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

Phylogenomics resolves a 100-year-old debate regarding the evolutionary history of caddisflies (Insecta: Trichoptera)

Trichoptera (caddisfly) phylogeny provides an interesting example of aquatic insect evolution, with rich ecological diversification, especially for underwater architecture. Trichoptera provide numerous critical ecosystem services and are also one of the most important groups of aquatic insects for assessing water quality. The phylogenetic relationships of Trichoptera have been debated for nearly a century. In particular, the phylogenetic position of the "cocoon-makers" within Trichoptera has long been contested. Here, we designed a universal single-copy orthologue and sets of ultraconserved element markers specific for Trichoptera for the first time. Simultaneously, we reconstructed the phylogenetic relationship of Trichoptera based on genome data from 111 species, representing 29 families and 71 genera. Our phylogenetic inference clarifies the probable phylogenetic relationships of "cocoon-makers" within Integripalpia. Hydroptilidae is considered as the basal lineage within Integripalpia, and the families Glossosomatidae, Hydrobiosidae, and Rhyacophilidae formed a monophyletic clade, sister to the integripalpian subterorder Phryganides. The resulting divergence time and ancestral state reconstruction suggest that the most recent common ancestor of Trichoptera appeared in the early Permian and that diversification was strongly correlated with habitat change.

Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki)

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

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.

Under the hood: Phylogenomics of hooded tick spiders (Arachnida, Ricinulei) uncovers discordance between morphology and molecules

Ricinulei or hooded tick-spiders are a cryptic and ancient group of arachnids. The order consists of around 100 highly endemic extant species restricted to the Afrotropics and the Neotropics along with 22 fossil species. Their antiquity and low vagility make them an excellent group with which to interrogate biogeographic questions. To date, only four molecular analyses have been conducted on the group and they failed to resolve the relationships of the main lineages and even recovering the non-monophyly of the three genera. These studies were limited to a few Sanger loci or phylogenomic analyses with at most seven ingroup samples. To increase phylogenetic resolution in this little-understood and poorly studied group, we present the most comprehensive phylogenomic study of Ricinulei to date leveraging the Arachnida ultra-conserved element probe set. With a data set of 473 loci across 96 ingroup samples, analyses resolved a monophyletic Neotropical clade consisting of four main lineages. Two of them correspond to the current genera Cryptocellus and Pseudocellus while topology testing revealed one lineage to likely be a phylogenetic reconstruction artefact. The fourth lineage, restricted to Northwestern, Andean South America, is consistent with the Cryptocellus magnus group, likely corresponding to the historical genus Heteroricinoides. Since we did not sample the type species for this old genus, we do not formally re-erect Heteroricinoides but our data suggest the need for a thorough morphological re-examination of Neotropical Ricinulei.

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.

Sizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in Epiperipatus broadwayi

Genome assemblies are growing at an exponential rate and have proved indispensable for studying evolution but the effort has been biased toward vertebrates and arthropods with a particular focus on insects. Onychophora or velvet worms are an ancient group of cryptic, soil dwelling worms noted for their unique mode of prey capture, biogeographic patterns, and diversity of reproductive strategies. They constitute a poorly understood phylum of exclusively terrestrial animals that is sister group to arthropods. Due to this phylogenetic position, they are crucial in understanding the origin of the largest phylum of animals. Despite their significance, there is a paucity of genomic resources for the phylum with only one highly fragmented and incomplete genome publicly available. Initial attempts at sequencing an onychophoran genome proved difficult due to its large genome size and high repeat content. However, leveraging recent advances in long-read sequencing technology, we present here the first annotated draft genome for the phylum. With a total size of 5.6Gb, the gigantism of the Epiperipatus broadwayi genome arises from having high repeat content, intron size inflation, and extensive gene family expansion. Additionally, we report a previously unknown diversity of onychophoran hemocyanins that suggests the diversification of copper-mediated oxygen carriers occurred independently in Onychophora after its split from Arthropoda, parallel to the independent diversification of hemocyanins in each of the main arthropod lineages.