Two new Poyntonophrynus species (Anura: Bufonidae) highlight the importance of Angolan centers of endemism
- Authors: Baptista, Ninda L , Pinto, Pedro V , Keates, Chad , Lobón-Rovira, Javier , Edwards, Shelley , Rödel, Mark-Oliver
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/461572 , vital:76214 , xlink:href="https://zoobank.org/7B5494CC-F8F2-46EA-BB73-D28B13D31CB6"
- Description: The pygmy toad genus Poyntonophrynus is endemic to southern Africa. The morphology of these small toads is conserved. They are usually dully colored, and are predominately adapted to arid conditions. During recent surveys in Angola we found Poyntonophrynus specimens that were not assignable to known species. Using an integrative approach, based on mitochondrial and nuclear DNA, morphology, osteology, biogeography and ecology, we identified three new lineages, and describe two of them as new species. All three lineages are closely related to P. pachnodes, an Angolan endemic species, but they are geographically isolated from it. The new species are morphologically distinguishable, and are associated with two of the most important Angolan centers of endemism: the western escarpment and the central highlands. In order to get a more comprehensive understanding of the osteology of the genus, we also provide an osteological characterization of P. dombensis, which was not available to date. Our findings i) increase the number of earless species in the genus Poyntonophrynus, ii) emphasize southwestern Africa as the cradle of diversification in this genus, iii) report the occurrence of Poyntonophrynus in humid environments, thus showing that these toads are ecologically more variable than previously thought, and iv) underline the importance of further biodiversity studies in Angolan centers of endemism.
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- Date Issued: 2023
Systematic revision of Afrogecko ansorgii (Boulenger, 1907)(Sauria: Gekkonidae) from western Angola
- Authors: Lobón-Rovira, Javier , Conradie, Werner C , Pinto, Pedro V , Keates, Chad , Edwards, Shelley , du Plessis, Anton , Branch, William R
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/461550 , vital:76212 , xlink:href="https://doi.org/10.11646/zootaxa.5124.4.1"
- Description: Here we provide the first phylogenetic analysis that include Afrogecko ansorgii and a detailed morphological comparison with other species of leaf-toed geckos. For this purpose, we used two mitochondrial (16S, ND2) and four nuclear (RAG1, RAG2, CMOS, PDC) genes to produce a robust phylogenetic reconstruction. This allowed us to show that A. ansorgii is not related as previously believed to circum-Indian Ocean leaf-toed geckos and is rather more closely related to other Malagasy leaf-toed geckos. Additionally, we explore and compare osteological variation in A. ansorgii skulls through High Resolution X-ray Computed Tomography with previously published material. This allowed us to describe herein a new genus, Bauerius gen. nov., and additionally provide a detailed redescription of the species (including the first description of male material), supplementing the limited original description and type series, which consisted of only two females.
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- Date Issued: 2022
Integrative systematic structuring of the widespread psammophiid snakes (Psammophiidae): a multi-evidence species delineation approach
- Authors: Keates, Chad
- Date: 2021-10-29
- Subjects: Psammophis South Africa , Herpetology , Herpetology Africa , Molecular biology , Psammophis Classification , Psammophis Genetics , Psammophis Morphology , Psammophis Phylogeny , Morphology Mathematics , Psammophylax
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/295077 , vital:57288 , DOI 10.21504/10962/295079
- Description: Species form the foundations upon which we build our understanding of the natural world. Although a focus of much scientific attention, our understanding of species is stunted by the intrinsic ‘fuzziness’ of boundaries within nature. Due to the complexity of the evolutionary process, coupled with an ever-changing abiotic landscape, species are hard to delineate, even at the best of times. Whilst various species concepts and sophisticated delimitation methods have helped scientists tease apart species, many species complexes persist. This is because taxonomy is a discrete ordering system imposed upon the continuous and intercalated structure of life. To improve our understanding of a wide-ranging family of snakes, I investigated the taxonomy and evolutionary structuring within Psammophiidae using both molecular and morphological approaches, employing phylogenetic, phylogeographic, and morphometric analyses on the group. The systematic complexity of the family (as evidenced by past research) coupled with the group’s widespread distribution and ecological importance, made the taxon an ideal candidate for a broad-sweeping multi-level systematic analysis using multiple species delimitation methods. Additionally, in this thesis I attempted to build on the ground-breaking work of Christopher Kelly by addressing several knowledge gaps identified within the family, and in so doing, produce the most thorough evolutionary and taxonomic study of Psammophiidae possible. Given the taxonomic uncertainty associated with the family, Chapter Two used a representative sampling from every available species (near complete taxon sampling approach) in the family. The chapter used both standard and time-calibrated phylogenetic modelling and distance/threshold-based species delimitation, to