Phylogeny of the Family.

Chloropidae, commonly known as grass flies, represent the most taxonomically diverse family of Diptera Carnoidea, comprising over 3000 described species worldwide. Previous phylogenetic studies of this family have predominantly relied on morphological characters, with mitochondrial genomes being reported in a few species. This study presents 11 newly sequenced mitochondrial genomes (10 Chloropidae and 1 Milichiidae) and provides the first comprehensive comparative analysis of mitochondrial genomes for Chloropidae. Apart from 37 standard genes and the control region, three conserved intergenic sequences across Diptera Cyclorrhapha were identified in all available chloropid mitochondrial genomes. Evolutionary rates within Chloropidae exhibit significant variation across subfamilies, with Chloropinae displaying higher rates than the other three subfamilies. Phylogenetic relationships based on mitochondrial genomes were inferred using maximum likelihood and Bayesian methods. The monophyly of Chloropidae and all four subfamilies is consistently strongly supported, while subfamily relationships within Chloropidae remain poorly resolved, possibly due to rapid evolution.

High-efficiency reinforcement learning with hybrid architecture photonic integrated circuit.

Reinforcement learning (RL) stands as one of the three fundamental paradigms within machine learning and has made a substantial leap to build general-purpose learning systems. However, using traditional electrical computers to simulate agent-environment interactions in RL models consumes tremendous computing resources, posing a significant challenge to the efficiency of RL. Here, we propose a universal framework that utilizes a photonic integrated circuit (PIC) to simulate the interactions in RL for improving the algorithm efficiency. High parallelism and precision on-chip optical interaction calculations are implemented with the assistance of link calibration in the hybrid architecture PIC. By introducing similarity information into the reward function of the RL model, PIC-RL successfully accomplishes perovskite materials synthesis task within a 3472-dimensional state space, resulting in a notable 56% improvement in efficiency. Our results validate the effectiveness of simulating RL algorithm interactions on the PIC platform, highlighting its potential to boost computing power in large-scale and sophisticated RL tasks.

Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea).

The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.

The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes.

The Diaprepes root weevil (DRW), Diaprepes abbreviatus, is a broadly polyphagous invasive pest of agriculture in the southern United States and the Caribbean. Its genome was sequenced, assembled, and annotated to study genomic correlates of specialized plant-feeding and invasiveness and to facilitate the development of new methods for DRW control. The 1.69 Gb D. abbreviatus genome assembly was distributed across 653 contigs, with an N50 of 7.8 Mb and the largest contig of 62 Mb. Most of the genome was comprised of repetitive sequences, with 66.17% in transposable elements, 5.75% in macrosatellites, and 2.06% in microsatellites. Most expected orthologous genes were present and fully assembled, with 99.5% of BUSCO genes present and 1.5% duplicated. One hundred and nine contigs (27.19 Mb) were identified as putative fragments of the X and Y sex chromosomes, and homology assessment with other beetle X chromosomes indicated a possible sex chromosome turnover event. Genome annotation identified 18,412 genes, including 43 putative horizontally transferred (HT) loci. Notably, 258 genes were identified from gene families known to encode plant cell wall degrading enzymes and invertases, including carbohydrate esterases, polysaccharide lyases, and glycoside hydrolases (GH). GH genes were unusually numerous, with 239 putative genes representing 19 GH families. Interestingly, several other beetle species with large numbers of GH genes are (like D. abbreviatus) successful invasive pests of agriculture or forestry.

A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins.

Butterflies are a diverse and charismatic insect group that are thought to have evolved with plants and dispersed throughout the world in response to key geological events. However, these hypotheses have not been extensively tested because a comprehensive phylogenetic framework and datasets for butterfly larval hosts and global distributions are lacking. We sequenced 391 genes from nearly 2,300 butterfly species, sampled from 90 countries and 28 specimen collections, to reconstruct a new phylogenomic tree of butterflies representing 92% of all genera. Our phylogeny has strong support for nearly all nodes and demonstrates that at least 36 butterfly tribes require reclassification. Divergence time analyses imply an origin ~100 million years ago for butterflies and indicate that all but one family were present before the K/Pg extinction event. We aggregated larval host datasets and global distribution records and found that butterflies are likely to have first fed on Fabaceae and originated in what is now the Americas. Soon after the Cretaceous Thermal Maximum, butterflies crossed Beringia and diversified in the Palaeotropics. Our results also reveal that most butterfly species are specialists that feed on only one larval host plant family. However, generalist butterflies that consume two or more plant families usually feed on closely related plants.

