Abstract Gene family expansions can reveal how genomes diverge in lineages shaped by ecological divergence. We examined gene family evolution in two South African dwarf chameleons, Bradypodion pumilum and B. ventrale, which occupy contrasting forested and open-canopy habitats and belong to different clades. Using newly annotated Bradypodion genomes and four published squamate genomes, we identified orthologous gene families and estimated changes in family composition within a phylogenetic framework. The Bradypodion crown group showed expansions enriched for neural connectivity, synaptic organization, cell–cell recognition, and genome maintenance, suggesting an ancestral background of neural wiring and cellular resilience. Bradypodion pumilum exhibited expansions centred on synaptic organization, postsynaptic receptor localization, and membrane-associated signalling, indicating lineage-specific functional differentiation in a forest-associated lineage. By contrast, B. ventrale showed expansions linked to neural morphogenesis, cell adhesion, tissue organization, and developmental pathways, indicating a distinct functional profile in an open-habitat lineage. These results show that habitat-associated lineages differ not simply in the presence of expanded gene families, but in the functional categories they display across expanded families. Our study highlights the value of gene family analyses for detecting lineage-specific genomic signatures in non-model taxa and underscores the importance of integrating evolutionary history with ecological context when interpreting genomic architecture in relation to diversification.

Horizon scans identify potential changes, enabling proactive rather than reactive conservation strategies. Here, in a follow up to the 2020 horizon scan, 14 biodiversity professionals from different sectors identify ten emerging issues potentially relevant to biodiversity conservation in South Africa over the next 5–10 years. The issues identified highlight three critical needs: adaptive governance systems, cross-sectoral collaboration capacity, and vigilance around new technologies that may simultaneously offer solutions and create new environmental pressures. We plotted these issues 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 condisderable levels of social disagreement) or "chaotic" (high social disagreement and highly scientifically challenging). Only one issue was likely to be addressed with improved science alone, but the remainder were all “complex”, requiring social, economic and political engagement.

Classifying the foraging mode of a species is challenging and is usually assessed through movement-based indices. Without considering what motivates movement, these indices may result in a biased interpretation of foraging mode-overlooking the fact that movement is influenced by multiple biological factors and not solely foraging. Conversely, while attack-based indices provide a more informative assessment of foraging mode because behavior is incorporated, the most comprehensive and reliable assessments should incorporate both movement- and attack-based indices. We applied a combination of movement- and attack-based indices to reevaluate foraging mode in chameleons, using Bradypodion pumilum as a case study. Focal observations were used to record the behaviors of 38 individuals, 12 of which were telemetered over two 10-day periods. Chameleons spent most of the day in stationary positions, perched in direct sunlight during mornings but in partial sunlight or shaded areas during afternoons. From >100 feeding events, chameleons had a significantly higher percentage of attacks and rate of attacks on prey while stationary than when moving. Most recorded intraspecific interactions were between females and males. Not only do our findings suggest that chameleons are motivated to move for several reasons but after considering life history traits in conjunction with our findings, we propose a paradigm shift in chameleon foraging mode suggesting that they should be considered ambush foragers instead of "cruise foragers" as previously classified. Overall, our findings demonstrate the importance of a multifaceted approach to foraging mode assessments, and we caution against using only one type of index in evaluations.

Most of the nine genera and 38 species in the family Pythonidae occur in south-east Asia and Australasia, but the genus Python is distinctive in that it also occurs in sub-Saharan Africa. There is a large distribution gap for Python between Africa and south-east Asia, but fossil evidence suggests Python once occurred in this gap, as well as in Europe until the mid-Miocene. However, because all African species have not previously been included in any previously published phylogeny, their monophyly has not been established. Further, it has been suggested that the genus Python may have an Asian origin, and this scenario would require the African species to be monophyletic. Otherwise, multiple independent dispersals into Africa would be required to explain current day biogeographic patterns. To test these competing hypotheses, a dated phylogeny was constructed based on one nuclear and two mitochondrial genes and biogeographic scenarios evaluated using ancestral range reconstruction. In addition, fossil evidence was appraised as supporting evidence for their paleo-distribution but also to evaluate the hypothesis that large pythons (e.g., > 6 m in body length) are restricted to warmer climatic zones, and we suggest this influenced their paleo- and present-day distributions. The dated phylogeny indicates monophyly for the African species, diverging from the Asian species approximately 33 Mya. Ancestral area reconstruction supports an Asian origin for the genus, with a single dispersal event to Africa after which species diversified across the continent. We find no support for multiple dispersal events into Africa. Accounting for the distribution of fossils, it appears that Python , including large-bodied species, were once more widespread, but ranges contracted in response to global cooling since the mid-Miocene, and they are now excluded from temperate (i.e., Europe, Iranian plateau) as well as hyper-arid areas (i.e., Arabian, Saharan and Namib deserts). The genus Python originated in Asia, with a single ancestral lineage entering Africa around 33 Mya where it diversified into four extant species. Fossil evidence reveals that Python was much more widespread but with mid to late Miocene global cooling, the African and south-east Asian clades became isolated geographically from each other. Large body size may have had an important influence on geographic range, limiting species to the warmer areas. Long-term global cooling has presumably driven range contractions, creating the distribution gap, and possibly causing extinctions of Python species.

