Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such envi... more Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships.
The girdled lizard genus Cordylus is represented in Angola by two species, Cordylus angolensis an... more The girdled lizard genus Cordylus is represented in Angola by two species, Cordylus angolensis and C. machadoi, sepa- rated from their nearest congeners by over 700 km. Here we describe a new species, Cordylus namakuiyus sp. nov., en- demic to the arid lowlands west of the southern Angolan escarpment. Phylogenetic analysis using three mitochondrial and eight nuclear genes shows that the low-elevation forms and the proximate, high-elevation species C. machadoi are genet- ically divergent and reciprocally monophyletic, and together form the earliest diverging lineage of the northern Cordylus clade. Morphological data, collected using computed tomography and traditional techniques (scalation and morphology), identify consistent phenotypic differences between these high- and low-elevation species and allows for a detailed descrip- tion of the osteology and osteodermal arrangements of the new species. A series of 50 specimens, collected during the 1925 Vernay expedition to southwestern Angola and housed at the American Museum of Natural History, are assigned to the new species, although the identity of Cordylus from northern Namibia remains ambiguous and requires further inves- tigation.
African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of thei... more African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolution- ary history of this group and describe six new species from west and central sub-Saharan Africa, including four tetraploids and two dodecaploids. We provide information on molecu- lar variation, morphology, karyotypes, vocalizations, and estimated geographic ranges, which support the distinctiveness of these new species. We resurrect Xenopus calcaratus from synonymy of Xenopus tropicalis and refer populations from Bioko Island and coastal Cameroon (near Mt. Cameroon) to this species. To facilitate comparisons to the new spe- cies, we also provide comments on the type specimens, morphology, and distributions of X. epitropicalis, X. tropicalis, and X. fraseri. This includes significantly restricted application of the names X. fraseri and X. epitropicalis, the first of which we argue is known definitively only from type specimens and possibly one other specimen. Inferring the evolutionary histo- ries of these new species allows refinement of species groups within Xenopus and leads to our recognition of two subgenera (Xenopus and Silurana) and three species groups within the subgenus Xenopus (amieti, laevis, and muelleri species groups).
Taxonomy of the Smaug warreni species complex remains contentious despite known morphological dif... more Taxonomy of the Smaug warreni species complex remains contentious despite known morphological differences and geographical separation of the various taxa. This study uses a six-gene dataset to recover phylogenetic rela- tionships between the seven nominal members of the S. warreni complex. Eight well-supported clades were re- turned, with S. warreni barbertonensis found to be paraphyletic. A time-calibrated analysis of molecular data indicates that all eight clades in the S. warreni complex separated in the late Miocene, much earlier than the date sug- gested by the existing hypothesis of vicariance through the ingression of Kalahari sands. Ecological niche mod- elling indicates that although all clades are allopatric, a slight decrease in temperature could potentially render them sympatric, supporting an hypothesis of range expansion through climatic change.
A phylogeny of the species-rich clade of the Neotropical frog genus Leptodactylus sensu stricto i... more A phylogeny of the species-rich clade of the Neotropical frog genus Leptodactylus sensu stricto is presented on the basis of a total evi- dence analysis of molecular (mitochondrial and nuclear markers) and non-molecular (adult and larval morphological and behavioral characters) sampled from > 80% of the 75 currently recognized species. Our results support the monophyly of Leptodactylus sensu stricto, with Hydrolaetare placed as its sister group. The reciprocal monophyly of Hydrolaetare and Leptodactylus sensu stricto does not require that we consider Hydrolaetare as either a subgenus or synonym of Leptodactylus sensu lato. We recognize Leptodactylus sensu stricto, Hydrolaetare, Adenomera, and Lithodytes as valid monophyletic genera. Our results generally support the traditionally recognized Leptodactylus species groups, with exceptions involving only a few species that are easily accommodated without proposing new groups or significantly altering contents. The four groups form a pectinate tree, with the Leptodactylus fuscus group diverging first, followed by the L. pentadactylus group, which is sister to the L. latrans and L. melanonotus groups. To evaluate the impact of non-molecular evidence on our results, we compared our total evidence results with results obtained from analy- ses using only molecular data. Although non-molecular evidence comprised only 3.5% of the total evidence matrix, it had a strong impact on our total evidence results. Only one species group was monophyletic in the molecular-only analysis, and support differed in 86% of the 54 Leptodac- tylus clades that are shared by the results of the two analyses. Even though no non-molecular evidence was included for Hydrolaetare, exclusion of that data partition resulted in that genus being nested within Leptodactylus, demonstrating that the inclusion of a small amount of non-molecular evidence for a subset of species can alter not only the placement of those species, but also species that were not scored for those data. The evolu- tion of several natural history and reproductive traits is considered in the light of our phylogenic framework. Invasion of rocky outcrops, larval oophagy, and use of underground reproductive chambers are restricted to species of the Leptodactylus fuscus and L. pentadactylus groups. In con- trast, larval schooling, larval attendance, and more complex parental care are restricted to the L. latrans and L. melanonotus groups. Construction of foam nests is plesiomorphic in Leptodactylus but their placement varies extensively (e.g., underground chambers, surface of waterbodies, natu- ral or excavated basins). Information on species synonymy, etymology, adult and larval morphology, advertisement call, and geographic distribu- tion is summarized in species accounts for the 30 species of the Leptodactylus fuscus group, 17 species of the L. pentadactylus group, eight species of the L. latrans group, and 17 species of the L. melanonotus group, as well as the three species that are currently unassigned to any species group.
