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Systematics of the Central African Spiny Reed Frog Afrixalus laevis (Anura: Hyperoliidae), with the description of two new species from the Albertine Rift
Abstract
The geographically widespread species Afrixalus laevis (Anura: Hyperoliidae) currently has a disjunct distribution in western Central Africa (Cameroon, Equatorial Guinea, Gabon, and possibly adjacent countries) and the area in and near the Albertine Rift in eastern Democratic Republic of the Congo and neighboring countries. At least two herpetologists have previously suggested that these disjunct populations represent distinct species, and herein, we utilize an integrative taxonomic approach with molecular and morphological data to reconcile the taxonomy of these spiny reed frogs. We sequenced 1554 base pairs of the 16S and RAG1 genes from 34 samples of A. laevis and one sample of A. orophilus (sympatric with eastern populations of A. laevis), and combined these data with previously sequenced GenBank Afrixalus samples via the bioinformatics toolkit SuperCRUNCH. Phylogenetic trees, dated phylogenetic analyses, and species-delimitation analyses were generated with RAxML, BEAST, and BPP, respectively. Eleven mensural characters were taken from multiple specimens of A. laevis and A. orophilus, and compared with paired t-tests and analyses of covariance. These combined results suggested populations of A. laevis in western Central Africa (Cameroon and Bioko Island, Equatorial Guinea) represent one species, whereas populations from the Albertine Rift and nearby forests represent two undescribed taxa that are sister to A. dorsimaculatus. The two new species (A. lacustris sp. nov. and A. phantasma sp. nov.) are distinguished by our phylogenetic and species-delimitation analyses, significant differences in several mensural characters, qualitative morphological differences, and by their non-overlapping elevational distribution.
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The fauna of the Central Congolian Lowland Forests ecoregion in the Democratic Republic of the Congo is poorly known due to the region’s remoteness and limited accessibility. An amphibian survey was conducted in Kokolopori, including the Kokolopori Bonobo Nature Reserve, to fill this gap in our knowledge of its amphibians. All major habitat types were surveyed using visual and acoustic encounter surveys, pitfall and funnel trapping, and active searching during four field sessions, totaling 48 days. A total of 37 species of
anuran amphibians were recorded, while caecilians were unknown to the local human population based on the photographs presented. Incidence-based species richness statistics estimated 37–41 amphibian species, indicating that our survey was probably nearly complete, but we assume that some rare species or species with secretive behaviors have probably remained overlooked. Approximately 75–80% of the total number of species were recorded during each of the two-week portions of the fieldwork, suggesting that two weeks of intensive surveys may have good potential for amphibian inventories in Afrotropical forests. The relatively low number of species for this equatorial rainforest is probably a consequence of its climatic history, with the central Congo being at a certain level of drought during the Pleistocene glaciations. The amphibian fauna is
mainly represented by forest species that inhabit the lowland forests of Central Africa. Species restricted to intact primary forests or more euryecious species of forested ecozones were recorded. Several representatives of genus Arthroleptis could not be assigned to any of the described species, and probably represent species new to science. Representatives of some other genera (Leptopelis, Sclerophrys) resembled species known from western Central Africa, but morphological differences suggested that they probably also represent new species. The taxonomic status of Arthroleptis procterae De Witte, 1921 and Hyperolius boulengeri Laurent, 1943 are revised. Range extensions were found for several taxa, including those known only from the original descriptions. The lack of ubiquitous synanthropic toad species of genus Sclerophrys can probably be attributed to the well-preserved Kokolopori forests and only narrow corridors of disturbed habitat (small paths) leading into the area. Interestingly, some degree of biofluorescence was recorded in Hyperolius phantasticus boulengeri, which to our knowledge is the first documented case in an African anuran. Despite the relatively low species richness, our results suggest that the Central Congolian Lowland Forests ecoregion harbors a unique
and partially endemic amphibian fauna that is to some degree differentiated from the anuran fauna to the north, east, and west of the wide arc of the Congo River. Therefore, this survey underscores the need to protect the central Congolian rainforests as a source of unique biodiversity, and the community-based Kokolopori Bonobo Nature Reserve serves as a good example.