Hot and dry weather conditions are known to impact the body condition and the fitness of many organisms. However, this relationship has not been extensively studied in snakes. We examined the impact of variation in rainfall and temperature on body condition for a population of cape cobras (Naja nivea) at Tswalu Kalahari Reserve (Northern Cape Province, South Africa) over a period of five years during which time environmental conditions fluctuated substantially. We measured the mass and body length of 105 cobras, 58 from which we collected repeat measures, and calculated a body condition index (BCI) for each observation. We tested whether BCI was impacted by season, sex, and/or differences from expected mean monthly rainfall (during the preceding four-, 12-, and 24-week periods) and mean daily maximum temperature (during the preceding four-, 12-, and 24week periods). Secondly, we tested whether BCI measures of cobras during the mating-season (September-November) were different between sexes and impacted by an index of environmental conditions (PC1 of rainfall and temperature) in the preceding summer. For our initial analysis, we found that the best-fitting model included season, sex, the relative amount of rain in the preceding twelve weeks (positive relationship), and the temperature in the preceding twelve weeks (negative relationship). Moreover, the BCI of cobras during the mating season was correlated with environmental conditions during the previous summer, with mating cobras exhibiting lower BCI measures following hot and dry summers. Our study reveals detrimental impacts of hot and dry conditions on cape cobra body condition, including measurable effects on body condition of mate-searching animals, following hot and dry summers. Taken together, we predict that prolonged hot dry periods, or increased frequency of hot dry periods in the future, might have detrimental effects on cape cobra populations in the Kalahari.

It has been hypothesized that biofluorescence is a trait linked to intraspecific signaling in many taxa, especially those with enhanced modes of conspecific signaling in complex habitats. Chameleons possess bone-based fluorescent tubercles (FTs) on their head ornaments that purportedly facilitate intraspecific signaling. We investigated the hypothesis that dwarf chameleons (Bradypodion) use biofluorescence for signaling by testing if the number of FTs associated with their ornaments can be explained by sexual dimorphism or ecological variation in five species from various habitats (i.e. fynbos, Afrotemperate forest, and shrublands). If the trait is used for signaling, we would expect males to have more FTs than females due to sexual selection, and/or forest species/populations to have more FTs than open-habitat species/populations via natural selection because forests are expected to be the most conducive terrestrial environment for fluorescent signals. Our results revealed that the number of FTs was greater for the larger sex (regardless of the direction of size dimorphism) but was not significantly different between sexes when adjusted for body size or head area. Forest species had more FTs than smaller-bodied fynbos species but fewer than the large-bodied shrublands species in absolute number, but there were no differences in FTs across species from different habitats when corrected for size and phylogeny. Moreover, there were no differences in FTs between natural and urban populations when correcting for body or head size. These findings suggest that larger-bodied species have more FTs than smaller-bodied species regardless of the conduciveness of their habitats toward facilitating biofluorescence. Therefore, FT trait magnitude is likely explained best by chameleon size rather than natural or sexual selection for increased signaling capability between sexes, species, or populations. We interpret these findings to suggest that it is unlikely that Bradypodion use biofluorescence as a signaling mechanism.

