Genomic footprint of cladogenesis revealed through RADseq and Sanger sequencing demonstrates congruent patterns in the velvet worm Peripatopsis sedgwicki species complex (Onychophora: Peripatopsidae)

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 1259 - 11,468 SNPs, in order to assess the species diversity and phylogeographic 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, statistically 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 spec..., , , # *Peripatopsis sedgwicki* genomic and mitochondrial sequence data

[https://doi.org/10.5061/dryad.z08kprrmw](https://doi.org/10.5061/dryad.z08kprrmw)

This dataset consists of genomic and mitochondrial sequence data for the *Peripatopsis sedgwicki* species complex, a forest-dwelling endemic species of velvet worm distributed from the Tsitsikamma Afrotemperate forests in the southern Cape of South Africa to Gqeberha and Makanda in the Eastern Cape, into the Baviaanskloof. This dataset consists of two files, namely genomic restriction enzyme-associated sequence (RADseq) data (output.fastq.gz) in compressed Illumina sequence data format, as well as mitochondrial cytochrome c oxidase subunit 1 (*COI*) data (Psedgwicki_COI_newout.nex) in Nexus format. The RADseq dataset was generated using the restriction enzyme *SbfI,* and based on 93 samples. The *COI* dataset was constructed using 195 samples, and are 648 base pairs in length.

## Description of the data and file structure

The raw RADse...