African amphibian diversity remains underestimated with many cryptic lineages awaiting formal description. An important hotspot of amphibian diversification is the Guineo-Congolian rainforest in Central Africa, its richness attributable to present day and ancestral range fragmentation through geological barriers, habitat expansion and contraction, and the presence of steep ecological gradients. The charismatic Nectophryne tree toads present an interesting case study for diversification in this region. The two formally described species comprising this genus show nearly identical geographic distributions extending across most of the Guineo-Congolian rainforest, but show little morphological disparity. Both species harbour extensive genetic diversity warranting taxonomic revisions, and interestingly, when comparing the subclades within each, the two species show remarkably parallel diversification histories, both in terms of timing of phylogenetic splits and their geographic distributions. This indicates that common processes may have shaped the evolutionary history of these lineages.
The reed frog genus Hyperolius (Afrobatrachia, Hyperoliidae) is a speciose genus containing over 140 species of mostly small to medium-sized frogs distributed in sub-Saharan Africa. Its high level of colour polymorphism, together with in anurans relatively rare sexual dichromatism, make systematic studies more difficult. As a result, the knowledge of the diversity and taxonomy of this genus is still limited. Hyperolius robustus known only from a handful of localities in rain forests of the central Congo Basin is one of the least known species. Here, we have used molecular methods for the first time to study the phylogenetic position of this taxon, accompanied by an analysis of phenotype based on external (morphometric) and internal (osteological) morphological characters. Our phylogenetic results undoubtedly placed H. robustus out of Hyperolius into a common clade with sympatric Cryptothylax and West African Morerella. To prevent the uncovered paraphyly, we place H. robustus into a new genus, Congolius. The review of all available data suggests that the new genus is endemic to the central Congolian lowland rain forests. The analysis of phenotype underlined morphological similarity of the new genus to some Hyperolius species. This uniformity of body shape (including cranial shape) indicates that the two genera have either retained ancestral morphology or evolved through convergent evolution under similar ecological pressures in the African rain forests.
1. Phylogenies with extensive taxon sampling have become indispensable for many types of ecological and evolutionary studies. Many large‐scale trees are based on a “supermatrix” approach, which involves amalgamating thousands of published sequences for a group. Constructing up‐to‐date supermatrices can be challenging, especially as new sequences may become available almost constantly. Additionally, genomic datasets (composed of thousands of loci) are becoming common in phylogenetics and phylogeography, and present novel challenges for constructing such datasets. 2. Here we present SuperCRUNCH, a Python toolkit for assembling large phylogenetic datasets. It can be applied to GenBank sequences, unpublished sequences, or combinations of GenBank and unpublished data. SuperCRUNCH constructs local databases and uses them to conduct rapid searches for user‐specified sets of taxa and loci. Sequences are parsed into putative loci and passed through rigorous filtering steps. A post‐filtering step allows for selection of one sequence per taxon (i.e. species‐level supermatrix) or retention of all sequences per taxon (i.e. population‐level dataset). Importantly, SuperCRUNCH can generate “vouchered” population‐level datasets, in which voucher information is used to generate multi‐locus phylogeographic datasets. SuperCRUNCH offers many options for taxonomy resolution, similarity filtering, sequence selection, alignment, and file manipulation. 3. We demonstrate the range of features available in SuperCRUNCH by generating a variety of phylogenetic datasets. Output datasets include traditional species‐level supermatrices, large‐scale phylogenomic matrices, and phylogeographic datasets. Finally, we briefly compare the ability of SuperCRUNCH to construct species‐level supermatrices to alternative approaches. SuperCRUNCH generated a large‐scale supermatrix (1,400 taxa and 66 loci) from 16GB of GenBank data in ~1.5 hours, and generated population‐level datasets (<350 samples, <10 loci) in <1 minute. It outperformed alternative methods for supermatrix construction in terms of taxa, loci, and sequences recovered. 4. SuperCRUNCH is a modular bioinformatics toolkit that can be used to assemble datasets for any taxonomic group and scale (kingdoms to individuals). It allows rapid construction of supermatrices, greatly simplifying the process of updating large phylogenies with new data. It is also designed to produce population‐level datasets. SuperCRUNCH streamlines the major tasks required to process phylogenetic data, including filtering, alignment, trimming, and formatting. SuperCRUNCH is open‐source, documented, and available at https://github.com/dportik/SuperCRUNCH.