Biomonitoring studies have documented the presence of contaminants in various urban wildlife species, but research has predominantly focused on avian and mammalian species. Despite snakes possessing several traits that make them excellent subjects for ecotoxicological studies, knowledge on their capacity to serve as bioindicators remains limited, particularly in African ecosystems where their utility has not previously been assessed. In this study, we investigated the use of black mambas (Dendroaspis polylepis), a large-bodied snake species native to sub-Saharan Africa, to serve as a bioindicator for heavy metal pollution within an urban environment. We examined concentrations of arsenic, cadmium, lead, and mercury in ventral scale clippings and compared these to concentrations in internal tissue samples from dead specimens opportunistically collected around the city of Durban, South Africa. Our findings demonstrated that black mambas are exposed to and accumulate heavy metals within their tissues. Metal concentrations tended to be higher in scales than liver and muscle tissue and displayed substantial variability, which was not strongly linked to body size or sex. We found a clear association between land use and heavy metal exposure in black mambas. Snakes living in connected green spaces around the city generally had significantly lower heavy metal concentrations in their scales compared to those in more industrial and commercial areas. Our findings indicate that black mambas can act as valuable sentinels of heavy metal pollution, enabling the detection of fine-scale local patterns. This suggests that snakes could be valuable models for environmental monitoring elsewhere in Africa.

Historically, snakes have been considered to have a weak functional response to changing prey abundance due to their ectothermic physiology and slow digestion. I measured aspects of food consumption in a captive colony of puff adders (Bitis arietans) to evaluate their functional response. I introduce a new metric for this evaluation, the 'factorial scope of ingestion', defined as the maximum food intake divided by maintenance consumption. Rates of weight loss during fasting were also quantified to assess the potential for puff adders to persist through periods of low prey abundance. To maintain a constant body mass, puff adders must consume 63% of their body mass in rodents annually. However, when provided with unlimited food, they increased their food intake by an average factor of 12 times above maintenance levels for extended periods, which resulted in dramatic increases in body mass. Regression analysis between annualized food intake and changes in body mass, and direct measures of weight loss, independently estimated an annualized weight loss of ~ 23% body mass for fasting puff adders while metabolising fat. This suggests that a puff adder with a high initial body condition index could fast for more than 2 years. The extreme flexibility of puff adder feeding biology suggests that this species has a significant functional response to high prey abundance, and this response is likely to be much more profound than the functional response of mammalian predators. These findings highlight the importance of snakes as potential ecosystem stabilizers and for the control of agricultural rodent pests.

Abstract Barking geckos, Ptenopus Gray, 1866 are burrowing geckos that occur across the xeric regions of southern Africa. They possess unique vocal abilities, with males producing loud advertisement calls to attract females. The taxonomy of the genus has remained stable for six decades, with three recognised species: Ptenopus garrulus (Smith, 1849), P. kochi Haacke, 1964, and P. carpi Brain, 1962. Within P. garrulus, two subspecies have been recognised since 1935: the nominotypical form (P. g. garrulus) and P. g. maculatus Gray, 1866. A recent phylogenetic analysis of the genus found that it contains eight to ten putative species. We used an integrated taxonomic approach to delimit a total of nine species, including evidence from phylogenetics, ecology, calls, and morphology. Ptenopus g. maculatus is elevated to full species, thereby restricting the geographic range of P. garrulus sensu stricto to the greater Kalahari. Additionally, four new species are named which were previously included in ‘P. g. maculatus’: Ptenopus adamanteus sp. nov. from the southern Namib Desert, P. circumsyrticus sp. nov. from the central Namib Desert, P. kenkenses sp. nov. from the northern Nama Karoo, and P. australis sp. nov. from southern Nama Karoo. As a result, the range of P. maculatus sensu stricto is restricted to the central northern Namib Desert. Furthermore, one new species previously included in P. carpi is named P. sceletus sp. nov. from the Skeleton Coast (northern coastal Namib Desert), thereby restricting the range of P. carpi sensu stricto to a small strip of coastal Namib Desert between the Swakop and Kuiseb rivers. The Namib Desert is the centre of diversity for the genus Ptenopus, containing seven of the nine species including the oldest divergent lineages. Two species-level keys are provided: a morphological key and a unique bioacoustic key to the advertisement calls.

Background Snakebite is a public health challenge that has a substantial impact on humans and snakes. Annually, millions of people are affected by snakebite globally but there is a paucity of detailed data on snakebite incidences. The aim of this study was to assess the patterns of snakebite incidences in South Africa.Methods We collected data from hospital records, information from the National Snakebite Database and records from the AfriTox Telelog database from 2011 to 2024.Results The combined dataset showed that 3496 snakebite incidences have been recorded over 12.5 years. The prevalence was calculated to be 5.63 per 100 000 individuals of the population for South Africa, with the highest prevalence in KwaZulu-Natal (8.89). Males made up 65.9% of snakebite incidences and most incidences were recorded between November and March. The snake species responsible for most snakebite incidences was Bitis arietans.Conclusion Snakebite is generally well managed in South Africa with few recorded deaths despite the relatively high number of bites. However, incidents are often not recorded or have missing information particularly regarding the circumstances of the bite. Our study provides insight on the snake species responsible for snakebite incidences in South Africa and can be used to create prevention measures.

