An ultraconserved element probe set for velvet worms (Onychophora)

Onychophora are cryptic, soil-dwelling invertebrates known for their biogeographic affinities, diversity of reproductive modes, close phylogenetic relationship to arthropods, and peculiar prey capture mechanism. The 216 valid species of Onychophora are grouped into two families - Peripatopsidae and Peripatidae - and apart from a few relationships among major lineages within these two families, a stable phylogenetic backbone for the phylum has yet to be resolved. This has hindered our understanding of onychophoran biogeographic patterns, evolutionary history, and systematics. Neopatida, the Neotropical clade of peripatids, has proved particularly difficult, with recalcitrant nodes and low resolution, potentially due to rapid radiation of the group during the Cretaceous. Previous studies have had to compromise between number of loci and number of taxa due to limitations of Sanger sequencing and phylotranscriptomics, respectively. Additionally, aspects of their genome size and structure have made molecular phylogenetics difficult and data matrices have been affected by missing data. To address these issues, we leveraged recent, published transcriptomes and the first high quality genome for the phylum and designed a high affinity ultraconserved element (UCE) probe set for Onychophora. This new probe set, consisting of ∼ 20,000 probes that target 1,465 loci across both families, has high locus recovery and phylogenetic utility. Phylogenetic analyses recovered the monophyly of major clades of Onychophora and revealed a novel lineage from the Neotropics that challenges our current understanding of onychophoran biogeographic endemicity. This new resource could drastically increase the power of molecular datasets and potentially allow access to genomic scale data from archival museum specimens to further tackle the issues exasperating onychophoran systematics.

An updated world checklist of velvet worms (Onychophora) with notes on nomenclature and status of names

More than a decade has passed since the publication of the only world checklist available for Onychophora. During this period, numerous nomenclatural acts and taxonomic changes have been suggested within the group and a wealth of novel data has been published on many taxa. Herein, the up-to-date taxonomic scenario within Onychophora is presented, with appraisal of name status. This checklist covers both extant (Peripatidae and Peripatopsidae) and fossil taxa, and each species is accompanied by information on synonyms, type designation, holotype location, type locality, and language of original description. Additional remarks include nomenclatural inconsistencies, synonymizations, name misspellings, conflicting collecting event data, availability of taxonomically informative molecular data, etc. According to the data, 237 species are currently assigned to Onychophora: 140 of Peripatopsidae, 92 of Peripatidae, and five fossil species with unclear relationship to extant taxa. Since the previous checklist, 37 species have been added to Onychophora, representing an increase of 18.5% in the diversity described for the group. Yet, taxonomic descriptions seem slow-paced, with an average of 3.6 onychophoran species being described annually. From the taxonomic standpoint, 216 species are valid, although many of them require morphological revision and molecular characterization; 21 species exhibit major taxonomic ambiguities and have been regarded as nomina dubia. Recurrent taxonomic issues identified in the literature include inaccurate collecting event data, doubtful taxonomic assignment of molecular sequences, and non-observance of nomenclatural rules. These and other taxonomic aspects are addressed herein in the light of the directives established by the International Code of Zoological Nomenclature.

Epiperipatus puri sp. nov., a new velvet worm from Atlantic Forest in Southeastern Brazil (Onychophora, Peripatidae)

Epiperipatus ohausi (Bouvier, 1900) is the first species known from Rio de Janeiro, and more than 120 years later a new species is described in the state of Rio de Janeiro (RJ). In this study, we describe the second species in the state of Rio de Janeiro, which we are naming in honor of the indigenous population called puri who resided in southeastern coastal Brazil. The species can be diagnosed mainly by large dorsal primary papillae close to the insertion of the legs drawing a light band from the anterior to the posterior region of the body, and large dorsal primary papillae alternating on the dorsal plicae. Moreover, they are recognized in vivo by the color of the diamond-shaped marks brownish orange on the dorsal portion of the body. Epiperipatus puri sp. nov. morphologically seems to be related to Epiperipatus acacioi (Marcus & Marcus, 1995) by the shape of the primary papillae apical piece and to E. ohausi by the resemblance of dorsal papillae. The phylogeny shows a close relationship between the new species and E. ohausi in a clade with a still undescribed species from Rio de Janeiro, Brazil located within the Atlantic Forest, one of the most threatened biomes in the world.

Phylogenomic Analysis of Velvet Worms (Onychophora) Uncovers an Evolutionary Radiation in the Neotropics

Onychophora ("velvet worms") are charismatic soil invertebrates known for their status as a "living fossil," their phylogenetic affiliation to arthropods, and their distinctive biogeographic patterns. However, several aspects of their internal phylogenetic relationships remain unresolved, limiting our understanding of the group's evolutionary history, particularly with regard to changes in reproductive mode and dispersal ability. To address these gaps, we used RNA sequencing and phylogenomic analysis of transcriptomes to reconstruct the evolutionary relationships and infer divergence times within the phylum. We recovered a fully resolved and well-supported phylogeny for the circum-Antarctic family Peripatopsidae, which retains signals of Gondwanan vicariance and showcases the evolutionary lability of reproductive mode in the family. Within the Neotropical clade of Peripatidae, though, we found that amino acid-translated sequence data masked nearly all phylogenetic signal, resulting in highly unstable and poorly supported relationships. Analyses using nucleotide sequence data were able to resolve many more relationships, though we still saw discordant phylogenetic signal between genes, probably indicative of a rapid, mid-Cretaceous radiation in the group. Finally, we hypothesize that the unique reproductive mode of placentotrophic viviparity found in all Neotropical peripatids may have facilitated the multiple inferred instances of over-water dispersal and establishment on oceanic islands.