Tortoise forensics: Conservation genetics of the leopard tortoise Stigmochelys pardalis in Southern Africa

Sub-Saharan Africa harbours an outstanding diversity of tortoises of which the leopard tortoise Stigmochelys pardalis is the most widespread. Across its’ range the species is impacted by habitat transformation, over-collection for human consumption and the pet trade, road mortality, and electrocution by electric fences. Most leopard tortoises in southern Africa are nowadays restricted to reserves and private farms. So far confiscated tortoises are frequently released into a nearby reserve without knowledge on their area of origin. This is problematic, as it has been demonstrated that the leopard tortoise harbours five distinct mitochondrial lineages, of which three occur in the southern portion of the species’ distributional range (South Africa, Namibia, and Botswana). Using 14 microsatellite loci corresponding to 270 samples collected throughout southern Africa, we found a clear substructuring in the north constituting four clusters (western, central, north-eastern, and eastern). Genetic diversity was particularly high in the north-east and decreased towards the south. In addition, we found a significant size difference between the studied populations. Our basic morphological analysis showed that tortoises from the southern cluster tend to grow bigger than tortoises from the north. We established a comprehensive genetic database for South Africa and Namibia that can serve as a conservation management tool for the assignment and potential release of translocated or seized leopard tortoises based on genetic affiliation

How many species of angulate tortoises occur in Southern Africa? (Testudines: Testudinidae: Chersina)

Using range-wide sampling and 1,143 bp of mtDNA (cytochrome b gene) and 14 microsatellite loci, we examined genetic differentiation in the widely distributed Southern African angulate tortoise (Chersina angulata). We found evidence for two genealogical lineages that differ in both genetic marker systems and their preferred habitat conditions. According to a fossil-calibrated molecular clock for all African tortoise lineages using 1,870 bp mitochondrial and 1,416 bp nuclear DNA, the two lineages of C. angulata diverged in the Pliocene (approx. 3.8 million years ago). Species distribution models reveal that the ranges of the two lineages shifted little since the Last Glacial Maximum, which is in agreement with the demographic population descriptors suggestive of stationary populations that did not experience expansion. One lineage occurs in the west, and the other in the south of the extant distribution range. In the geographic contact zone, the two lineages hybridize extensively, providing evidence for their conspecificity under the biological species concept. Each lineage could be recognized as a distinct subspecies, but the ill-defined geographic origins of the type material of the available names prevent their identification with any taxon

Unraveling the diversification and systematic puzzle of the highly polymorphic Psammobates tentorius (Bell, 1828) complex (Reptilia: Testudinidae) through phylogenetic analyses and species delimitation approaches

The high level of phenotypic diversity in southern African tent tortoises (Psammobates tentorius complex) has for decades prevented systematists from developing a stable taxonomy for the group. Here, we used a comprehensive DNA sequence dataset (mtDNA: Cytb, ND4, ND4 adjacent tRNA-His, and tRNA-Ser, 12S, 16S; and nDNA: PRLR gene) of 455 specimens, and the latest phylogenetic and species delimitation analytical procedures, to unravel the long-standing P. tentorius complex systematic puzzle. Our results for mtDNA and nDNA were incongruent, with the poorly supported nDNA phylogeny differentiating the three recognized subspecies, and showing potential hybridization in some regions. In contrast, the concatenated mtDNA phylogeny identified seven operational taxonomic units, with strong support. Clades 1, 4, 5, and 7 corresponded to tortoises identified as P. t. tentorius, clade 3 to P. t. trimeni, and clades 2 and 6 to P. t. verroxii. Our analyses showed conflicting topologies for the placement of C6 (P. t. verroxii north of the Orange River), with stronger support for it being sister to C2 + C3 than to the other clades. Clades 1, 2, and 6 had significantly higher genetic diversity than clades 3, 4, 5, and 7, perhaps because these clades inhabit substantially larger areas

