Worming my way into onychophorology: a multilevel approach to an enigmatic panarthropod

Abstract

The field of onychophorology has come a long way since the description of the first onychophoran as a legged mollusk that often walks backwards. Lansdown Guilding had only found one individual for his description in 1826 and would not see another in the span of his short life. He wrote that the subkingdom Mollusca was greatly disturbed by this paradoxical genus. What was originally his single species, Peripatus juliformis, has been elevated to a phylum unrelated to mollusks that now includes over 200 species. However, they remain just as puzzling. There are still many undescribed species, sometimes indistinguishable from each other without molecular data. We still do not understand the internal relationships of major groups within the phylum. And despite the other two panarthropods (Tardigrada, Arthropoda) being some the best studied groups of animals, Onychophora are almost completely lacking in molecular resources and are the last of them to enter the genomic era. I present here a dissertation on these enigmatic creatures exploring their biology from multiple levels: from individual (genomic), to population (species delimitation), to phylum (phylogenomic). In Chapter 1, leveraging recent advances in long read sequencing technology and bioinformatics, I present the first high quality, annotated genome for the phylum. To demonstrate the utility of the resource, I also conduct an analysis revealing an unknown diversity of hemocyanins, a molecule implicated in the success of the closest living relatives of Onychophora, the arthropods. In Chapter 2, I describe three new species of Kumbadjena from the biodiversity hotspot of Western Australia. For the first time in this phylum, I use DNA sequences as diagnostic characters to describe the hidden diversity obscured by morphology. Finally in Chapter 3, I develop an ultra-conserved element probeset for Onychophora targeting 1,465 loci and test it on the most comprehensive phylogenomic dataset to date spanning 66 specimens and 1,458 loci. The resulting phylogeny largely agrees with our current understanding of onychophoran relationships and increased resolution in the difficult clade, Neopatida. This resource will help tackle the difficult phylogenetic questions that have plagued Onychophora, particularly in the family Peripatidae, by allowing us to obtain phylogenomic data from archival museum specimens.