Mitochondrial phylogeography and subspecies of the wide-ranging sub-Saharan leopard tortoise Stigmochelys pardalis (Testudines: Testudinidae) - a case study for the pitfalls of pseudogenes and GenBank sequences

Abstract

The leopard tortoise (Stigmochelys pardalis) is the most widely distributed sub‐Saharan tortoise species, with a range extending from the Horn of Africa all over eastern Africa to the Republic of South Africa, Namibia and southernmost Angola. Using 1938 bp of mitochondrial DNA (cyt b gene, partial ND4 gene plus adjacent tRNA genes) from a nearly range‐wide sampling, we examined its phylogeographic structure and compared our findings with previously published GenBank sequences. We identified seven major clades that are largely parapatrically distributed. A few records of distinct haplotypes at the same locality or in close proximity could be the result of translocation of tortoises by man. The greatest diversity occurs in the south of the species’ range, with five out of the seven clades. Testing for isolation‐by‐distance suggests that the observed phylogeographic structure is the result of restricted geographical gene flow and not of historical vicariance. This is in sharp contrast to wide‐ranging thermophilic reptiles from the western Palaearctic, whose phylogeographic structure was significantly shaped by Pleistocene range interruptions, but also by earlier dispersal and vicariant events. Most cyt b sequences of S. pardalis from GenBank turned out to be nuclear pseudogenes, or to be of chimerical origin from such pseudogenes and authentic mitochondrial sequences, which argues for caution regarding uncritical usage of GenBank sequences. The recent revalidation of the two subspecies of S. pardalis was based on such a chimerical sequence that was erroneously identified with the subspecies S. p. babcocki. Furthermore, according to our data, the distribution of mitochondrial clades does match neither the traditional subspecies ranges nor the pronounced geographical size variation of leopard tortoises. We conclude that there is no rationale for recognizing subspecies within S. pardalis.

The genetic crisis of the Mexican Bolson Tortoise (Gopherus flavomarginatus: Testudinidae)

“…The available molecular evidence, however, does not support such interpopulation differences. Apparently, this is a well-known pattern in tortoises (see Fritz et al, 2010; and references therein). To our knowledge, nonetheless, this is the first time that such fact is confirmed for any of the species within the genus Gopherus.…”

Physically Effective Fiber Threshold, Apparent Digestibility, and Novel Fecal Microbiome Identification of the Leopard Tortoise (Stigmochelys pardalis)

“…A recent study proposes that there are no subspecies of S. pardalis, but rather phylogeographical differences in tortoises inhabiting different regions of Africa (Fritz et al, 2010b). This was previously predicted by Boycott and Bourqin (1988).…”

“…Some chelonians, including S. pardalis, have serrated tooth-like structures on the outer edges of the internal hard palate, although further research is needed to identify origin and function (Spellerberg, 1982). Without teeth, chelonians do not have the ability to masticate, and therefore, cannot mechanically reduce ingested food particle size (Bjorndal, 1997;Fritz et al, 2010b).…”

Molecular phylogeny of African hinge-back tortoises (Kinixys): implications for phylogeography and taxonomy (Testudines: Testudinidae)

“…This primer did not work in a few samples of Kinixys erosa ; then, the forward primer mt‐a‐neu was used instead. The authenticity of obtained mtDNA sequences was verified as in Fritz et al. (2010).…”