elucidate the finer-level structuring within the family. Geometric morphometrics was used to determine whether there were diagnosable differences in head structure between the different genera. The final phylogenetic tree incorporated 320 samples, representing the most comprehensive phylogenetic reconstruction of the family to date. By using a near-complete taxon sampling approach, I was able to resolve previously unsupported relationships within the family whilst also identifying several novel instances of an under- and over-appreciation of species diversity within the family. Geometric morphometrics also identified clear distinctions between genera based on head shape (head width and ‘beakedness’). This chapter showcased the importance of complete taxon sampling and robust methodology for species delimitation and the deleterious effect of species concepts when implemented in isolation. In Chapter Three, I narrowed the scope of the study to focus on the genus level. Psammophylax (Fitzinger 1843) is an abundant, yet poorly studied genus of grass snakes, endemic to Africa. The generalist nature of the genus and wide-spanning distributions of the constituent species has given rise to several subspecies and a poor understanding of the taxonomic structuring within the genus. The overlapping distributions (sympatry) of many of Psammophylax species, coupled with the potential for cryptic speciation via mechanisms such as convergent evolution, made the group the ideal candidate for a broad-sweeping systematic study (as evidenced in Chapter Two). By applying the suite of analyses used in Chapter Two to the generic level, we aimed to determine the effectiveness of a multi-evidence species delineation approach when tackling systematic problems at lower taxonomic levels. A genetic phylogeny of six of the seven species was estimated using multiple phylogenetic and distance/ threshold-based species delimitation methods. To support the molecular analyses, we conducted morphological analyses on the body (traditional morphology) and head (geometric morphometrics) separately. Phylogenetic analyses recovered a similar topology to past studies, but with better resolution and node support. I found substantial genetic structuring within the genus, supported by significantly different head shapes between Ps. a. acutus and other Psammophylax species. Psammophylax a. acutus was recovered as sister to its congeners, and sequence divergence values and morphometrics supported its recognition as a new genus. Increased sampling in East Africa (Tanzania, Kenya, and Ethiopia) revealed that Psammophylax multisquamis is polyphyletic, necessitating the description of a new, morphologically cryptic, species from northern Tanzania. The distribution of Ps. multisquamis sensu stricto is likely restricted to Kenya and Ethiopia. Within this chapter, taxon-specific phylogenetic analyses yielded stronger intrageneric support as compared to Chapter Two, allowing for more defensible conclusions about taxonomical amendments. Geometric morphometrics proved similarly useful (as compared to Chapter Two) in teasing apart genera within the family but lacked the robustness to delineate species within Psammophylax with confidence, highlighting the apparent convergence of form within the genus. In Chapter Four, I investigated the evolutionary structuring within the Southern African endemic Psammophylax rhombeatus. The structural and environmental heterogeneity within the region has given rise to many morphological forms distributed throughout the country, with previous studies neglecting the associated molecular significance of these forms. Irrespective of their small sample sizes, both Chapter Two and Three identified substantial phylogenetic structuring within the species, making Ps. rhombeatus the ideal candidate for a multi-faceted systematic review, using a combination of phylogenetics, geometric morphometrics and, for the first time in this species, phylogeographic analyses. By investigating a single species, in detail, I was able to assess the effectiveness of the methodologies implemented in previous chapters on systematic sorting using the multi-evidence species delineation approach. Phylogenetic and haplotype analysis retrieved four well-supported clades: southeast South Africa (SESA), southwest South Africa (SWSA), north-eastern South Africa (NESA) and western South Africa (WSA). Although not variable enough to warrant taxonomic re-evaluation, the clades represented important genetic hotspots, with relatively high intraspecific genetic divergence values separating them, irrespective of the small geographic distances separating populations. This is likely a product of the taxon’s habitat-generalist lifestyle, enabling them to bypass vicariant barriers that might otherwise cause speciation in less versatile species. The clades are also geographically distinct, with little overlap, indicating previous vicariance, a finding that is supported by the split of Ps. rhombeatus from Ps. ocellatus in the mid-Pliocene, followed by the diversification of Ps. rhombeatus into four clades throughout the Pleistocene. The genetic structuring observed in Ps. rhombeatus may be a product of population expansion following ancient refugial isolation (potentially Last Glacial Maximum [LGM]). The molecular distinctiveness of the clades was not replicated in the morphological component of this chapter, with neither dorsal nor lateral geometric morphometric analyses of head shape showing any discernible distinctiveness based on geography. Whilst head shape has not been shown to