Evolutionary timescale of chalcidoid wasps inferred from over one hundred mitochondrial genomes.

Chalcidoidea is one of the most biologically diverse groups among Hymenoptera. Members are characterized by extraordinary parasitic lifestyles and extensive host ranges, among which several species attack plants or serve as pollinators. However, higher-level chalcidoid relationships remain controversial. Here, we performed mitochondrial phylogenomic analyses for major clades (18 out of 25 families) of Chalcidoidea based on 139 mitochondrial genomes. The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences. Our phylogenetic results supported the monophyly of 16 families and polyphyly of Aphelinidae and Pteromalidae. Our preferred topology recovered the relationship (Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+ remaining Chalcidoidea)))). The monophyly of Agaonidae and Sycophaginae was rejected, while the gall-associated ((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae)) relationship was supported in most results. A six-gene inversion may be a synapomorphy for most families, whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes. Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea. We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea. Ancestral state reconstruction analyses supported the hypothesis that gall-inducers were mainly derived from parasitoids of gall-inducers, while other gall-inducers were derived from phytophagous groups. Taken together, these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.

Phylogeny of the Chinese Subgenera of the Genus Homoneura (Diptera, Lauxaniidae, Homoneurinae) Based on Morphological Characters.

The genus Homoneura comprises over 700 described species in eight known subgenera distributed worldwide and has the highest species richness of Lauxaniidae. Five subgenera and more than 200 species have currently been recorded from China. Despite its high diversity, the monophyly of Homoneura and its subgenera, and the phylogenetic relationships among its subgenera remain to be investigated. One maximum-parsimony tree was generated based on 105 morphological characters scored from 24 species, representing all five subgenera of Homoneura recorded from China. The results did not support the monophyly of the genus Homoneura and subgenus Homoneura. The subgenus Chaetohomoneura is a sister to subgenus Neohomoneura. The monophyly of the subgenera Euhomoneura and Neohomoneura is supported. Much of the current classification of the genus Homoneura needs a revision before taxonomy can reflect natural groupings.

First records of the subfamilies Ecliminae and Lomatiinae (Diptera, Bombyliidae) from China with description of two new species.

Two subfamilies of bee flies, Ecliminae and Lomatiinae, are first reported from China with the description of the following two new species: Lomatia shanguii sp. nov. and Thevenetimyia cingulata sp. nov. A key to the Chinese subfamilies of Bombyliidae and a key to the Palaearctic species of Thevenetimyia Bigot are also presented.

A diversification relay race from Caribbean-Mesoamerica to the Andes: historical biogeography of Xylophanes hawkmoths.

The regions of the Andes and Caribbean-Mesoamerica are both hypothesized to be the cradle for many Neotropical lineages, but few studies have fully investigated the dynamics and interactions between Neotropical bioregions. The New World hawkmoth genus Xylophanes is the most taxonomically diverse genus in the Sphingidae, with the highest endemism and richness in the Andes and Caribbean-Mesoamerica. We integrated phylogenomic and DNA barcode data and generated the first time-calibrated tree for this genus, covering 93.8% of the species diversity. We used event-based likelihood ancestral area estimation and biogeographic stochastic mapping to examine the speciation and dispersal dynamics of Xylophanes across bioregions. We also used trait-dependent diversification models to compare speciation and extinction rates of lineages associated with different bioregions. Our results indicate that Xylophanes originated in Caribbean-Mesoamerica in the Late Miocene, and immediately diverged into five major clades. The current species diversity and distribution of Xylophanes can be explained by two consecutive phases. In the first phase, the highest Xylophanes speciation and emigration rates occurred in the Caribbean-Mesoamerica, and the highest immigration rates occurred in the Andes, whereas in the second phase the highest immigration rates were found in Amazonia, and the Andes had the highest speciation and emigration rates.

Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data.

Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade "LAMPO" (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade "AMO" (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the "LAMPO" clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous-Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.

First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing.

We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called mandibulate archaic moths (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 Ma and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly contiguous genome with a contig N50 of nearly 17 Mb. The assembled genome length of 541,115,538 bp is about half the length of the largest published Amphiesmenoptera genome (Limnephilus lunatus, Trichoptera) and double the length of the smallest (Papilio polytes, Lepidoptera). We find high recovery of universal single copy orthologs with 98.1% of BUSCO genes present and provide a genome annotation of 15,643 genes aided by resolved isoforms from PacBio IsoSeq data. This high-quality genome assembly provides an important resource for studying ecological and evolutionary transitions in the early evolution of Amphiesmenoptera.

Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae).

Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the main lineages in our AHE tree to build a data set with more genes (550 loci versus 216 loci) and higher support levels. Our overall results show strong congruence with the current classification of the family, with 11 out of 14 included subfamilies recovered as monophyletic. Heterotropinae and Mythicomyiinae are successive sister groups to the remainder of the family. We examined the evolution of key morphological characters through our phylogenetic hypotheses and show that neither the "sand chamber subfamilies" nor the "Tomophthalmae" are monophyletic in our phylogenomic analyses. Based on our results, we reinstate two tribes at the subfamily level (Phthiriinae stat. rev. and Ecliminae stat. rev.) and we include the genus Sericosoma Macquart (previously incertae sedis) in the subfamily Oniromyiinae, bringing the total number of bee fly subfamilies to 19. Our dating analyses indicate a Jurassic origin of the family (165-194 Ma), with the sand chamber evolving early in bee fly evolution, in the late Jurassic or mid-Cretaceous (100-165 Ma). We hypothesize that the angiosperm radiation and the hothouse climate established during the late Cretaceous accelerated the diversification of bee flies, by providing an expanded range of resources for the parasitoid larvae and nectarivorous adults.

Revision of the Australian bee fly genus Meomyia Evenhuis, 1983, with description of three new species (Bombyliidae, Bombyliinae, Bombyliini).

The endemic Australian bee fly genus Meomyia Evenhuis is revised, including six described species and three newly described: Meomyia hortorum sp. nov., Meomyia kochae sp. nov., Meomyia melanocincta sp. nov. Bombylius tetratrichus Walker is excluded from Meomyia and placed in Dissodesma Bowden Li. Meomyia is characterised by the slender and elongate antennal flagellum, and the black abdominal band and dense black tuft on apex of abdomen. A key to species of Meomyia is provided. Species are found in southern Australia.

Sand wasp (Hymenoptera: Crabronidae) parasites emerging from mud wasp nests (Hymenoptera: Sphecidae)-a reliable host record of Thraxan Yeates amp; Lambkin (Diptera: Bombyliidae: Anthracinae) with description of the pupal exuviae of three Thraxan species.

Two female Thraxan sp. (Diptera: Bombyliidae: Anthracinae) emerged from parasitised Pison simillimum Smith (Hymenoptera: Crabronidae) larvae found inside a Sceliphron formosum Smith (Hymenoptera: Sphecidae) mud wasps nest. Thraxan sp. larvae are endoparasites of P. simillimum larvae. The endoparasite pupates inside the host larva, kills it, and emerges free of the host body. We describe and illustrate the pupal exuviae of the newly found species and two known species, T. luteus Yeates Lambkin and T. misatulus Yeates Lambkin, and we compare these pupal exuviae to those of Anthrax Scopoli.

Revision of the Australian bee fly genus Sisyromyia White, 1916 (Bombyliidae, Bombyliinae, Acrophthalmydini).

We review Sisyromyia White (Bombyliidae, Bombyliinae), a remarkable Australian endemic bee fly genus, which includes 11 species, including six species we describe as new here: Sisyromyia albisquama sp. nov., Sisyromyia angustivitta sp. nov., Sisyromyia elongata sp. nov., Sisyromyia maculipennis sp. nov., Sisyromyia umbra sp. nov., Sisyromyia vittata sp. nov. The genus can be easily distinguished from other Australian genera in the subfamily by having a one-segmented antennal flagellum, subapex of flagellum with some long hairs; a pale median stripe present on the abdomen consisting of dense, decumbent short scales, cell r5 open; cell br nearly as long as cell bm, crossvein m-m located on base of cell dm; crossvein m-m long, nearly as long as crossvein r-m. We also recognized one new synonym, and propose a new combination for Sisyromyia binghi Evenhuis. A key to species of Sisyromyia is provided, and we extensively illustrate their internal and external morphology.

Revision of the Australian bee fly genus Pilosia Hull, 1973 (Bombyliidae, Bombyliinae) from Western Australia.

A restricted Western Australia bee fly genus Pilosia Hull (Bombyliidae, Bombyliinae) is reviewed with the description of two new species, Pilosia incana Bowden Li sp. nov. and Pilosia flava Li Yeates sp. nov., and the type species, Pilosia flavopilosa Hull, 1973 is identified as a new junior synonym of Pilosia immutatus (Walker, 1849). This genus can easily be distinguished from other Australian genera in the subfamily by having a three-segmented antennal flagellum, a closed cell cup and a haired mediotergite. A recent morphological phylogeny of Australian Bombyliinae suggested Pilosia is sister to all the remaining Bombyliinae genera (Li Yeates, 2018). A key to all three known species of Pilosia is provided.