The African mambas (Dendroaspis) comprise an iconic genus of four large-bodied, highly venomous elapid snakes: the black mamba (D. polylepis) from open formations across sub-Saharan Africa is comprised of two allopatric populations, and three species of green mamba (D. angusticeps, D. jamesoni, and D. viridis) from tropical and sub-tropical forests. Dendroaspis angusticeps occurs in multiple isolated forest patches, and the presence of cryptic species within D. angusticeps has been suggested. The striking coloration of the three green species, a trait unique among elapids, suggests their monophyly to the exclusion of D. polylepis. We generated a dated, multilocus phylogeny of the mambas and assessed species boundaries. Species distribution modelling (SDM) was used to assess the past and present potential connectivity between allopatric populations of D. angusticeps and D. polylepis. The phylogeny suggests that diversification of the crown clade began c. 6 Mya and, contrary to previous suggestions, we found no convincing signal of species-level diversification within D. polylepis or D. angusticeps. The hypothesis of green mamba monophyly was rejected, with D. angusticeps being sister to D. polylepis. The SDMs suggested that allopatric populations of D. polylepis and D. angusticeps were historically connected, and that their vicariance is recent.

Kinetic feeding bones of macrostomatan Afrophidian snakes enable them to consume diverse prey types. While significant research has focused on functional feeding morphology in snakes, it often emphasizes broad taxonomic comparisons or species with distinct dietary ecologies. There is limited knowledge of how small variations in prey type composition may influence feeding morphology among closely related species sharing similar ecological niches. African Green and Bush Snakes (Philothamnus) feed primarily on frogs (anurophagous) and lizards (saurophagous), but the degree of intraspecific dietary generalization and specialization remains unclear. Thus, our study had three objectives: (1) to evaluate proportional differences in anurophagy and saurophagy between Philothamnus species, (2) quantitatively assess the shape differences in four of the main cranial bones functional in feeding, and (3) explore models of diet evolution. We hypothesized that differences in feeding morphology would reflect the extent of dietary specialization and/or generalization. Macroevolution diet analysis results indicated two main diet groups: anurophagous specialists and anuro-saurophagous generalists. We included 14 species to reconstruct ancestral dietary states within a phylogenetic framework and analysed five representative species using geometric morphometric methods to assess skull shape variation related to dietary specialization and generalization. Geometric morphometric shape analyses show that the jawbones of anurophagous specialists (P. angolensis and P. hoplogaster) have higher mechanical advantage (MA), pronounced posteriorly curved maxillary teeth, deeper mandibular fossae on a more convex shaped compound, wider proximal quadrates, and deeper quadromandibular joint articulations. Conversely, anuro-saurophagous generalists (P. occidentalis, P. natalensis and P. semivariegatus) have longer and thinner jaw bones with lower MA, a more horizontal dorsal quadrate, and high shape variation in maxillae and pterygoids. These findings suggest that dietary morphology is malleable and pervasive even among congeners with fine-scaled differences in prey type proportions. Dietary specialization and generalizations among the African Green and Bush Snakes appear to exist along a continuum. Dietary ecomorphology appears to be influenced by phylogenetic relationships and may have evolved in dual mode, i.e., gradual specialization and punctuated shifts in dietary generalisation in response to ecological opportunity.

Climate and land use changes are eroding biodiversity globally, and reptiles are highlighted as being particularly susceptible. In South Africa, global changes threaten the persistence of an assemblage of dwarf chameleons (Bradypodion) located in a biodiversity hotspot. We used ecological niche modelling to assess the combined effect of climate change and habitat transformation on these species and assessed their susceptibility in a vulnerability framework under optimistic and pessimistic change scenarios. Although our models showed a gain in suitable climatic space for all coastal species in some scenarios, considerable losses were predicted for most species under the most pessimistic change scenarios. Bradypodion ngomeense, for example is predicted to incur a complete loss of climatic suitability by 2050. The vulnerability framework predicts inland species to be more adversely affected by climate change than coastal species. However, no species show resilience to the combined effects of climate change and habitat transformation. Our models predicted a loss of climatically suitable habitat for most species in protected areas. These findings highlight the importance of a protected area network design to remain a step ahead of these anticipated changes.

