Substrate specialisation drives an unexpectedly diverse radiation in barking geckos (Ptenopus: Gekkonidae).

Barking geckos (genus Ptenopus) are terrestrial, burrowing lizards endemic to southern Africa, currently with three recognised species. Two species are range-restricted (P. kochi and P. carpi) and display clear differences in substrate preference (soft sand vs. hard gravel). The third and most widespread species, P. garrulus, occurs on a variety of substrates of differing hardness, across potential geographic barriers, and over a steep climatic gradient. Variations in morphology and advertisement calls indicates that P. garrulus may be a species complex. Two subspecies of P. garrulus are currently recognised: P. g. maculatus and P. g. garrulus. To investigate species boundaries, we produced the first comprehensive phylogeny for the genus. We used a novel application of multiple regression on matrices models to assess multiple environmental drivers of diversification, as contrasted to isolation by distance. We show that P. kochi, P. carpi, and P. g. garrulus are valid species, but that P. g. maculatus is a paraphyletic complex of five previously unrecognised taxa. Specialisation onto different substrates was likely the main driver of divergence, with parapatric occurrence of two to four clades occurring at each of the three substrate transition zones identified a priori. The region encompasses diverse bioclimatic regions and potential geographic barriers, and these likely played a role in some divergence events.

The bii4africa dataset of faunal and floral population intactness estimates across Africa's major land uses.

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.

De Novo Whole Genome Assemblies for Two Southern African Dwarf Chameleons (Bradypodion, Chamaeleonidae).

A complete and high-quality reference genome has become a fundamental tool for the study of functional, comparative, and evolutionary genomics. However, efforts to produce high-quality genomes for African taxa are lagging given the limited access to sufficient resources and technologies. The southern African dwarf chameleons (Bradypodion) are a relatively young lineage, with a large body of evidence demonstrating the highly adaptive capacity of these lizards. Bradypodion are known for their habitat specialization, with evidence of convergent phenotypes across the phylogeny. However, the underlying genetic architecture of these phenotypes remains unknown for Bradypodion, and without adequate genomic resources, many evolutionary questions cannot be answered. We present de novo assembled whole genomes for Bradypodion pumilum and Bradypodion ventrale, using Pacific Biosciences long-read sequencing data. BUSCO analysis revealed that 96.36% of single copy orthologs were present in the B. pumilum genome and 94% in B. ventrale. Moreover, these genomes boast scaffold N50 of 389.6 and 374.9 Mb, respectively. Based on a whole genome alignment of both Bradypodion genomes, B. pumilum is highly syntenic with B. ventrale. Furthermore, Bradypodion is also syntenic with Anolis lizards, despite the divergence between these lineages estimated to be nearly 170 Ma. Coalescent analysis of the genomic data also suggests that historical changes in effective population size for these species correspond to notable shifts in the southern African environment. These high-quality Bradypodion genome assemblies will support future research on the evolutionary history, diversification, and genetic underpinnings of adaptation in Bradypodion.

When to shed? Patterns and drivers of time to first ecdysis in snakes.

Time from birth or hatching to the first shed (postnatal ecdysis) in snakes ranges from about an hour to several weeks depending upon the species. We assessed patterns in time to postnatal ecdysis in 102 snake species for which we could source appropriate information, covering 2.6% of all extant snake species, and related measures to various biological traits. Reconstruction revealed ancestral time to postnatal ecdysis to be 11 days. Since time to postnatal ecdysis can be shorter or longer than the ancestral state, we argue that there are several competing drivers for time to postnatal ecdysis. A reduced time to postnatal ecdysis has evolved in several lineages, commonly in ambush-foraging, viviparous vipers, while extended time to postnatal ecdysis is associated with oviparous species with maternal care. Of central importance is the impact of postnatal ecdysis on the scent levels of neonates, resulting in a reduction of time to postnatal ecdysis in chemically cryptic species, while the pivotal role of scent in mother-neonate recognition has resulted in the retention or extension of time to postnatal ecdysis. We showed that postnatal ecdysis improves chemical crypsis. The patterns revealed in this study suggest that measures of time to postnatal ecdysis can provide insights into the biology of snakes and be used as an indicator of certain life history traits.

A global reptile assessment highlights shared conservation needs of tetrapods.