The lizard family Cordylidae is mainly endemic to southern Africa and comprises 80 named taxa, pl... more The lizard family Cordylidae is mainly endemic to southern Africa and comprises 80 named taxa, placed in 10 genera. We mapped parity mode and the timing of gametogenesis in males and females on a genus-level phylogenetic tree for the family, derived from the literature. For those genera for which reproduction data were not available, we investigated male reproductive activity for representative species using museum material. In addition, we constructed an area cladogram to recover ancestral ranges. Our parsimony analysis retrieved two equally parsimonious solutions for evolutionary transformations in parity mode and reproductive timing in the Cordylidae. Both solutions suggest that oviparity and spring gametogenesis in both males and females (synchronized breeding) is the basal condition in the family. The correlated evolution of viviparity and autumn breeding has been noted in many lizard clades, and we therefore prefer the solution suggesting (1) that the transformations from oviparity to viviparity and from spring to autumn gametogenesis occurred simultaneously in the most recent common ancestor of the Cordylinae, and (2) that a subsequent return to spring spermatogenesis occurred in the most recent common ancestor of the Ouroborus-Karusasaurus-Namazonurus-Hemicordylus-Cordylus clade, a distinctly western clade. The evolution of viviparity and autumn spermatogenesis in the most recent common ancestor of the Cordylinae appears to have been correlated with the onset of cooler climates during the Oligocene while the return to spring spermatogenesis appears to be have been correlated with the aridification of the western parts of southern Africa during the early Miocene.
Abstract.*Currently there are 20 recognised species of the widespread lizard genus Cordylus, whic... more Abstract.*Currently there are 20 recognised species of the widespread lizard genus Cordylus, which is distributed throughout sub-Saharan Africa’s non-forested habitats from Ethiopia to South Africa. Most recent taxonomic work has focused on forms in southern Africa, where several subspecific taxa have been elevated to full species status. Herein, we focus on the widespread species Cordylus tropidosternum, which occurs from Mozambique (its type locality) to south-eastern Kenya and Tanzania, and west to Katanga Province of Democratic Republic of the Congo (DRC). We sequenced 3 779 bp from two mitochondrial (12S, 16S) and four nuclear (MYH, Kif24, PrLR and MC1R) genes from multiple samples of C. tropidosternum and several sympatric species; these data were analysed with maximum parsimony, maximum likelihood and Bayesian inference optimality criteria. One morphologically and genetically distinct clade of Cordylus from the Marungu Plateau of Katanga Province, DRC is described as a new species. The new species was found under rocks in montane grassland, but further study is needed to assess Cordylus populations in the lowlands of Katanga. We also provide the first detailed morphometric data for the poorly known species C. angolensis, which was described from a single specimen that has since been destroyed.
