On the importance of fine-scale sampling in detecting alpha taxonomic diversity among saproxylic invertebrates: A velvet worm (Onychophora:Opisthopatus amaxhosa) template

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.

Ngāokeoke Aotearoa: The Peripatoides Onychophora of New Zealand

(1) Background: Originally described as a single taxon, Peripatoides novaezealandiae (Hutton, 1876) are distributed across both main islands of New Zealand; the existence of multiple distinct lineages of live-bearing Onychophora across this spatial range has gradually emerged. Morphological conservatism obscured the true endemic diversity, and the inclusion of molecular tools has been instrumental in revealing these cryptic taxa. (2) Methods: Here, we review the diversity of the ovoviviparous Onychophora of New Zealand through a re-analysis of allozyme genotype data, mitochondrial DNA cytochrome oxidase subunit I sequences, geographic information and morphology. (3) Results: New analysis of the multilocus biallelic nuclear data using methods that do not require a priori assumptions of population assignment support at least six lineages of ovoviviparous Peripatoides in northern New Zealand, and mtDNA sequence variation is consistent with these divisions. Expansion of mitochondrial DNA sequence data, including representation of all existing taxa and additional populations extends our knowledge of the scale of sympatry among taxa and shows that three other lineages from southern South Island can be added to the Peripatoides list, and names are proposed here. In total, 10 species of Peripatoides can be recognised with current data.

Sample design in biodiversity studies matters: a fine-scale study of Lawrence's velvet worm, Peripatopsis lawrencei (Onychophora: Peripatopsidae), reveals hidden diversity

A fine-scale phylogenetic and phylogeographic analysis of Peripatopsis lawrencei s.l. was conducted with both mitochondrial and nuclear DNA sequence data, using both external morphology and scanning electron microscopy of taxonomically important characters. A total of 119 sequences were used for the mitochondrial cytochrome c oxidase subunit I (COI ) whereas a single representative specimen from each locality was sequenced for the nuclear 18S rRNA locus. Phylogenetic analyses were conducted on the total COI data set and the combined COI + 18S rRNA data set using a Bayesian analysis and maximum likelihood analyses. For the combined DNA sequence data set, a divergence time estimation was further undertaken in BEAST and specimens placed in a phylogenetic framework including all the described Peripatopsis species from South Africa. In addition, a phylogeographic study was conducted exclusively on P. lawrencei s.s. (clade A) using an analysis of molecular variance and haplotype network. Phylogenetic results indicated that, at the Oubos sample locality, two highly distinct genetic lineages were present (clades A and B), whereas a divergence time estimation suggests a Miocene cladogenesis of the novel Oubos lineage. Marked phylogeographic structure was observed for P. lawrencei s.s. (restricted to clade A) across the distribution range with limited maternal dispersal. Morphologically, the two sympatric lineages at Oubos A and B differed in leg pair number, ventral colour and dorsal scale rank counts, as evident from scanning electron microscopy. Our results support the recognition of a distinct species that occurs in sympatry with P. lawrencei s.s. The new species, P. aereus sp. nov. (clade B) is described and the implication for fine-scale taxonomic studies on saproxylic taxa is discussed. ZooBank: urn:lsid:zoobank.org:pub:AB6E0BDA-7B5F-4FD3-A863-BA7C814E278C.

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.

Description of a new montane freshwater crab (Arthropoda, Malacostraca, Decapoda, Potamonautidae) from the Eastern Cape, South Africa

A new species of freshwater crab, Potamonautesamatholesp. nov., is described from the Winterberg-Amathole mountain range in the Eastern Cape Province, South Africa. Morphologically, P.amathole Peer & Gouws, sp. nov. most closely resembles P.tuerkayi but can be distinguished by key morphological characters including the variation in the shape of the subterminal segment of gonopod 2 between both species. Genetically, P.amathole Peer & Gouws, sp. nov. is placed within the clade of small-bodied, mountain-dwelling crabs including P.parvispina, P.parvicorpus, P.brincki, P.tuerkayi, P.baziya, and P.depressus. The new species is found in slow-moving mountain streams and pools at high altitudes. The continued discovery and description of new freshwater crab species reinforces the need for ongoing research, especially in under-sampled regions.