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.

Elucidating factors that drive microhabitat selection in a species is important for informing the conservation management of the species. For species that use microhabitats as long-term refuge sites, selection pressures are likely to be strong because the microhabitat must fulfil their eco-physiological and life history requirements. Smaug giganteus (Sungazer) is a threatened (Vulnerable) cordylid lizard species in the highveld grasslands of South Africa - a key agricultural area in the country. Individuals dig burrows as refuges, which increases their sensitivity to habitat transformation. In addition, previous attempts to translocate populations have failed due to a lack of knowledge about their specific microhabitat requirements. We assessed microhabitat characteristics that may influence burrow site selection by measuring vegetation characteristics surrounding Sungazer burrows and comparing these to vegetation at randomly selected sites. We also recorded orientation, aspect, soil composition, and the presence of other animal dung. Sungazers selected sites with sparse vegetation cover, and where grass height was short, but had no preference for soil composition. There was no relationship between the presence of ungulate dung and the placement of Sungazer burrows. Most Sungazer burrows were orientated in a northerly direction on north-facing slopes, suggesting that burrow placement has thermoregulatory advantages. We recommend that to identify suitable sites for Sungazer translocations, landscapes are thoroughly surveyed with cognisance to the findings in this study, and that a soft-release translocation protocol follows to maximise translocation success.

The sungazer (Smaug giganteus) is a strict grassland specialist lizard endemic to South Africa's highveld grasslands. It is currently listed as Vulnerable (IUCN) and is primarily threatened by anthropogenic activities. Because sungazers are habitat specialists, climate change may be detrimental to the species, considering their life-history traits, and the area of available suitable habitat. We assessed how climate change may impact the sungazers' geographic range by first producing an ecological niche model (ENM) for the species within a buffered region of its extent of occurrence (buffered EOO). The ENM was then projected to 2040, 2060, 2080 and 2100 under two climate change scenarios using Shared Socioeconomic Pathways (SSP); SSP245 (moderate-case) and SSP585 (worst-case). A mean ensemble of three global circulation models for each time period and scenario was used to create habitat suitability maps which were refined using a natural grassland variable overlay. Resulting maps were clipped to the sungazers' EOO and interpreted distribution. Within the interpreted distribution, models predicted an area of 10 198 km(2) of current suitable habitat. At this scale, future habitat suitability is predicted to remain relatively stable (area: 9910 km(2); 3% decline) under SSP245 by 2100. However, a 24% decline (area: 7705 km(2)) in habitat suitability was predicted under SSP585. Within the buffered EOO, habitat suitability increased in south-western regions, which was more prominent under SSP585. Although this finding suggests that sungazers could track favourable conditions, their life history and low dispersal ability makes climate tracking unlikely. Because sungazers only occur in primary grasslands, regions dominated by agricultural activities, further land use developments are likely to affect the species survival. Thus, careful conservation management is essential, and we recommend the establishment of protected areas with cognizance of our predictions for current and future suitable habitat within the sungazers' interpreted distribution.

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.

The North West Province, South Africa, is centrally situated in southern Africa and is characterised by savannah with a mesic, temperate climate in the east and a hot, arid climate in the west. While the eastern region is fairly well-documented for herpetofauna, the arid central and western regions are poorly surveyed. Given that the Province has been targeted by the national government for development of infrastructure, the overall deficiency of biodiversity data could result in impact assessments that are not well-informed. We, therefore, carried out herpetofaunal surveys over two years (2019–2020) in the North West Province to improve knowledge on the distributions of reptiles and amphibians. Our surveys added a total of 578 new records to an earlier baseline of 1340 records. In addition, over 300 records were added to a citizen-science platform in connection with our surveys. As compared to the previous 100 years, our surveys increased the herpetofaunal dataset by 68% in just two years, increased geographic coverage by 20% and brought the total number of species with accurate records for the Province to 102 reptiles and 23 amphibians. We also recorded range extensions for five reptile species and confirmed the presence of Dendroaspis polylepis (Black Mamba) in the west where it had been last recorded in 1996. Our surveys resulted in a significant increase in biodiversity data for the Province and provided a better foundation for spatial planning that accounts for biodiversity and the maintenance of ecological function.