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Abstract We review the developments in caddisfly (Insecta: Trichoptera) systematics starting with Linnaeus through to the present time. We give a brief introduction to the natural history and biology of the order, survey the contributions of prominent caddisfly taxonomists, explore the history of Trichoptera phylogenetics, define synapomorphies for the major caddisfly clades, identify gaps in our knowledge, and make recommendations for the future research in caddisfly systematics. While the pattern of early evolutionary divergences within the order is becoming clearer with phylogenomic data, much work remains to be done to describe unknown caddisfly diversity and to fully resolve their tree of life. This will require the training of a new generation of Trichoptera systematists, particularly in tropical regions, equipped with broad knowledge in natural history, taxonomy, systematics, genomics, and phylogenetics. 

Abstract Mountains and islands provide an opportunity for studying the biogeography of diversification and population fragmentation. Aotearoa (New Zealand) is an excellent location to investigate both phenomena due to alpine emergence and oceanic separation. While it would be expected that separation across oceanic and elevation gradients are major barriers to gene flow in animals, including aquatic insects, such hypotheses have not been thoroughly tested in these taxa. By integrating population genomic from subgenomic Anchored-Hybrid Enrichment sequencing, ecological niche modeling, and morphological analyses from scanning-electron microscopy, we show that tectonic uplift and oceanic vicariance are implicated in speciation and population structure in Kapokapowai (Uropetala) dragonflies. Although Te Moana o Raukawa (Cook Strait) is likely responsible for some of the genetic structure observed, speciation has not yet occurred in populations separated by the strait. We find that the altitudinal gradient across Kā Tiritiri-o-te-Moana (the Southern Alps) is not impervious, but it significantly restricts gene flow between the aforementioned species. Our data support the hypothesis of an active colonization of Kā Tiritiri-o-te-Moana by the ancestral population of Kapokapowai, followed by a recolonization of the lowlands. These findings provide key foundations for the study of lineages endemic to Aotearoa. 

Abstract We present the first long-read de novo assembly and annotation of the luna moth (Actias luna) and provide the full characterization of heavy chain fibroin (h-fibroin), a long and highly repetitive gene (>20 kb) essential in silk fiber production. There are >160,000 described species of moths and butterflies (Lepidoptera), but only within the last 5 years have we begun to recover high-quality annotated whole genomes across the order that capture h-fibroin. Using PacBio HiFi reads, we produce the first high-quality long-read reference genome for this species. The assembled genome has a length of 532 Mb, a contig N50 of 16.8 Mb, an L50 of 14 contigs, and 99.4% completeness (BUSCO). Our annotation using Bombyx mori protein and A. luna RNAseq evidence captured a total of 20,866 genes at 98.9% completeness with 10,267 functionally annotated proteins and a full-length h-fibroin annotation of 2,679 amino acid residues. 

Abstract While most species of butterflies and moths (Lepidoptera) have entirely terrestrial life histories, ∼0.5% of the described species are known to have an aquatic larval stage. Larvae of aquatic Lepidoptera are similar to caddisflies (Trichoptera) in that they use silk to anchor themselves to underwater substrates or to build protective cases. However, the physical properties and genetic elements of silks in aquatic Lepidoptera remain unstudied, as most research on lepidopteran silk has focused on the commercially important silkworm, Bombyx mori. Here, we provide high-quality PacBio HiFi genome assemblies of 2 distantly-related aquatic Lepidoptera species [Elophila obliteralis (Pyraloidea: Crambidae) and Hyposmocoma kahamanoa (Gelechioidea: Cosmopterigidae)]. As a step toward understanding the evolution of underwater silk in aquatic Lepidoptera, we used the genome assemblies and compared them to published genetic data of aquatic and terrestrial Lepidoptera. Sequences of the primary silk protein, h-fibroin, in aquatic moths have conserved termini and share a basic motif structure with terrestrial Lepidoptera. However, these sequences were similar to aquatic Trichoptera in that the percentage of positively and negatively charged amino acids was much higher than in terrestrial Lepidoptera, indicating a possible adaptation of silks to aquatic environments. 

Abstract Insects have evolved complex and diverse visual systems in which light-sensing protein molecules called “opsins” couple with a chromophore to form photopigments. Insect photopigments group into three major gene families based on wavelength sensitivity: long wavelength (LW), short wavelength (SW), and ultraviolet wavelength (UV). In this study, we identified 123 opsin sequences from whole-genome assemblies across 25 caddisfly species (Insecta: Trichoptera). We discovered the LW opsins have the most diversity across species and form two separate clades in the opsin gene tree. Conversely, we observed a loss of the SW opsin in half of the trichopteran species in this study, which might be associated with the fact that caddisflies are active during low-light conditions. Lastly, we found a single copy of the UV opsin in all the species in this study, with one exception: Athripsodes cinereus has two copies of the UV opsin and resides within a clade of caddisflies with colorful wing patterns. 

Abstract The use of gDNAs isolated from museum specimens for high throughput sequencing, especially targeted sequencing in the context of phylogenetics, is a common practice. Yet, little understanding has been focused on comparing the quality of DNA and results of sequencing museum DNAs. Dragonflies and damselflies are ubiquitous in freshwater ecosystems and are commonly collected and preserved insects in museum collections hence their use in this study. However, the history of odonate preservation across time and museums has resulted in wide variability in the success of viable DNA extraction, necessitating an assessment of their usefulness in genetic studies. Using Anchored Hybrid Enrichment probes, we sequenced DNA from samples at 2 museums, 48 from the American Museum of Natural History (AMNH) in NYC, USA and 46 from the Naturalis Biodiversity Center (RMNH) in Leiden, Netherlands ranging from global collection localities and across a 120-year time span. We recovered at least 4 loci out of an >1,000 locus probe set for all samples, with the average capture being ~385 loci (539 loci on average when a clade of ambiguous taxa omitted). Neither specimen age nor size was a good predictor of locus capture, but recapture rates differed significantly between museums. Samples from the AMNH had lower overall locus capture than the RMNH, perhaps due to differences in specimen storage over time.