be an effective delineator of evolutionary units at the species level (within this taxon), body colour, scalation, and snout-vent length has been linked to morphotypes within the species based on the work of Broadley (1966). These morphological groupings are loosely attributable to the molecular clades identified in the phylogenetic analyses, highlighting the complex interplay of genetic and morphological characteristics in the process of speciation, and their representation in systematic accounts. This thesis represents the most thorough evolutionary and systematic study of the family currently possible. In addition to identifying and describing both a new genus and species, this thesis also highlighted several instances of an over- and under-appreciation of species diversity within Psammophiidae. By applying a multi-evidence species delineation approach to this thesis, I show the intricacy of the evolutionary process (at various taxonomic levels) and showcase the ease to which species boundaries can be confounded when species concepts are implemented in isolation. These findings also highlighted the importance of sample size, sample range, species delimitation method on the outcome of taxonomic analyses, and their interpretation. Lastly, this thesis addressed the knowledge gaps left by Christopher Kelly’s PhD work and investigated the findings of recent papers that attempted to do the same. Whilst this study answers the questions of old, the taxon-intensive focus revealed several new knowledge gaps within the family, highlighting how much we know about snake systematics, and furthermore, how much we still need to learn about evolutionary structuring. , Thesis (PhD) -- Faculty of Science, Environmental Science, 2021
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- Date Issued: 2021-10-29
A new species of red toad, Schismaderma Smith, 1849 (Anura: Bufonidae), from central Angola
- Authors: Baptista, Ninda L , Pinto, Pedro V , Keates, Chad , Edwards, Shelley , Rödel, Mark-Oliver , Conradie, Werner C
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/461462 , vital:76204 , xlink:href="https://www.biotaxa.org/Zootaxa/article/view/zootaxa.5081.3.1"
- Description: A new species of red toad, from the previously monotypic genus Schismaderma, is described. The new species was found in Malanje Province, and seems endemic to central Angola, occurring approximately 500 km west of the closest known records of Schismaderma carens. Unusual adult colouration and geographical distance to remaining S. carens populations suggested specific differentiation. In an integrative approach, we compared the red toads from central Angola with S. carens from across the entire range, including molecular data, morphology of adults and tadpoles, and male advertisement calls. Phylogenetic analysis based on mitochondrial (12S, 16S, COI) and nuclear (CXCR4, RAG1) markers, retrieved the Angolan clade as monophyletic, and revealed intra-specific substructuring among the remaining Schismaderma. Genetic distances supported specific differentiation of the central Angolan material compared with other S. carens. Adults from the new Angolan species have bolder ventral patterning and smaller body size than S. carens. No obvious differences were detected between the tadpoles and the advertisement calls of the two Schismaderma species. This discovery adds to the knowledge of the herpetofauna of the Angolan Miombo woodlands, a poorly understood ecoregion, and likely more biodiverse than previously assumed. The result of past river basin dynamics in central Angola likely led to the evolution of this new species of Schismaderma.
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- Date Issued: 2021
New insights into the geographical distribution, ecology and conservation status of South Africa’s endemic Coastal Leaf-toed Gecko, Cryptactites peringueyi (Boulenger, 1910)
- Authors: Nicolau, Gary K , Petford, Melissa , Edwards, Shelley , Busschau, Theo , Lynch, Kier , Kemp, Luke , Balmer, Jonathan P , Keates, Chad , Hundermark, Courtney R , Weeber, Joshua , Conradie, Werner C
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/461517 , vital:76209 , xlink:href="https://www.biotaxa.org/hn/article/view/63908"
- Description: Range-restricted species are generally poorly known and at higher risk of extinction than species with wider distributions. In the past, the Coastal Leaf-toed Gecko, Cryptactites peringueyi (Boulenger, 1910) caused much confusion and was once referred to as “one of the herpetological mysteries of the region”. Knowledge on the species has grown substantially, predominately due to new insights into its ecological preferences. Surveys from 2018 through early 2020 re-established the presence of C. peringueyi at three of four historical localities, as well as documenting four new localities. In 2018, preliminary data from these surveys resulted in an IUCN Red List downgrading from Critically Endangered to Near Threatened. However, with further investigation into the distribution of the species, the results from the present study more than doubled the previously estimated Extent of Occurrence from 785 km2 to 1504 km2 and the populations appear to be stable, despite environmental and anthropogenic disturbance. By incorporating environmental niche modelling, we further discuss the distribution, habits and ecology of C. peringueyi. The results presented here highlight the importance of fully understanding a species’ ecology to address its conservation status and we suggest that a new listing of Least Concern is appropriate for C. peringueyi.
