Krystal Tolley

South African National Biodiversity Institute · Biodiversity Research, Assessment and Monitoring Division

In biodiversity research, the retrieval of genetic material from organisms is a common and essential component for assessing genetic diversity. The welfare of the organism, however, needs to be balanced against the overall goal of the intended research. One sampling technique often applied to retrieve DNA material from small reptiles is the removal...

In biodiversity research, the retrieval of genetic material from organisms is a common and essential component for assessing genetic diversity. The welfare of the organism, however, needs to be balanced against the overall goal of the intended research. One sampling technique often applied to retrieve DNA material from small reptiles is the removal...

Urbanisation creates novel environments, not only through (abiotic) microhabitat alterations, but also due to changes in (biotic) inter- and intraspecific interactions. Where sheltering sites in urban habitats are limited, intra or interspecific interactions may increase, resulting in increased competition and changes in predation risk in urban are...

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 rel...

The Open Institute of the African BioGenome Project empowers African scientists and institutions with the skill sets, capacity and infrastructure to advance scientifc knowledge and innovation and drive economic growth.

Africa, a continent of 1.3 billion people, had 326 researchers per one million people in 2018 (Schneegans, 2021; UNESCO, 2022), despite the global average for the number of researchers per million people being 1368 (Schneegans, 2021; UNESCO, 2022). Nevertheless, a strong research community is a requirement to advance scientific knowledge and innova...

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 b...

The IUCN recently coordinated the first assessment of extinction risk of the world's reptile species. This monumental undertaking allows, for the first time, an examination of threats and prioritization of conservation effort, not just for reptiles, but for land vertebrates as a whole. Reptiles are now the largest class of land vertebrates in terms...

The Red List Index (RLI) measures change in the aggregate extinction risk of species. It is a key indicator for tracking progress toward nine of the Aichi and many proposed post‐2020 Global Biodiversity Framework Targets. Here, we consider two formulations of the RLI used for reporting biodiversity trends at national scales. Disaggregated global RL...

Previous molecular phylogenetic studies of pygmy chameleons have identified several cases of undescribed cryptic diversity of species, some of which have remained undescribed due to a lack of morphological information. Here, we combine descriptive morphology with principal component analysis, to quantify the overall morphological variation, and phy...

Species-level phylogeny and especially phylogeography of African chelonians is a comparatively under-studied field of research. We review the current knowledge of phylogeny and phylogeography, highlight congruence of spatial phylogeographic patterns amongst chelonians and other taxa and suggest future research directions to address gaps in knowledg...

Arboreal chameleons must navigate a complex, three-dimensional landscape consisting of trees, bushes and/or grasses of various sizes. This complexity equates to the microhabitat of chameleons, that is, the branches upon which they perch and through which they move. Therefore, chameleons rely on their ability to grip perches available to them, and t...

The genus Heliobolus comprises four recognized species, all endemic to sub-Saharan Africa. Of these, only Heliobolus lugubrisoccurs in southern Africa, its distribution extending from Angola in the west to Mozambique in the east and reaching as far south as parts of northern South Africa. Like many of the reptile species that occur in southern Afri...

Genetic diversity provides the capacity for species to evolve in response to environmental change, and its importance in assessing the status of species is well established. However, there is a paucity of genetic monitoring studies. The Endangered western leopard toad (Sclerophrys pantherina), endemic to South Africa, is a good candidate for geneti...

Estimating and planning for the impacts of climate change on the biodiversity of protected areas is a major challenge for conservation managers. When these areas are topographically heterogenous and contain species' entire ranges, this challenge is exacerbated because the coarse spatial scales of Global Circulation Model projections provide limited...

Molecular phylogenetics and the application of species delimitation methods have proven useful in addressing limitations associated with morphology based taxonomy and have highlighted the inconsistencies in the current taxonomy for many groups. For example, the genus Chamaeleo, which comprises 14 species with large distributions across mainland Afr...