As the fields of molecular systematics and phylogeography are advancing, it is necessary to incor... more As the fields of molecular systematics and phylogeography are advancing, it is necessary to incorporate multiple loci in both population and species-level inference. Here, we present primer sets for 104 intronless orthologus exons designed for amplification in all squamates. When comparing the Anolis genome to the Gallus genome, all the markers have less than 67.2% DNA sequence identity, the percent identity of the first third of the commonly used nuclear marker RAG-1. The rate of evolution in these markers is therefore greater than nuclear markers commonly used, and we demonstrate their usefulness for both phylogeographic and phylogenetic studies
Girdled lizards (Cordylidae) are sub-Saharan Africa’s only endemic squamate family and contain 80... more Girdled lizards (Cordylidae) are sub-Saharan Africa’s only endemic squamate family and contain 80 nominal taxa, traditionally divided into four genera: Cordylus, Pseudocordylus, Chamaesaura and Platysaurus. Previous phylogenetic analysis revealed Chamaesaura and Pseudocordylus to be nested within Cordylus, and the former genera were sunk into the later. This taxonomic revision has received limited support due to the study’s poor taxon sampling, weakly supported results and possible temporary nomenclatural instability. Our study analyzes three nuclear and three mitochondrial genes from 111 specimens, representing 51 ingroup taxa. Parsimony, likelihood and Bayesian analyses of concatenated and partitioned datasets consistently recovered a comb-like tree with 10, well-supported, monophyletic lineages. Our taxonomic reassessment divides the family into 10 genera, corresponding to these well-supported lineages. Short internodes and low support between the non-platysaur lineages are consistent with a rapid radiation event at the base of the viviparous cordylids.
There is considerable laboratory-based evidence that social learning plays a role in the behaviou... more There is considerable laboratory-based evidence that social learning plays a role in the behaviour of many animals, including fish. However, a weakness of such studies in fish, is that in virtually all to date, the behaviour showed could be learned asocially, with the social influence merely accelerating the rate of learning. Lefebvre & Palameta (1988. Social Learning: Psychological and Biological Perspectives. pp. 141–164) argued that the most compelling evidence for social learning comes from studies where inexperienced animals are unlikely to learn the target behaviour by themselves. The present study is designed to address this concern, by employing a feeding tube task in which fish gain access to food by swimming in a manner that they would not normally show. Employing a transmission chain design, we show foraging traditions in guppies, Poecilia reticulata, and southern platyfish, Xiphophorus maculatus, in which shoal members continue to exploit the food available in the feeding tube, in spite of changes in the composition of the shoal due to the gradual removal of demonstrators. Two experiments provide strong evidence for social learning underlying traditional behaviour, such as migratory routes, in fish, and reveal how the stability of such traditions (duration within a population) is affected by group size (2, 4 or 6 fish) and rate of turnover (16.5%, 25% or 50% per day). While larger shoals of fish showed more stable traditions than smaller shoals, this was found to be related to their slower rate of turnover rather than a direct effect of group size.
Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such envi... more Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships.
The girdled lizard genus Cordylus is represented in Angola by two species, Cordylus angolensis an... more The girdled lizard genus Cordylus is represented in Angola by two species, Cordylus angolensis and C. machadoi, sepa- rated from their nearest congeners by over 700 km. Here we describe a new species, Cordylus namakuiyus sp. nov., en- demic to the arid lowlands west of the southern Angolan escarpment. Phylogenetic analysis using three mitochondrial and eight nuclear genes shows that the low-elevation forms and the proximate, high-elevation species C. machadoi are genet- ically divergent and reciprocally monophyletic, and together form the earliest diverging lineage of the northern Cordylus clade. Morphological data, collected using computed tomography and traditional techniques (scalation and morphology), identify consistent phenotypic differences between these high- and low-elevation species and allows for a detailed descrip- tion of the osteology and osteodermal arrangements of the new species. A series of 50 specimens, collected during the 1925 Vernay expedition to southwestern Angola and housed at the American Museum of Natural History, are assigned to the new species, although the identity of Cordylus from northern Namibia remains ambiguous and requires further inves- tigation.
African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of thei... more African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolution- ary history of this group and describe six new species from west and central sub-Saharan Africa, including four tetraploids and two dodecaploids. We provide information on molecu- lar variation, morphology, karyotypes, vocalizations, and estimated geographic ranges, which support the distinctiveness of these new species. We resurrect Xenopus calcaratus from synonymy of Xenopus tropicalis and refer populations from Bioko Island and coastal Cameroon (near Mt. Cameroon) to this species. To facilitate comparisons to the new spe- cies, we also provide comments on the type specimens, morphology, and distributions of X. epitropicalis, X. tropicalis, and X. fraseri. This includes significantly restricted application of the names X. fraseri and X. epitropicalis, the first of which we argue is known definitively only from type specimens and possibly one other specimen. Inferring the evolutionary histo- ries of these new species allows refinement of species groups within Xenopus and leads to our recognition of two subgenera (Xenopus and Silurana) and three species groups within the subgenus Xenopus (amieti, laevis, and muelleri species groups).