Comprehensive assessments of species' extinction risks have documented the extinction crisis1 and underpinned strategies for reducing those risks2. Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction3. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods4-7. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs6. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened-confirming a previous extrapolation8 and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods-agriculture, logging, urban development and invasive species-although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles-including most species of crocodiles and turtles-require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.

Correction to: Male energy reserves, mate-searching activities, and reproductive success: alternative resource use strategies in a presumed capital breeder.

The authors would like to correct the error in table 4 which was incorrectly published in original version. Correct version of Table 4 is updated here.

Male energy reserves, mate-searching activities, and reproductive success: alternative resource use strategies in a presumed capital breeder.

Sexual selection studies often focus on morphological traits that are important only in the later stages of mate acquisition. Comparatively little is known about traits that lead to mate acquisition, such as mate-searching activities. We experimentally manipulated body condition (i.e., the energy reserves) in male puff adders (Bitis arietans) prior to the mating season using supplemental feeding in the field, and used radio-telemetry and DNA paternity analyses to characterize the relationships between male energy reserves, mating activities, and reproductive success. We found that male mobility is a strongly sexually selected trait because males that travelled further in search of females have higher female encounter rates and reproductive success. However, supplemental feeding did not have a significant effect on mating activities or reproductive success, because control snakes compensated by foraging more often during the mating season. The time invested in foraging by control snakes did not come at the costs of decreased mating activities or opportunity compared to fed snakes, because the latter spent the spare time resting. Our experimental field research directly demonstrates the link between male mobility and reproductive success, identifying the ultimate mechanism leading to the evolution of prolonged male mate-searching activities in snakes, and indicates that male puff adders, presumed capital breeders, adjust their breeding tactics according to resource availability.

Horizon scanning for South African biodiversity: A need for social engagement as well as science.

A horizon scan was conducted to identify emerging and intensifying issues for biodiversity conservation in South Africa over the next 5-10 years. South African biodiversity experts submitted 63 issues of which ten were identified as priorities using the Delphi method. These priority issues were then plotted along axes of social agreement and scientific certainty, to ascertain whether issues might be "simple" (amenable to solutions from science alone), "complicated" (socially agreed upon but technically complicated), "complex" (scientifically challenging and significant levels of social disagreement) or "chaotic" (high social disagreement and highly scientifically challenging). Only three of the issues were likely to be resolved by improved science alone, while the remainder require engagement with social, economic and political factors. Fortunately, none of the issues were considered chaotic. Nevertheless, strategic communication, education and engagement with the populace and policy makers were considered vital for addressing emerging issues.

The cutting-edge morphology of the mole snake's dental apparatus.

The mole snake (Pseudaspis cana) is capable of inflicting unusual bites in defence and during male combat that present as two parallel lacerations. We investigated the dental morphology of the mole snake by making SEM images, and by CT-scanning and digitally reconstructing the skulls of 14 specimens comprising both sexes. The lengths, volumes, shapes and positions of maxillary and dentary teeth were compared within individuals, between individuals, and between sexes. CT reconstructions show the occurrence of large, flat triangular teeth at the posterior end of the maxilla that are angled to point towards the posterior of the skull. SEM imagery highlights the presence of sharp ridges (carinae) on the posterior edges of the posterior dentary and maxillary teeth. Males have greater dental specialization, maxillary tooth variation, enlargement of the posterior-most maxillary teeth, and dentary teeth with posterior carinae. We hypothesize that mole snake dental specializations are adaptations for their particular form of male combat and possibly for subduing prey in the confines of underground burrows. Our findings reveal a complex dental morphology in mole snakes and provide impetus for further studies on the functional morphology of snake teeth.

Foraging mode, relative prey size and diet breadth: A phylogenetically explicit analysis of snake feeding ecology.