Comprehensive assessments of species’ extinction risks have documented the extinction crisis and underpinned strategies for reducing those risks. Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction. Because global assessments have been lacking, reptiles have been o...

The Great Karoo is an ecologically fragile, poorly studied arid region in central South Africa. With the discovery of shale gas as a potential resource in the Great Karoo, it is expected that a substantial footprint will be left in this region if gas extraction proceeds. This highlights the need for biodiversity surveys of the Great Karoo of taxono...

Comprehensive assessments of species’ extinction risks have documented the extinction crisis and underpinned strategies for reducing those risks. Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction. Because global assessments have been lacking, reptiles have been o...

Angola has experienced an incredible increase of the knowledge of its herpetofauna over the past decade. However, accurate biodiversity inventories remain deficient for certain regions of particular conservation interest. We therefore provide an updated checklist of Iona National Park’s herpetofauna, with 75 recorded species, including five amphibi...

The mechanisms that underpin ecological speciation, morphological convergence and the evolution of ecological morphotypes (ecomorphs) in squamates have allowed for a better appreciation of the speciation process in chameleons. In particular, attention has been drawn to several populations of chameleons (Sauria, Chamaeleonidae, Bradypodion) from the...

Open access to sequence data is a cornerstone of biology and biodiversity research, but has created tension under the United Nations Convention on Biological Diversity (CBD). Policy decisions could compromise research and development, unless a practical multilateral solution is implemented. Ensuring international benefit-sharing from sequence data...

It is commonly recognised that natural history datasets contain locality errors that can compromise the utility of those datasets. However, another source of error in these datasets is taxonomic misidentifications, and this type of error is potentially common, particularly with regards to morphologically conservative species. For example, in the Af...

Although reproductive strategies are poorly documented in chameleons, sperm storage has been confirmed among some species for which male reproductive success may be maximised by increasing the number of females inseminated and/or preventing subsequent female copulation with rival males. Behaviour, such as mate searching, may enable males to maximis...

Detecting occupied sites of rare species, and estimating the probability that all occupied sites are known within a given area, are desired outcomes for many ecological or conservation projects. Examples include managing all occupied sites of a threatened species, or eradicating an emerging invader. Occupied sites may remain undetected because 1) s...

The Great Karoo and Namaqualand of South Africa are home to a species complex of morphologically conserved lizards that occur in allopatry (Karoo: Cordylus aridus, Cordylus cloetei, Cordylus minor; Namaqualand: Cordylus imkeae). However, there are negligible morphological differences and a lack of obvious physical or climatic barriers, particularly...

Climate shifts during the Quaternary Period have driven changes in regional range dynamics for many species, influencing population structure of species and in some cases promoting speciation. Within southern Africa, the psammophine snakes Psammophis trinasalis and P. namibensis were historically considered subspecies of P. leightoni but were eleva...

The genus Pedioplanis reaches its northernmost limit in western Angola, where it is represented by three species, Pedioplanis benguelensis, P. haackei and P. huntleyi. The taxonomic status of P. benguelensis remains problematic, mainly due to the vague original escription and the loss of the original type material. Here we provide a revision of the...

Background The African continent is comprised of several different biomes, although savanna is the most prevalent. The current heterogeneous landscape was formed through long-term vegetation shifts as a result of the global cooling trend since the Oligocene epoch. The overwhelming trend was a shift from primarily forest, to primarily savanna. As su...

The Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum is endemic to the low elevation rainforest of the Malawi Hills in southern Malawi. Much of this forest has been converted to agriculture and it was uncertain whether chameleon populations have persisted. We used current and historical satellite imagery to identify remaining...

Despite increasing awareness of issues affecting inclusivity, equity and diversity, change has been slow in science and academia, and gender disparities remain significant. Biogeography has not escaped this pattern. Here, we present a virtual issue compiling some of the most cited papers led by women that have been published in the Journal of Bioge...

Burrowing is a common behavior in vertebrates. An underground life‐style offers many advantages but also poses important challenges including the high energetic cost of burrowing. Scolecophidians are a group of morphologically derived subterranean snakes that show great diversity in form and function. Although it has been suggested that leptotyphlo...