Taxonomy of the Smaug warreni species complex remains contentious despite known morphological dif... more Taxonomy of the Smaug warreni species complex remains contentious despite known morphological differences and geographical separation of the various taxa. This study uses a six-gene dataset to recover phylogenetic rela- tionships between the seven nominal members of the S. warreni complex. Eight well-supported clades were re- turned, with S. warreni barbertonensis found to be paraphyletic. A time-calibrated analysis of molecular data indicates that all eight clades in the S. warreni complex separated in the late Miocene, much earlier than the date sug- gested by the existing hypothesis of vicariance through the ingression of Kalahari sands. Ecological niche mod- elling indicates that although all clades are allopatric, a slight decrease in temperature could potentially render them sympatric, supporting an hypothesis of range expansion through climatic change.
A phylogeny of the species-rich clade of the Neotropical frog genus Leptodactylus sensu stricto i... more A phylogeny of the species-rich clade of the Neotropical frog genus Leptodactylus sensu stricto is presented on the basis of a total evi- dence analysis of molecular (mitochondrial and nuclear markers) and non-molecular (adult and larval morphological and behavioral characters) sampled from > 80% of the 75 currently recognized species. Our results support the monophyly of Leptodactylus sensu stricto, with Hydrolaetare placed as its sister group. The reciprocal monophyly of Hydrolaetare and Leptodactylus sensu stricto does not require that we consider Hydrolaetare as either a subgenus or synonym of Leptodactylus sensu lato. We recognize Leptodactylus sensu stricto, Hydrolaetare, Adenomera, and Lithodytes as valid monophyletic genera. Our results generally support the traditionally recognized Leptodactylus species groups, with exceptions involving only a few species that are easily accommodated without proposing new groups or significantly altering contents. The four groups form a pectinate tree, with the Leptodactylus fuscus group diverging first, followed by the L. pentadactylus group, which is sister to the L. latrans and L. melanonotus groups. To evaluate the impact of non-molecular evidence on our results, we compared our total evidence results with results obtained from analy- ses using only molecular data. Although non-molecular evidence comprised only 3.5% of the total evidence matrix, it had a strong impact on our total evidence results. Only one species group was monophyletic in the molecular-only analysis, and support differed in 86% of the 54 Leptodac- tylus clades that are shared by the results of the two analyses. Even though no non-molecular evidence was included for Hydrolaetare, exclusion of that data partition resulted in that genus being nested within Leptodactylus, demonstrating that the inclusion of a small amount of non-molecular evidence for a subset of species can alter not only the placement of those species, but also species that were not scored for those data. The evolu- tion of several natural history and reproductive traits is considered in the light of our phylogenic framework. Invasion of rocky outcrops, larval oophagy, and use of underground reproductive chambers are restricted to species of the Leptodactylus fuscus and L. pentadactylus groups. In con- trast, larval schooling, larval attendance, and more complex parental care are restricted to the L. latrans and L. melanonotus groups. Construction of foam nests is plesiomorphic in Leptodactylus but their placement varies extensively (e.g., underground chambers, surface of waterbodies, natu- ral or excavated basins). Information on species synonymy, etymology, adult and larval morphology, advertisement call, and geographic distribu- tion is summarized in species accounts for the 30 species of the Leptodactylus fuscus group, 17 species of the L. pentadactylus group, eight species of the L. latrans group, and 17 species of the L. melanonotus group, as well as the three species that are currently unassigned to any species group.
The lizard family Cordylidae is mainly endemic to southern Africa and comprises 80 named taxa, pl... more The lizard family Cordylidae is mainly endemic to southern Africa and comprises 80 named taxa, placed in 10 genera. We mapped parity mode and the timing of gametogenesis in males and females on a genus-level phylogenetic tree for the family, derived from the literature. For those genera for which reproduction data were not available, we investigated male reproductive activity for representative species using museum material. In addition, we constructed an area cladogram to recover ancestral ranges. Our parsimony analysis retrieved two equally parsimonious solutions for evolutionary transformations in parity mode and reproductive timing in the Cordylidae. Both solutions suggest that oviparity and spring gametogenesis in both males and females (synchronized breeding) is the basal condition in the family. The correlated evolution of viviparity and autumn breeding has been noted in many lizard clades, and we therefore prefer the solution suggesting (1) that the transformations from oviparity to viviparity and from spring to autumn gametogenesis occurred simultaneously in the most recent common ancestor of the Cordylinae, and (2) that a subsequent return to spring spermatogenesis occurred in the most recent common ancestor of the Ouroborus-Karusasaurus-Namazonurus-Hemicordylus-Cordylus clade, a distinctly western clade. The evolution of viviparity and autumn spermatogenesis in the most recent common ancestor of the Cordylinae appears to have been correlated with the onset of cooler climates during the Oligocene while the return to spring spermatogenesis appears to be have been correlated with the aridification of the western parts of southern Africa during the early Miocene.
