Data from: Exploring the impact of habitat size on phylogeographic patterning in the Overberg velvet worm Peripatopsis overbergiensis (Onychophora: Peripatopsidae)

Evolutionary relationships in the velvet worm species, Peripatopsis
overbergiensis, were examined in 3 forest areas in the Overberg region of
South Africa to explore the impact of historical habitat fragmentation on
the population genetic structure of the species. We collected 84 P.
overbergiensis specimens from Grootvadersbosch, Koppie Alleen, and Marloth
Nature Reserves and sequenced all these specimens for the cytochrome c
oxidase subunit I (COI) locus, whereas a subset of 13 specimens were also
sequenced for the 18S rRNA locus. Phylogenetic analyses of the 20 unique
COI haplotypes revealed 4 genetically distinct clades, a result that is
corroborated by the haplotype network. A hierarchical analysis of genetic
variation was performed on the COI haplotype data within the 2 large
forested areas, Grootvadersbosch and Marloth Nature Reserves, and across
all 3 of the sample localities. These results revealed low haplotypic and
nucleotide diversity within the largest Grootvadersbosch Nature Reserve
forest and high haplotypic and nucleotide diversity within the fragmented
Marloth Nature Reserve forest, whereas Koppie Alleen had the lowest
haplotypic and nucleotide diversity. Across all 3 main localities
statistically significant F ST values were found, together with the
absence of shared haplotypes indicating the absence of maternal gene flow.
Divergence time estimations based on the 20 COI haplotypes calculated in
BEAST suggest a Pleistocene/Holocene divergence between the 4 clades as a
result of habitat fragmentation and the aridification of the region. Our
results indicate that conservation efforts should also prioritize linked,
smaller fragmented habitats together with continuous habitats to maximize
the genetic diversity of saproxylic fauna.