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- Date Issued: 2021
New insights into the taxonomic status, distribution and natural history of De Witte's Clicking Frog (Kassinula wittei Laurent, 1940)
- Authors: Conradie, Werner C , Keates, Chad , Lobón-Rovira, Javier , Vaz Pinto, Pedro , Verburgt, Luke , Baptista, Ninda L , Harvey, James , Júlio, Timóteo
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443572 , vital:74134 , https://hdl.handle.net/10520/ejc-afzoo-v55-n4-a6
- Description: Kassinula is a monotypic genus of small frog in the family Hyperoliidae, only represented by Kassinula wittei. This species morphologically resembles both Kassina Girard, 1853 and Afrixalus Laurent, 1944, and its taxonomic status has been debated for decades. It has previously been subsumed within Kassina, and is currently placed as a sister genus to Afrixalus, although it has not been included in any phylogenetic studies until now. This species is poorly represented in museum collections and is only known from fewer than 35 specimens from southern Democratic Republic of the Congo and adjacent Zambia. Newly collected material from central Angola, a range extension of 400-800 km west of previously known localities, allowed us to revisit the taxonomic placement of the genus with the aid of phylogenetic analysis and shed light on its geographic distribution, morphology and natural history. Although our phylogenetic analysis is limited to a single mitochondrial gene (16S), we place Kassinula in the subfamily Hyperoliinae and closely related to Afrixalus, with a high degree of confidence. Further phylogenetic studies are needed before formally synonymising Afrixalus with Kassinula.
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- Date Issued: 2020
A snake in the grass: Genetic structuring of the widespread African grass snake (Psammophylax Fitzinger 1843), with the description of a new genus and a new species
- Authors: Keates, Chad , Conradie, Werner C , Greenbaum, Eli , Edwards, Shelley
- Date: 2019
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/461473 , vital:76205 , xlink:href="https://doi.org/10.1111/jzs.12337"
- Description: Psammophylax (Fitzinger 1843) is a widespread yet poorly studied genus of African grass snakes. A genetic phylogeny of six of the seven species was estimated using multiple phylogenetic and distance‐based methods. To support the genetic analyses, we conducted morphological analyses on the body (traditional morphology) and head (geometric morphometrics) separately. Phylogenetic analyses recovered a similar topology to past studies, but with better resolution and node support. We found substantial genetic structuring within the genus, supported by significantly different head shapes between P. a. acutus and other Psammophylax. Psammophylax a. acutus was recovered as sister to its congeners, and sequence divergence values and morphometrics supported its recognition as a new genus. Increased sampling in East Africa (Tanzania, Kenya, and Ethiopia) revealed that Psammophylax multisquamis is polyphyletic, necessitating the description of a new, morphologically cryptic species from northern Tanzania. The distribution of P. multisquamis sensu stricto is likely restricted to Kenya and Ethiopia. The study has further resolved multiple aspects of Psammophylax systematics, including the taxonomic validity of two central African subspecies, P. variabilis vanoyei (Laurent 1956) and P. tritaeniatus subniger (Laurent 1956). Inclusion of specimens from the more remote parts of Africa, in future analyses, may result in the recovery of additional diversity within Psammophylax.
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- Date Issued: 2019
Rediscovery, taxonomic status, and phylogenetic relationships of two rare and endemic snakes (Serpentes: Psammophiinae) from the southwestern Angolan plateau
- Authors: Branch, William R , Baptista, Ninda L , Keates, Chad , Edwards, Shelley
- Date: 2019
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/462658 , vital:76323 , xlink:href="https://zoobank.org/References/7FEE7CB2-9A74-407A-A9DB-DB714FEF1E0F"
- Description: Two rare and endemic psammophines (Serpentes: Psammophiinae) occur in Angola. The taxonomic status of Psammophylax rhombeatus ocellatus Bocage, 1873 and Psammophis ansorgii Boulenger, 1905 have long remained problematic, with both having varied past and present taxonomic assignments, and whose distributions may therefore present zoogeographic anomalies. Little was known of their biology, habitat associations, or phylogenetic relationships. New material was collected during biodiversity surveys of the Humpata Plateau, near Lubango, Angola. It allowed fuller descriptions of scalation and live coloration for both species, and resolution of their taxonomic status. Genetic analysis confirms that both are distinct at the specific level. In addition, within Psammophis, Jalla’s Sand Snake (Psammophis jallae Peracca, 1896), of which P. rohani Angel, 1925, remains a synonym, is sister to P. ansorgii, and Boulenger’s comment on similarities with P. crucifer are not supported. The status of an unusual skaapsteker from Calueque, Cunene Province, Angola, is discussed and its assignment to Ps. ocellatus is provisional and requires additional material for taxonomic resolution. The new P. ansorgii records from Tundavala represent a range (+ 400 km southwest) and altitude (1800 m to 2286 m asl) extension from the previous only known precise locality of Bela Vista (= Catchiungo), Huambo Province, whilst that for Ps. ocellatus doubles the known altitude from 1108 m to 2286 m asl and extends the range about 122 km to the northwest from historical material from the plateau of Huíla and Cunene provinces.
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- Date Issued: 2019