Abstract.*Currently there are 20 recognised species of the widespread lizard genus Cordylus, whic... more Abstract.*Currently there are 20 recognised species of the widespread lizard genus Cordylus, which is distributed throughout sub-Saharan Africa’s non-forested habitats from Ethiopia to South Africa. Most recent taxonomic work has focused on forms in southern Africa, where several subspecific taxa have been elevated to full species status. Herein, we focus on the widespread species Cordylus tropidosternum, which occurs from Mozambique (its type locality) to south-eastern Kenya and Tanzania, and west to Katanga Province of Democratic Republic of the Congo (DRC). We sequenced 3 779 bp from two mitochondrial (12S, 16S) and four nuclear (MYH, Kif24, PrLR and MC1R) genes from multiple samples of C. tropidosternum and several sympatric species; these data were analysed with maximum parsimony, maximum likelihood and Bayesian inference optimality criteria. One morphologically and genetically distinct clade of Cordylus from the Marungu Plateau of Katanga Province, DRC is described as a new species. The new species was found under rocks in montane grassland, but further study is needed to assess Cordylus populations in the lowlands of Katanga. We also provide the first detailed morphometric data for the poorly known species C. angolensis, which was described from a single specimen that has since been destroyed.
As the fields of molecular systematics and phylogeography are advancing, it is necessary to incor... more As the fields of molecular systematics and phylogeography are advancing, it is necessary to incorporate multiple loci in both population and species-level inference. Here, we present primer sets for 104 intronless orthologus exons designed for amplification in all squamates. When comparing the Anolis genome to the Gallus genome, all the markers have less than 67.2% DNA sequence identity, the percent identity of the first third of the commonly used nuclear marker RAG-1. The rate of evolution in these markers is therefore greater than nuclear markers commonly used, and we demonstrate their usefulness for both phylogeographic and phylogenetic studies
Girdled lizards (Cordylidae) are sub-Saharan Africa’s only endemic squamate family and contain 80... more Girdled lizards (Cordylidae) are sub-Saharan Africa’s only endemic squamate family and contain 80 nominal taxa, traditionally divided into four genera: Cordylus, Pseudocordylus, Chamaesaura and Platysaurus. Previous phylogenetic analysis revealed Chamaesaura and Pseudocordylus to be nested within Cordylus, and the former genera were sunk into the later. This taxonomic revision has received limited support due to the study’s poor taxon sampling, weakly supported results and possible temporary nomenclatural instability. Our study analyzes three nuclear and three mitochondrial genes from 111 specimens, representing 51 ingroup taxa. Parsimony, likelihood and Bayesian analyses of concatenated and partitioned datasets consistently recovered a comb-like tree with 10, well-supported, monophyletic lineages. Our taxonomic reassessment divides the family into 10 genera, corresponding to these well-supported lineages. Short internodes and low support between the non-platysaur lineages are consistent with a rapid radiation event at the base of the viviparous cordylids.
There is considerable laboratory-based evidence that social learning plays a role in the behaviou... more There is considerable laboratory-based evidence that social learning plays a role in the behaviour of many animals, including fish. However, a weakness of such studies in fish, is that in virtually all to date, the behaviour showed could be learned asocially, with the social influence merely accelerating the rate of learning. Lefebvre & Palameta (1988. Social Learning: Psychological and Biological Perspectives. pp. 141–164) argued that the most compelling evidence for social learning comes from studies where inexperienced animals are unlikely to learn the target behaviour by themselves. The present study is designed to address this concern, by employing a feeding tube task in which fish gain access to food by swimming in a manner that they would not normally show. Employing a transmission chain design, we show foraging traditions in guppies, Poecilia reticulata, and southern platyfish, Xiphophorus maculatus, in which shoal members continue to exploit the food available in the feeding tube, in spite of changes in the composition of the shoal due to the gradual removal of demonstrators. Two experiments provide strong evidence for social learning underlying traditional behaviour, such as migratory routes, in fish, and reveal how the stability of such traditions (duration within a population) is affected by group size (2, 4 or 6 fish) and rate of turnover (16.5%, 25% or 50% per day). While larger shoals of fish showed more stable traditions than smaller shoals, this was found to be related to their slower rate of turnover rather than a direct effect of group size.
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Papers by Edward L Stanley