Search

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

Aspects of the life history and biology of two Prorops spp. are explored, Prorops maya sp. nov. and Prorops umiehu sp. nov. Aspects of their behavior are deduced through dissection of plant material and through the use of “phloem sandwich” style observation chambers. Both were found to be ectoparasitoids of adult Hypothenemus eruditus beetles. They thus show a novel feeding behavior as, along with a Plastanoxus sp., the only bethylids known to parasitize the adult stage of their hosts, and the only known ectoparasitoids of adult scolytids. Searching, stinging, host feeding, and oviposition behaviors are reported and illustrated with photographs and video. Oviposition occurs on the ventral side of the membraneous region between the pro- and mesothorax of the beetle, and larvae feed through this location. The projection on the frons, a defining character of the genus Prorops, is observed to function as a tongue and groove mechanism with which the adult female pushes on the edge of the prothoracic sclerite of the host beetle while maintaining use of its mandibles to chew on the membrane underneath for host feeding and in preparation for oviposition. Defensive action of a Hypothenemus sp. against the wasp's sting by clamping down on the intruding ovipositor between its pro- and mesothorax is also reported, though this behavior was only observed once and thus its generality is uncertain.

The Hawaiian Drosophilidae radiation is an ecologically and morphologically diverse clade of almost 700 described species. A phylogenetic approach is key to understanding the evolutionary forces that have given rise to this diverse lineage. Here we infer the phylogeny for the antopocerus, modified tarsus and ciliated tarsus (AMC) clade, a lineage comprising 16% (91 of 687 species) of the described Hawaiian Drosophilidae. To improve on previous analyses we constructed the largest dataset to date for the AMC, including a matrix of 15 genes for 68 species. Results strongly support most of the morphologically defined species groups as monophyletic. We explore the correlation of increased diversity in biogeography, sexual selection and ecology on the present day diversity seen in this lineage using a combination of dating methods, rearing records, and distributional data. Molecular dating analyses indicate that AMC lineage started diversifying about 4.4 million years ago, culminating in the present day AMC diversity. We do not find evidence that ecological speciation or sexual selection played a part in generating this diversity, but given the limited number of described larval substrates and secondary sexual characters analyzed we can not rule these factors out entirely. An increased rate of diversification in the AMC is found to overlap with the emergence of multiple islands in the current chain of high islands, specifically Oahu and Kauai.

Large parts of the Pacific were thought to host low bee diversity. In Fiji alone, our recent estimates of native bee diversity have rapidly increased by a factor of five (from 4 to >22). Here, we show how including sampling of the forest canopy has quickly uncovered a new radiation of Hylaeus (Hymenoptera: Colletidae) bees in Fiji. We also show that Hylaeus are more common across the Pacific than previously thought and solve one of Charles Michener’s mysteries by linking the previously enigmatic French Polynesian Hylaeus tuamotuensis to relatives in Fiji. We use systematic techniques to describe eight new Hylaeus species in Fiji (n = 6), French Polynesia (n = 1), and Micronesia (n = 1), and discuss impressive dispersal events by this genus. These clades also double the number of Hylaeus dispersals out of Australia from two to four. Our discovery highlights the severe impact of bee sampling methods on ecological interpretations and species discovery, specifically that canopy sampling is needed to correctly assess forest bee diversity even where there is a very long record of sampling. It further highlights the potential for forests to host higher-than-anticipated diversity and conservation value. This has broad methodological and regulatory impacts for land managers seeking to make choices about pollination services and diversity. The new species are Hylaeus (Euprosopoides) chuukensis Dorey, Davies, and Parslow; H. (Prosopisteron) albaeus Dorey, Davies, and Parslow; H. (P.) apertus Dorey, Davies, and Parslow; H. (P.) aureaviridis Dorey, Magnacca, and Parslow; H. (P.) breviflavus Magnacca; H. (P.) derectus Dorey, Davies, and Parslow; H. (P.) navai Dorey, Davies, and Parslow; and H. (P.) veli Dorey, Davies, and Parslow.

Insects associate with a diversity of microbes that can shape host ecology and diversity by providing essential biological and adaptive services. For most insect groups, the evolutionary implications of host–microbe interactions remain poorly understood. Geographically discrete areas with high biodiversity offer powerful, simplified model systems to better understand insect–microbe interactions. Hawaii boasts a diverse endemic insect fauna (~6000 species) characterized by spectacular adaptive radiations. Despite this, little is known about the role of bacteria in shaping this diversity. To address this knowledge gap, we inaugurate the Native Hawaiian Insect Microbiome Initiative (NHIMI). The NHIMI is an effort intended to develop a framework for informing evolutionary and biological studies in Hawaii. To initiate this effort, we have sequenced the bacterial microbiomes of thirteen species representing iconic, endemic Hawaiian insect groups. Our results show that native Hawaiian insects associate with a diversity of bacteria that exhibit a wide phylogenetic breadth. Several groups show predictable associations with obligate microbes that permit diet specialization. Others exhibit unique ecological transitions that are correlated with shifts in their microbiomes (e.g., transition to carrion feeding from plant-feeding in Nysius wekiuicola). Finally, some groups, such as the Hawaiian Drosophila, have relatively diverse microbiomes with a conserved core of bacterial taxa across multiple species and islands.