Rose’s dwarf mountain toadlet, Capensibufo rosei (Hewitt, 1926), is endemic to fire-dependent, montane fynbos vegetation on South Africa’s Cape Peninsula. The area undergoes natural fire cycles that are disrupted due to increasing urban pressure from the City of Cape Town. In this natural history observation, we report on C. rosei microhabitats use...

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to...

The Angolan Adder, Bitis heraldica (Bocage, 1889), is endemic to the Angolan central plateau and is one of the most poorly known and rarely observed species of African snakes. The phylogenetic placement of B. heraldica within the four subgenera of the genus Bitis (Bitis, Macrocerastes, Calechidna, Keniabitis) has been problematic. The few recent ta...

The Scaled Sandveld Lizard Nucras scalaris Laurent, 1964 is a poorly known lacertid endemic to north-eastern Angola and is only known from the type series collected more than half a century ago. The original description provided a comprehensive morphological description, but there was a lack of information regarding its evolutionary relationships a...

The African colubrid snake genus Crotaphopeltis currently comprises six species and occurs throughout sub‐Saharan Africa. The most widespread of these, Crotaphopeltis hotamboeia, inhabits most biomes, aside from rainforest and hyper‐arid regions, and its catholic niche has presumably facilitated substantial gene flow. Despite this, the geographical...

A new endemic Sandveld Lizard, genus Nucras, is described from south-western Angola. Morphologically it resembles members of the Nucras tessellata group, but it is genetically separated and is sister to the larger tessellata + lalandii group. Although the genus is generally very conservative morphologically, the new species differs from other conge...

The NBA 2018 Synthesis report can be downloaded from the NBA website: http://nba.sanbi.org.za

Previous studies on leaf-tailed geckos of the genus Uroplatus identified a lineage from the Ankarana karst massif in northern Madagascar as genetically highly divergent, but only fragmentary information was available on these geckos. Here, we provide an integrative analysis based on molecular and morphological data, including a newly collected spec...

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 scient...

There are notable examples of repeated evolution of ecomorphs within groups of closely related species, these are typically viewed as remarkable cases of natural selection. In most cases, directional selection for certain phenotypic traits under specific (and differing) environmental conditions is implicated. Differing ecomorphological forms for cl...

A new species of tree snake Dipsadoboa montisilva Branch, Conradie & Tolley sp. nov. (Serpentes: Colubridae) is described from the ‘sky islands’ of Mount Mabu and Mount Ribáuè in northern Mozambique. Features of scalation, colour, body form and habitat distinguish the new species from other Dipsadoboa. This is supported by a phylogenetic analysis u...

Aim The expansion of open habitats during the mid‐Miocene has been hypothesized as a driver of allopatric speciation for many African taxa. This habitat‐dependent mode of diversification has been implicated in the shift from C3 (e.g. forest/woodland) to C4 dominated systems (i.e. open savanna, grasslands) in a number of African squamates. We examin...

Scaling evolutionary trees to time is essential for understanding the origins of clades. Recently developed methods allow including the entire fossil record known for the group of interest and eliminated the need for specifying prior distributions for node ages. Here we apply the fossilized birth-death (FBD) approach to reconstruct the diversificat...

Compared to the global average, extinction risk for mainland African reptiles, particularly for South Africa, appears to be relatively low. Despite this, African reptiles are under threat primarily due to habitat loss as a result of agriculture, resource extraction, and urbanisation, and these pressures are expected to increase into the future. Sou...

Life on earth relates directly to the diversity of genes in space and time. The genomes of organisms encode the basic biological structures that define them, and allows individuals to survive and persist through time in changing environments. To this end, DNA can best be described as the foundation of all life on earth, it is recognised as an impor...

