Leopard tortoises in southern Africa have greater genetic diversity in the north than in the south (Testudinidae)

Abstract

In contrast to mammals, little is known about the phylogeographic structuring of widely distributed African reptile species. With the present study, we contribute data for the leopard tortoise (Stigmochelys pardalis). It ranges from the Horn of Africa southward to South Africa and westwards to southern Angola. However, its natural occurrence is disputed for some southern regions. To clarify the situation, we used mtDNA sequences and 14 microsatellite loci from 204 individuals mainly from southern Africa. Our results retrieved five mitochondrial clades; one in the south and two in the north‐west and north‐east of southern Africa, respectively, plus two distributed further north. Using microsatellites, the southern clade matched with a well‐defined southern nuclear cluster, whilst the two northern clades from southern Africa corresponded to another nuclear cluster with three subclusters. One subcluster had a western and central distribution, another occurred mostly in the north‐east, and the third in a small eastern region (Maputaland), which forms part of a biodiversity hotspot. Genetic diversity was low in the south and high in the north of our study region, particularly in the north‐east. Our results refuted that translocations influenced the genetic structure of leopard tortoises substantially. We propose that Pleistocene climatic fluctuations caused leopard tortoises to retract to distinct refugia in southern and northern regions and ascribe the high genetic diversity in the north of southern Africa to genetic structuring caused by the survival in three refuges and subsequent admixture, whereas tortoises in the south seem to have survived in only one continuous coastal refuge.

Phylogeny and phylogeography of chelonians from sub-Saharan Africa—A review of current knowledge in tribute to Margaretha D. Hofmeyr

“…Fritz et al (2010) revealed that mtDNA sequences that were previously identified with the distinct subspecies S. p. babcocki represent nuclear mitochondrial insertions (numts), whereas they found no evidence for the validity of this subspecies and recommended to synonymize it into the nominotypical subspecies. Building on these results, two later studies (Spitzweg et al 2019;Dajčman et al 2021) focused on the southern part of the distribution of S. pardalis. Using mtDNA sequences (1,136 bp) and 14 microsatellite loci, Spitzweg et al (2019) identified two major genetic clusters: A southern cluster from southern coastal South Africa and a northern cluster, distributed from Namibia across northern South Africa to adjacent Mozambique.…”

“…Building on these results, two later studies (Spitzweg et al 2019;Dajčman et al 2021) focused on the southern part of the distribution of S. pardalis. Using mtDNA sequences (1,136 bp) and 14 microsatellite loci, Spitzweg et al (2019) identified two major genetic clusters: A southern cluster from southern coastal South Africa and a northern cluster, distributed from Namibia across northern South Africa to adjacent Mozambique. Microsatellite data indicated further substructure and greater genetic diversity within the northern cluster.…”

“…Compared to C. sulcata, the phylogeography of the second widely distributed African testudinid, Stigmochelys pardalis, has been well studied (Fritz et al 2010;Spitzweg et al 2019;Dajčman et al 2021). This species is distributed in East Africa from the Horn of Africa in Ethiopia southwest to Angola and through southern Africa to the southernmost extent of the continent in the Cape of Good Hope in South Africa (TTWG 2021).…”