Custom phylogenomics pipeline elucidates the evolutionary history and biogeography of Simuliidae

Black flies (Diptera:Simuliidae), or simuliids, perform valuable ecosystem services as larvae and are economic pests of humans and wildlife as adults. Despite their large ecological and economic impacts, relationships between taxa, beyond closely related species groups, are poorly understood. Intrafamilial relationships of black flies remain unknown, as neither conventional genetic markers nor morphology reliably demonstrate monophyletic groupings between genera or species groups. Extensive genomic translocations, which are hypothesized to drive adaptive radiation in simuliids, further impede genetic efforts to elucidate relationships between taxa. Previous efforts to establish the underpinnings of intrafamilial systematics for simuliids so far have been unsuccessful due to the cosmopolitan distribution of black flies required to infer intergeneric relationships and a lack of genomic sequence data. The advent of next-generation sequencing and emergent phylogenomic tools now allows for a robust examination of simuliid evolutionary history.

OrthoGarden, an automated assembly-based phylogenomics pipeline, was used to generate a Maximum Likelihood (ML) reconstruction of 47 identified simuliids and 8 outgroup taxa collected internationally. To this end, short reads were trimmed, assembled, annotated, and gathered for orthology inference. 3,254 annotated genes orthologous in 50% of taxa were recovered and then translated, aligned, and concatenated for a preliminary ML phylogenetic reconstruction. Collection data for ingroup taxa will be leveraged alongside the recovered topology to derive an ancestral state reconstruction to model biogeographical shifts across simuliid evolutionary history. This preliminary phylogeny reflects established relationships between tribes and notably reveals two monophyletic subclades within Simulinii with extensive radiation within each.