Climatic oscillations during the Mio/Pliocene epochs induced cladogenesis in the terrestrial snail genus Gittenedouardia (Mollusca: Gastropoda: Cerastidae) from South Africa

In South Africa, the terrestrial snail genus Gittenedouardia is the most species-rich member of the Cerastidae, where it is primarily distributed in the highly fragmented Afrotemperate and Indian Ocean coastal belt (IOCB) forest biomes. Phylogenetic relationships and cladogenetic events within the genus remain unstudied. In this respect, we reconstructed a dated phylogeny for eight Gittenedouardia species, and two populations identified to genus level using a combined mitochondrial (16S rRNA and COI) DNA sequencing dataset analysed using Bayesian inference and Maximum Likelihood framework. Furthermore, we investigated the population genetic substructure of the three widely distributed species (Gittenedouardia spadicea, G. natalensis and G. arenicola) for the COI locus, while also subsampling these species using the nuclear DNA ITS-2 locus. Phylogenetic results based on the combined mtDNA dataset supported the monophyly of Gittenedouardia and revealed three major clades and deep genetic structure among the three widely distributed species. Divergence-time estimates suggest that diversification within Gittenedouardia occurred during the middle Miocene/late Pliocene, a period characterised by a decrease in precipitation and the contraction of the Afrotemperate and IOCB forest biomes. We used two species delimitation methods, (PTP and STACEY) to infer putative species in G. spadicea, G. natalensis and G. arenicola. The two methods recovered a large number of evolutionary distinct units, with minimal consensus in the exact number of lineages. Our findings suggest the presence of undescribed diversity, necessitating the need for taxonomic revisionary work on Gittenedouardia. We discuss the climatic factors which may have contributed to the observed cladogenesis and compare our results with other studies of forest dwelling faunal taxa.

Systematics of the Peripatopsis clavigera species complex (Onychophora : Peripatopsidae) reveals cryptic cladogenic patterning, with the description of five new species

During the present study, DNA sequence data, gross morphology and scanning electron microscopy (SEM) were used to examine cryptic species boundaries in the velvet worm, Peripatopsis clavigera species complex, from the southern Cape Afrotemperate forest belt in South Africa. Sequence data were generated for the mitochondrial COI and the nuclear 18S rRNA loci and phylogenetically analysed using both a Bayesian inference and a maximum-likelihood approach. Both the COI data and the combined DNA sequence topology (COI+18S) revealed the presence of five clades within the Peripatopsis clavigera species complex, and revealed that specimens from Tulbagh were distantly related and represented a sixth clade. The evolutionary distinction of the five clades was corroborated to varying degrees by the four species-delimitation methods (ABGD, PTP, GMYC and STACEY); however, both the gross morphological data and the SEM provided limited diagnostic differences between the five clades. Furthermore, the COI haplotype network and phylogeographic analyses provided evidence of genetic isolation between lineages that are currently syntopic. The distribution of genealogically exclusive and widespread maternal lineages was atypical among velvet worms and did not reflect the general trend of genetic and geographical isolation. Instead, lineages exhibited admixture among localities, a result most likely due to fluctuations in climatic conditions affecting the southern Cape Afrotemperate forest during the Pliocene–Pleistocene period as evident from our divergence time estimations. Four novel, narrow-range endemic species – P. ferox, sp. nov., P. mellaria, sp. nov., P. edenensis, sp. nov. and P. mira, sp. nov. – are described within the P. clavigera species complex, whereas the Tulbagh specimens are described as P. tulbaghensis, sp. nov. Collectively, these results demonstrate that Peripatopsis likely contains several undescribed species.