Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains

Toward a comparative framework for studies of altitudinal migration

The study and importance of altitudinal migration has attracted increasing interest among zoologists. Altitudinal migrants are taxonomically widespread and move across altitudinal gradients as partial or complete migrants, subjecting them to a wide array of environments and ecological interactions. Here, we present a brief synthesis of recent developments in the field and suggest future directions toward a more taxonomically inclusive comparative framework for the study of altitudinal migration. Our framework centers on a working definition of altitudinal migration that hinges on its biological relevance, which is scale-dependent and related to fitness outcomes. We discuss linguistic nuances of altitudinal movements and provide concrete steps to compare altitudinal migration phenomena across traditionally disparate study systems. Together, our comparative framework outlines a "phenotypic space" that contextualizes the biotic and abiotic interactions encountered by altitudinal migrants from divergent lineages and biomes. We also summarize new opportunities, methods, and challenges for the ongoing study of altitudinal migration. A persistent, primary challenge is characterizing the taxonomic extent of altitudinal migration within and among species. Fortunately, a host of new methods have been developed to help researchers assess the taxonomic prevalence of altitudinal migration-each with their own advantages and disadvantages. An improved comparative framework will allow researchers that study disparate disciplines and taxonomic groups to better communicate and to test hypotheses regarding the evolutionary and ecological drivers underlying variation in altitudinal migration among populations and species.

Holotype sequencing of Silvataresholzenthali Rázuri-Gonzales, Ngera & Pauls, 2022 (Trichoptera, Pisuliidae)

While DNA barcodes are increasingly provided in descriptions of new species, the whole mitochondrial and nuclear genomes are still rarely included. This is unfortunate because whole genome sequencing of holotypes allows perpetual genetic characterization of the most representative specimen for a given species. Thus, de novo genomes are invaluable additional diagnostic characters in species descriptions, provided the structural integrity of the holotype specimens remains intact. Here, we used a minimally invasive method to extract DNA of the type specimen of the recently described caddisfly species Silvataresholzenthali Rázuri-Gonzales, Ngera & Pauls, 2022 (Trichoptera: Pisuliidae) from the Democratic Republic of the Congo. A low-cost next generation sequencing strategy was used to generate the complete mitochondrial and draft nuclear genome of the holotype. The data in its current form is an important extension to the morphological species description and valuable for phylogenomic studies.

The impact of sequencing depth and relatedness of the reference genome in population genomic studies: A case study with two caddisfly species (Trichoptera, Rhyacophilidae, Himalopsyche)

Whole genome sequencing for generating SNP data is increasingly used in population genetic studies. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. It is thus imperative to select an appropriate reference genome and sequencing depth to ensure the accuracy of the results for a specific research question, while balancing cost and feasibility. To evaluate the effect of the choice of the reference genome and sequencing depth on downstream analyses, we used five confamilial reference genomes of variable relatedness and three levels of sequencing depth (3.5×, 7.5× and 12×) in a population genomic study on two caddisfly species: Himalopsyche digitata and H. tibetana. Using these 30 datasets (five reference genomes × three depths × two target species), we estimated population genetic indices (inbreeding coefficient, nucleotide diversity, pairwise F ST, and genome-wide distribution of F ST) based on variants and population structure (PCA and admixture) based on genotype likelihood estimates. The results showed that both distantly related reference genomes and lower sequencing depth lead to degradation of resolution. In addition, choosing a more closely related reference genome may significantly remedy the defects caused by low depth. Therefore, we conclude that population genetic studies would benefit from closely related reference genomes, especially as the costs of obtaining a high-quality reference genome continue to decrease. However, to determine a cost-efficient strategy for a specific population genomic study, a trade-off between reference genome relatedness and sequencing depth can be considered.

A preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): an exploration of combined targeted enrichment data and legacy sequence data

Hydroptilidae is an extremely diverse family within Trichoptera, containing over 2,600 known species, that displays a wide array of ecological, morphological, and habitat diversity. However, exploration into the evolutionary history of microcaddisflies based on current phylogenetic methods is mostly lacking. The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies. Here, a preliminary exploration of the hydroptilid phylogeny is presented using a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.