Foraging modes (ambush vs. active foraging) are often correlated with a suite of morphological, physiological, behavioural and ecological traits known as the "adaptive syndrome" or "syndrome hypothesis." In snakes, an ecological correlate often reported in the literature is that ambush-hunting snakes have a higher relative meal size compared to actively foraging snakes which feed on smaller prey items. This "large meal versus small meal" feeding hypothesis between ambush and active foragers has become a widely accepted paradigm of snake feeding ecology, despite the fact that no rigorous meta-analysis has been conducted to support this generalization. We conducted a phylogenetically explicit meta-analysis, which included ca. 100 species, to test this paradigm of snake feeding ecology. We gathered data on prey size by inducing regurgitation by palpation in free-ranging snakes and by examining the stomach contents of preserved museum specimens. When we found prey, we recorded both snake and prey mass to estimate relative prey mass (prey mass/snake mass). We also reviewed published studies of snake feeding ecology to gather similar information for other species. Ambush and active foragers did not differ in minimum or average meal size but the maximum meal sizes consumed by ambush-foraging snakes were larger than the maximum meal sizes eaten by active foragers. This results in ambush-foraging snakes consuming a significantly wider range of meal sizes, rather than being large meal specialists compared to active foragers. We argue that ambush foragers evolved to be more opportunistic predators because they encounter prey less frequently compared to active foragers. This hypothesis is further supported by the fact that ambush foragers also exhibited marginally wider diet breadths, consuming a broader range of prey types in comparison with active foragers. Our study challenges aspects of the foraging syndrome as it is currently conceived, and our results have important implications for our understanding of how foraging mode has shaped the behaviour and physiology of ambush-foraging snakes.

Diversifying into the branches: Species boundaries in African green and bush snakes, Philothamnus (Serpentes: Colubridae).

The African green and bush snakes of the genus Philothamnus currently comprises 21 species and three subspecies and occurs throughout sub-Saharan Africa. The genus has been the subject of previous taxonomic revisions based on traditional morphological characters and limited genetic assessment, and may not reflect their evolutionary history. Indeed, previous findings based on phylogenetics show discordant results of interspecific relationships and question the monophyly of the genus, although taxon sampling has been limited to date. We investigated phylogenetic affinities within Philothamnus with more inclusive genetic and geographical sampling, with the aim of better understanding their evolutionary history, so that future taxonomic revision of Philothamnus can be better informed. Species relationships were examined within a phylogenetic context and sampling included 133 ingroup samples from 16 taxa. Phylogenies were constructed in Bayesian and likelihood frameworks using three mitochondrial (16S, cyt b and ND4) and two nuclear (c-mos and RAG1) markers. Competing hypotheses relating to the monophyly of the genus were tested with a Shimodaira-Hasegawa test. To examine species boundaries, Bayesian General Mixed Yule-Coalescent Model and multi-rate Poisson Tree Processes analyses were conducted. In addition, a barcoding approach was used to further clarify species-level relationships by comparing frequency distributions between intra- and interspecific sequence divergence. The genus was recovered as monophyletic; however, species-delimitation results suggest that the current taxonomy does not reflect the evolutionary history of this group. For example, Philothamnus s. semivariegatus is paraphyletic, with at least four distinct clades. Philothamnus carinatus consists of two cryptic (sister) lineages from Central and West Africa that are deeply divergent, suggesting a long history of isolation between those regions. Furthermore, the subspecies P. n. natalensis and P. n. occidentalis show strong support for species-level divergence, which reflects their morphological and ecological differences. Accordingly, we elevate P. occidentalisnov. comb. to a full species. A fully informed taxonomic revision of these taxa will require additional morphological and ecological data for corroboration, but it seems that the morphological characters (e.g. scalation, dentition) used to describe these species to date are labile within and between species. This most likely has clouded our understanding of the species boundaries within the genus. Our phylogeny and species-delimitation analyses should provide a sounder framework for taxonomy, but may also prove useful toward understanding the morphological adaptations of these species to their respective habitats.

The impact of posture and basking orientation on thermoregulation in the Sungazer (Smaug giganteus).