Multiple sequence alignment is a prerequisite for many evolutionary analyses. MACSE is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates downstream analyses such as selection pressure estimation based on the ratio of non-synonymous to synonymous substitutions. Here, we present MACSE v2, a major update with an improved version of the initial algorithm enriched with a complete toolkit to handle multiple alignments of protein-coding sequences. A graphical interface now provides user-friendly access to the different subprograms.
The multispecies coalescent (MSC) provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program bpp includes a full-likelihood implementation of the MSC, using trans-model Markov chain Monte Carlo (MCMC) to calculate the posterior probabilities of different species trees. Bpp is suitable for analyzing multi-locus sequence datasets and it accommodates the heterogeneity of gene trees (both the topology and branch lengths) among loci and gene tree uncertainties due to limited phylogenetic information at each locus. Here we provide a practical guide to the use of bpp in species tree estimation. Bpp is a command-line program that runs on linux, macosx, and windows. This protocol shows how to use both bpp 3.4 (http://abacus.gene.ucl.ac.uk/software/) and bpp 4.0 (https://github.com/bpp/).
Aim
To investigate how putative barriers, forest refugia, and ecological gradients across the lower Guineo‐Congolian rain forest shape genetic and phenotypic divergence in the leaf‐folding frog Afrixalus paradorsalis, and examine the role of adjacent land bridge and sky‐islands in diversification.
Location
The Lower Guineo‐Congolian Forest, the Cameroonian Volcanic Line (CVL), and Bioko Island, Central Africa.
Taxon
Afrixalus paradorsalis (Family: Hyperoliidae), an African leaf‐folding frog.
Methods
We used molecular and phenotypic data to investigate diversity and divergence among the A. paradorsalis species complex distributed across lowland rain forests, a land bridge island, and mountains in Central Africa. We examined the coincidence of population boundaries, landscape features, divergence times, and spatial patterns of connectivity and diversity, and subsequently performed demographic modelling using genome‐wide SNP variation to distinguish among divergence mechanisms in mainland (riverine barriers, forest refugia, ecological gradients) and land bridge island populations (vicariance, overwater dispersal).
Results
We detected four genetically distinct allopatric populations corresponding to Bioko Island, the CVL, and two lowland rain forest populations split by the Sanaga River. Although lowland populations are phenotypically indistinguishable, pronounced body size evolution occurs at high elevation, and the timing of the formation of the high elevation population coincides with mountain uplift in the CVL. Spatial analyses and demographic modelling revealed population divergence across mainland Lower Guinea is best explained by forest refugia rather than riverine barriers or ecological gradients, and that the Bioko Island population divergence is best explained by vicariance (marine incursion) rather than overseas dispersal.
Main conclusions
We provide growing support for the important role of forest refugia in driving intraspecific divergences in the Guineo‐Congolian rain forest. In A. paradorsalis, sky‐islands in the CVL have resulted in greater genetic and phenotypic divergences than marine incursions of the land bridge Bioko Island, highlighting important differences in patterns of island‐driven diversification in Lower Guinea.
Emerald Labyrinth is a scientist and adventurer’s chronicle of years exploring the rainforests of sub-Saharan Africa. The richly varied habitats of the Democratic Republic of the Congo offer a wealth of animal, plant, chemical, and medical discoveries. But the country also has a deeply troubled colonial past and a complicated political present. Author Eli Greenbaum is a leading expert in sub-Saharan herpetology—snakes, lizards, and frogs—who brings a sense of wonder to the question of how science works in the twenty-first century. Along the way he comes face to face with spitting cobras, silverback mountain gorillas, wild elephants, and the teenaged armies of AK-47-toting fighters engaged in the continent’s longest-running war.
As a bellwether of the climate and biodiversity crises now facing the planet, the Congo holds the key to our planet’s future. Writing in the tradition of books like The Lost City of Z, Greenbaum seeks out the creatures struggling to survive in a war-torn, environmentally threatened country. Emerald Labyrinth is an extraordinary book about the enormous challenges and hard-won satisfactions of doing science in one of the least known, least hospitable places on earth.