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

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 refug

Important new records of Pelomedusa species for South Africa and Ethiopia

Because of a recent taxonomic revision, the species identity of helmeted terrapins (Pelomedusa) became unclear in many regions of their wide distribution range. Based on mtDNA sequence data, here we present the first record of Pelomedusa subrufa sensu stricto for the South African province of Mpumalanga. In South Africa, this species was previously known only from a single record in the province of Limpopo. In addition, we provide evidence for the occurrence of at least two distinct Pelomedusa species in Ethiopia. A sample from southern Ethiopia (Omo Region) turned out as P. neumanni, while another sample from Koka Lake (Oromia Region, central Ethiopia) represents P. somalica. Also a historical museum specimen from Ethiopia, most likely collected south of the Shebelle River (Oromia Region), belongs to P. somalica. However, these two Ethiopian specimens of P. somalica represent highly distinct genetic lineages, which may actually correspond to two different species

Body of evidence: forensic use of baseline health assessments to convict wildlife poachers

CONTEXT. Given the immense impact of wildlife trade, disease and repatriations on populations, health assessments can" "provide powerful forensic material to help convict wildlife poachers and minimise risks of releasing unhealthy wildlife." AIMS. We aimed to use reference ranges to assess the health of confiscated tortoises, to illustrate forensic application of these ranges, and to advance analyses for future applications." METHODS. We used analyses of variance (ANOVA) and covariance (ANCOVA), and composite indices, to compare wild and confiscate tortoise body condition, haematocrit and haemoglobin concentration of males and females of three tortoise species. Subsequently, we used multivariate statistics (e.g. discriminant analyses) to evaluate the relative importance of species, sex and group (wild or confiscate) on tortoise condition and haematology." KEY RESULTS. Our initial statistical tests demonstrated, at P < 0.05 to P < 0.0005, that confiscate body condition and haematology were compromised compared with that of wild tortoises. Subsequently, discriminant analyses strongly discriminated between most wild and confiscate groups (P < 0.0001), correctly classified individual health as wild or confiscate 80–90% of the time, indicated that species and sex effects were stronger than was the wild-confiscate category, and provided discriminant functions for use on other taxa and studies." CONCLUSIONS. The health assessments discriminated well between wild and confiscate tortoises. The results had considerable forensic value, being relevant, quickly generated using portable field equipment, reliable, accurate, easy to explain and convey in terms of likelihood in a court of law, synergistically consistent among variables and groups, a strong rebuttal to the poachers’ specific statements, and consistent with other types of evidence. Multivariate analyses were consistent with, and more prudent and powerful than, the original statistical analyses. Discriminant functions can be applied in future studies and on other chelonian species, and should be developed for other wildlife species." IMPLICATIONS. Reference ranges provide considerable value for forensics, diagnostics and treatment. Given the disease risks resulting from the massive scale of wildlife trade and release, reference ranges should be developed for more species."Web of Scienc

Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises ( Cylindraspis spp.)

The five extinct giant tortoises of the genus Cylindraspis belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of Cylindraspis, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. Cylindraspis is an ancient lineage that diverged as early as the late Eocene. Diversification of Cylindraspis commenced in the mid-Oligocene, long before the formation of the Mascarene Islands. This rejects any notion suggesting that the group either arrived from nearby or distant continents over the course of the last millions of years or had even been translocated to the islands by humans. Instead, Cylindraspis likely originated on now submerged islands of the Réunion Hotspot and utilized these to island hop to reach the Mascarenes. The final diversification took place both before and after the arrival on the Mascarenes. With Cylindraspis a deeply divergent clade of tortoises became extinct that evolved long before the dodo or the Rodrigues solitaire, two other charismatic species of the lost Mascarene fauna