Body temperature (Tb) is one of the most influential factors affecting physiological processes in ectothermic animals. Reptiles use behaviours such as shuttling, and postural and orientation adjustments to ensure that Tb remains close to a target. It is thought that target body temperature (Ttarget) is aligned to the physiological and behavioural thermal optima of the animal. The Sungazer (Smaug giganteus), a Threatened lizard species, is unique amongst the Cordylidae in that lizards inhabit self-excavated burrows in open grasslands, a habitat in which there are few exposed rock basking sites. In this situation, Tbs are likely to be greatly influenced by postural and orientation adjustments during basking. We measured Tbs using modified iButtons, and calculated Ttarget of free-ranging Sungazers in order to assess the impact of body posture and orientation in the thermoregulation of the species. We used camera traps to record lizard behaviour at burrow entrances and aligned these measures to measures of Tb. Ttarget was 30 ±â€¯1.4 °C, and Tbs remained within this range for 371 ±â€¯162 min per day. The anterior body-up postures resulted in faster heating and higher Tbs. Lizards heated faster when facing away from the sun and spent proportionally more time in this orientation in the morning when Tbs were lower than Ttarget. Our findings suggest that their wide behavioural repertoire allows Sungazers to thermoregulate effectively over a broad range of environmental conditions and may thus be able to effectively respond to changing climatic conditions.

An ambusher's arsenal: chemical crypsis in the puff adder (Bitis arietans).

Ambush foragers use a hunting strategy that places them at risk of predation by both visual and olfaction-oriented predators. Resulting selective pressures have driven the evolution of impressive visual crypsis in many ambushing species, and may have led to the development of chemical crypsis. However, unlike for visual crypsis, few studies have attempted to demonstrate chemical crypsis. Field observations of puff adders (Bitis arietans) going undetected by several scent-orientated predator and prey species led us to investigate chemical crypsis in this ambushing species. We trained dogs (Canis familiaris) and meerkats (Suricata suricatta) to test whether a canid and a herpestid predator could detect B. arietans using olfaction. We also tested for chemical crypsis in five species of active foraging snakes, predicted to be easily detectable. Dogs and meerkats unambiguously indicated active foraging species, but failed to correctly indicate puff adder, confirming that B. arietans employs chemical crypsis. This is the first demonstration of chemical crypsis anti-predatory behaviour, though the phenomenon may be widespread among ambushers, especially those that experience high mortality rates owing to predation. Our study provides additional evidence for the existence of an ongoing chemically mediated arms race between predator and prey species.

Digestive efficiencies are independent of gut passage times in rainbow skinks (Trachylepis margaritifer).

Constraints on physiological processes imposed on ectotherms by environmental temperatures can be severe, affecting many aspects of their biology. Included in the suite of physiological processes affected is gut motility, with below optimum temperatures generally resulting in slow gut passage. Trachylepis margaritifer (rainbow skink) however presents an unusual pattern whereby gut passage time decreases at a low temperature compared to when at an intermediate temperature. It has been suggested that this may be a 'cutting-your-losses' response whereby nutritional gain is sacrificed by voiding the digesta to reduce the risk of these rotting within the gut at these low temperatures, and if this is so, it should result in reduced digestive performance at 25°C. We tested this hypothesis by measuring appetite, apparent digestive efficiency (ADE) and apparent assimilation efficiency (AAE) in T. margaritifer. We found that although temperature significantly affected appetite and gut passage time, it did not affect digestive efficiency. Both ADE (>90%) and AAE (>80%) were high and temperature-independent across the range tested. Thus, the 'cutting-your-losses' hypothesis does not explain faster gut passage at 25°C. High digestive parameters could be maintained by increasing concentrations of digestive enzyme at low temperatures but remains to be tested in this species.

Sex-based differences and similarities in locomotor performance, thermal preferences, and escape behaviour in the lizard Platysaurus intermedius wilhelmi.

Differences between sexes in physiological performance have received little attention in animals. We tested for sex differences in maximum sprint speed and maximal exertion over a range of temperatures in a population of Platysaurus intermedius wilhelmi lizards. We also examined sex-based differences in selected temperature range, mean field body temperatures (T(b)), and thermal activity limits. Finally, we conducted field studies to quantify male and female responses to a potential predator, which may be affected by their respective performance capabilities. Males were faster than females at all temperatures, and body size had no significant effect on sprint speeds. Males and females also selected similar T(b)'s when placed in a thermal gradient, but in the field, male lizards' T(b)'s were different from those of the females. However, predicted sprint speeds for males and females at their field T(b)'s are similar. No significant differences were found between males and females with regard to maximal exertion. When approached in the field, adult male lizards took refuge significantly earlier than did adult females and also fled over shorter distances, suggesting that females rely on crypsis as an escape strategy.