One hundred years of solitude ended: A second species of Marmasoma White, 1916 (Diptera, Bombyliidae, Bombyliinae, Eclimini) from Australia.

Known as a monotypic genus for over a century, Marmasoma White, 1916 is an endemic Australian bee fly genus belonging to the tribe Eclimini of the subfamily Bombyliinae. A new species: Marmasoma hortorum sp. nov. is described based on a series of specimens from Western Australia and South Australia. This new species can be easily distinguished from the congener by the inconspicuous pale wing markings and mostly white to pale yellow scales on the body, as well as characters of both male and female genitalia. M. sumptuosum is found in south-eastern Australia, including Tasmania, and some specimens have been collected on Kangaroo Island, South Australia. M. hortorum sp. nov. occurs in south Western Australia, and a pair of specimens has been taken just north of Port Augusta in South Australia. A key to species of Marmasoma is provided.

Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha).

The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), were corroborated; however, the higher-level relationships between cyclorrhaphan superfamilies are mostly poorly supported.

Effect of surfactants on the aggregation and sedimentation of zinc oxide nanomaterial in natural water matrices.

The wide application of surfactants and engineered nanomaterials (ENMs) in industrial and consumer products lead to the high possibility of their co-presence in natural water environment, making it important to study the effect of surfactants on the environmental behavior and fate of ENMs. In this work, we selected an anionic sodium dodecyl sulfate (SDS) and a nonionic nonylphenol ethoxylate (NPEO, Tergitol NP-9) to study their effects on the aggregation and sedimentation of a 20nm ZnO ENM in different water matrices. The adsorption of SDS and NP-9 by ZnO ENM were fitted with Langmuir model, and the maximum adsorption capacities were 43.73±4.62mg/g and 13.79±1.09 respectively. As the surfactant concentration increased from 0 to 0.030% (m:v), SDS reduced the zeta potential of ZnO ENM from 17.56±2.13 to -27.96±2.59mV, whereas NP-9 did not affect the zeta potential. After a 24-h batch reactor experiment, SDS and NP-9 reduced 93.02% and 80.26% of the aggregate size of ZnO ENM (50mgL-1) in maximum at surfactant concentrations≥0.015%. The ZnO ENM was not stable in natural aqueous matrices, mainly because of the relatively high ionic strength. However, surfactants were found to reduce the aggregation and sedimentation of ZnO ENM in six natural water matrices in different degrees. With the presence of 0.030% SDS in tap water, maximum reduction rates of aggregate size and sedimentation were recorded as 69.54% and 26.69%, respectively. The results of this study indicate that the presence of surfactants may alter the behaviors and fate of ENMs in natural water environment.

Effect of surfactants on the aggregation and stability of TiO2 nanomaterial in environmental aqueous matrices.

The high likelihood of the coexistence of surfactants and engineered nano-materials (ENMs) in aqueous environments redoubles the need to study the effects of surfactants on the behavior and transport of nano-materials. In this study, we chose anionic sodium dodecyl sulfate (SDS) and nonionic nonylphenol ethoxylate (NPEO, Tergitol NP-9) to study the effect of surfactants on the behaviors of a typical TiO2 ENM in water environment. An adsorption isotherm and zeta potential study showed that both surfactants could be adsorbed onto the surface of nano-TiO2 but that only SDS can significantly decrease the zeta potential of TiO2. For a better simulation of the dynamic natural water environment, we conducted a 24-h batch experiment to study the aggregation behaviors of nano-TiO2 in the presence of SDS or NP-9 surfactants and recorded the sedimentation of the aggregates in solutions containing the surfactants over a 24h-period. SDS and NP-9 both reduced the growth of the TiO2 aggregates and retarded the aggregate sedimentation at surfactant concentrations ≥0.015% (w:v). The aggregation of TiO2 was far more remarkable in six environmental water matrices from different natural origins than in Milli-Q water, mainly because of the relatively high ionic strength of the former. The introduction of surfactants, however, still retarded the aggregation and sedimentation of TiO2 in the six environmental water matrices. SDS exerted a stronger reductive effect than NP-9. This study reveals that the presence of surfactants may increase the bioavailability and environmental risk of nanomaterial contaminants by retarding the aggregation and promoting the transport of nanomaterials in natural aqueous environments.