The padloper’s tortuous path (Chelonia: Testudinidae): Two genera, not one

<p>Since 1957, all padlopers were considered <i>Homopus</i>, which was an anomaly, because only two species have four claws on the front and hind limbs. The revival of the genus <i>Chersobius</i> for the five-toed species (<i>signatus</i>, <i>boulengeri</i> and <i>solus</i>) now limits <i>Homopus</i> to the four-toed species (<i>areolatus</i> and <i>femoralis</i>). Molecular data indicate that <i>Homopus</i> is paraphyletic with two well-supported clades: the four-toed <i>Homopus</i> in one clade and the five-toed <i>Chersobius</i> together with <i>Chersina angulata</i> in a second clade. There are numerous distinct morphological and ecological differences between the genera. All <i>Chersobius</i> species have a single, large inguinal scute, whereas the number is variable in <i>Homopus</i>. The midline pectoral scute of <i>Chersobius</i> is consistently longer, and the nuchal scute shorter, than in <i>Homopus</i>. The fourth to fifth vertebral suture is narrow in <i>Homopus</i> and broad in <i>Chersobius</i>. Forelimb scales also differ with 3–4 large rows and 5–6 smaller rows, respectively, in <i>Homopus</i> and <i>Chersobius</i>. <i>Chersobius</i> males have a plastral concavity and <i>Homopus</i> males not. Two <i>Chersobius</i> species (<i>C. signatus</i> and <i>C. boulengeri</i>) are distinguishable from <i>Homopus</i> by having 12 or more marginal scutes, whereas <i>Homopus</i> species have 11 or fewer. The glans penes are respectively V-shaped and heart-shaped in <i>Homopus</i> and <i>Chersobius.</i> Ecological differences include that <i>Chersobius</i> species are rupicolous and inhabit arid regions, whereas <i>Homopus</i> species inhabit more mesic habitats. <i>Homopus</i> females produce multi-egg clutches and tend to be bigger compared to single-egg clutching <i>Chersobius</i> females. Females of all species are larger than conspecific males, and all males have larger shell openings than females have.</p> <p><b>ZooBank</b>—urn:lsid:zoobank.org:pub: 18229454-6662-46F3-8B15-836BF2AC38EB</p

Sexual disparity in activity patterns and time budgets of angulate tortoises (Chersina angulata) on Dassen Island, South Africa

Behavioural frequencies and time budgets for male and female Chersina angulata were recorded in spring, September 2004. The daily activity of the population was 10.51 ± 0.42 h (mean ± CI), but individual males and females were in the open for 2.57 ± 1.12 h and 1.58 ± 1.44 h, respectively. Both sexes spent nearly 3.5 h per day basking with 90% of the basking time in the cover of sparse vegetation. Feeding and walking were the most frequent active behaviours. The activity pattern of the sexes differed between 10:00 and 12:00 in the morning when males spent more time out of cover on active behaviours, particularly feeding, than females did. The daily activity pattern of the population peaked between 10:00 and 12:00, reflecting the activity pattern of the more active sex, males. Females were out of cover, active, and feeding at higher temperatures than were males. The high temperatures  probably allowed  females to complete activities more efficiently, reducing their exposure time and  predation risk. Although fighting and mating represented small fractions of male time budgets, the extended physical presence through walking and feeding may help  males to establish dominance hierarchies and enhance mating success.Key words: activity pattern, behaviour, temperature, thread-trailing, time budget, tortoise

Season, sex and age variation in the haematology and body condition of geometric tortoises Psammobates geometricus

Body condition and haematological indices provide powerful information when assessing wildlife health. Reference intervals for these indices can facilitate wildlife management, and would benefit initiatives to save the Critically Endangered geometric tortoise (Psammobates geometricus). We collected data from 126 geometric tortoises to establish baseline values reflecting variation over four seasons (spring 2000 to winter 2001) and among three groups (female, male and juvenile). We measured body condition index (BCI; mass to shell volume), blood urea nitrogen (BUN), plasma chloride, packed cell volume (PCV), haemoglobin concentration (Hb) and red blood cell count (RBC), and used PCV, Hb and RBC to calculate erythrocyte indices. BCI correlated poorly with haematological measures but had a strong inverse relationship with BUN. BCI did not vary among groups, but all groups had low condition indices in autumn, the end of the dry season. High BUN and chloride values in autumn indicate dehydration, particularly in males. Males had the highest PCV, Hb and RBC values, especially during summer and autumn when they moved long distances, likely pursuing mates. Female and juvenile indices were similar, except that female Hb was higher than juvenile Hb, possibly to meet female energy needs associated with their large size and reproductive metabolism. Low Hb levels in winter coincided with low temperatures and reduced movements. Our results illustrate how intrinsic and extrinsic factors influence the physiology of geometric tortoises and provide reference intervals to monitor their health.Keywords: blood urea nitrogen, erythrocyte indices, haemoglobin, packed cell volume, red blood cell count, reference interval