IUCN assessment of Scolecoseps boulengeri, Boulenger's Limbless Skink (2019)

IUCN assessment of Proscelotes aenea, Montane Skink (2019)

This chapter discusses the status of genetic monitoring in South Africa, highlighting key considerations for future genetic monitoring programmes, such as which species to prioritize, how often should they be monitored, what molecular markers to use, and the type of indicators to be evaluated

Throughout the Miocene, the African landscape underwent broad climatic shifts that profoundly influenced the distribution of fauna and flora. Since the late Miocene, these shifts have created a landscape in southern Africa that is strongly characterised by savanna and arid environments. Forests persist in small fragments, primarily in mountainous o...

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,...

Several biogeographic barriers in the Central African highlands have reduced gene flow among populations of many terrestrial species in predictable ways. Yet, a comprehensive understanding of mechanisms underlying species divergence in the Afrotropics can be obscured by unrecognized levels of cryptic diversity, particularly in widespread species. W...

The spatial genetic structure of a species, and whether distinct genetic lineages are present, is strongly influenced by their biology and habitat requirements. Given habitat specificity and low vagility, many herpetofaunal species are reservoirs for high levels of cryptic diversity; chameleons are a case in hand. The common flap-necked chameleon C...

Given the ever-increasing anthropogenic changes to natural ecosystems, it is imperative that temporal changes in genetic diversity be monitored to help safeguard the future viability of species. Capensibufo rosei is a small, range-restricted bufonid from South Africa, believed to have experienced an enigmatic decline likely due to the suppression o...

The sub-Saharan African file snake genus Gonionotophis is currently comprised of 15 species. However, the concept of this genus has been confounded by morphological and genetic differences between the constituent taxa. Due to the dearth of DNA samples, a taxonomic assessment has been impractical to date. We therefore sequenced two mitochondrial and...

Pachydactylus is the most species-rich reptile genus in southern Africa. Most species are habitat specialists adapted to hyper-arid conditions of the Namibian and north-western South African xeric regions. Although a fair number of phylogenetic studies and taxonomic revisions have been published, some species still remain rather enigmatic. In the t...

Nothophryne Poynton, 1963 is a monotypic genus of frog, with the nominal species N. broadleyi found only on Mount Mulanje, in southern Malawi. Recent surveys in northern Mozambique, however, have uncovered at least four new species associated with four inselbergs (Mount Inago, Mount Namuli, Mount Ribáuè and Taratibu Hills). Previous phylogenetic an...

Age-specific survival and reproduction are closely linked to fitness and therefore subject to strong selection that typically limits their variability within species. Furthermore, adult survival rate in vertebrate populations is typically less variable over time than other life-history traits, such as fecundity or recruitment. Hence, adult survival...

Intraspecific genetic diversity provides the basis for evolutionary change and is therefore considered the most fundamental level of biodiversity. Mitochondrial DNA (mtDNA) and microsatellite loci are the markers most typically used in population-level studies; however, their patterns of genetic variation are not always congruent. This can result i...

Ecological niche models (ENMs) have been used in a wide range of ecological and evolutionary studies. In biogeographic studies these models have, among other things, helped in the discovery of new allopatric populations, and even new species. However, small sample sizes and questionable taxonomic delimitation can challenge models, often decreasing...

Direct anthropogenic factors (e.g., habitat loss, fragmentation, and degradation) threaten many amphibian populations, however some declines have occurred in supposedly pristine environments with no obvious causes. These enigmatic declines may be due to shifts in environmental factors influencing development and ultimately adult survival. Rose’s mo...

Aim To investigate whether morphological variation in a continental radiation of lizards (Chamaeleonidae) was driven by ecological opportunity. Location KwaZulu‐Natal, South Africa. Methods Chameleons from all morphotypes were genotyped ( n = 279) using 10 microsatellite and one mitochondrial marker ( n = 130). Genetic spatial structure was exami...

A molecular and morphological study of the Mountain Toadlets, previously included in Capensibufo rosei, showed that there are several previously unrecognised species in this group. We describe three new species from the Hawekwas, Hot-tentots-Holland, Groenland and Riviersonderend Mountains; the DuToitskloof Mountains, and the Akkedis, Koeël and Kle...