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects hundreds of amphibian species and is implicated in global amphibian declines. Bd is comprised of several lineages that differ in pathogenicity, thus, identifying which Bd strains are present in a given amphibian community is essential for understanding host–pathogen dynamics. The presence of Bd has been confirmed in Central Africa, yet vast expanses of this region have not yet been surveyed for Bd prevalence, and the genetic diversity of Bd is largely unknown in this part of the world. Using retrospective surveys of museum specimens and contemporary field surveys, we estimated the prevalence of Bd in Central African island and continental amphibian assemblages, and genotyped strains of Bd present in each community. Our sampling of museum specimens included just a few individuals collected in the Gulf of Guinea archipelago prior to 1998, yet one of these individuals was Bd-positive indicating that the pathogen has been on Bioko Island since 1966. We detected Bd across all subsequent sample years in our study and found modest support for a relationship between host life history and Bd prevalence, a positive relationship between prevalence and host community species richness, and no significant relationship between elevation and prevalence. The Global Panzootic Lineage (BdGPL) was present in all the island and continental amphibian communities we surveyed. Our results are consistent with a long-term and widespread distribution of Bd in amphibian communities of Gabon and the Gulf of Guinea archipelago.
The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers, and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses. We found that a majority of population divergences are best explained by allopatric models consistent with the forest refugia hypothesis, and involve divergence in isolation with subsequent expansion and gene flow. These population divergences occurred simultaneously and conform to predictions based on climatically stable regions inferred through ecological niche modeling. Though forest refugia played a prominent role in the intraspecific diversification of S. gabonicus, we also find evidence for potential interactions between landscape features and historical refugia, including major rivers and elevational barriers such as the Cameroonian Volcanic Line. We outline the advantages of using genome-wide variation in a model-testing framework to distinguish between alternative allopatric hypotheses, and the pitfalls of limited geographic and molecular sampling. Although phylogeographic patterns are often species-specific and related to life history traits, additional comparative studies incorporating genomic data are necessary for separating shared historical processes from idiosyncratic responses to environmental, climatic, and geological influences on diversification. This article is protected by copyright. All rights reserved.
The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift towards using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans. This article is protected by copyright. All rights reserved.
We describe two new frog species of Cardioglossa (Family Arthroleptidae) from
Central Africa. The new species are found in the rainforests of western-central Democratic
Republic of the Congo and the Republic of the Congo near the Gabonese border, respectively.
We demonstrate that these species are morphologically and genetically distinct from each other
and all other species of Cardioglossa. Both new species lack the dorsal hour-glass pattern
present in many species of the genus, but they can be distinguished from each other and related
species by distinctive colour patterns on their lateral surfaces and extremities. Both new species
most closely resemble C. gratiosa, which occurs in the Atlantic coastal forests extending from
Cameroon through Gabon. The new species can be differentiated from C. gratiosa by the
absence of black transverse bars on all limbs or by distinctive lateral colouration. Analysis of
mitochondrial ribosomal 16S DNA sequences reveals low to moderate levels (1.9–7.5%) of
divergence between these new species and closely related species of Cardioglossa. The
floodplains of the Congo and Ubangi Rivers may be important geographic barriers for many of
these species. The occurrence of these two new lowland species in the Congo Basin reveals that
the distribution and diversity of Cardioglossa in this region was underestimated. In addition,
we elevate C. nigromaculata inornata to species-level status, based in part on newly available
colour photographs from 1950 of specimens from the only known locality.
The identities of two reed frog taxa are re-assessed. Rappia papyri WERNER, 1908 is shown to represent a distinct and valid species in the H. nasutus group of the genus Hyperolius. Rappia pachyderma WERNER, 1908 is removed from the synonymy of Hyperolius viridiflavus (DUMERIL & BIBRON, 1841) and referred to the synonymy of H. papyri.
This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis.
BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne's Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. ABSTRACT.—We describe a new species of Leptopelis from the L. modestus complex. The new species is described from forest and lacustrine habitats of the Albertine Rift of Central Africa, is superficially similar to topotypic L. modestus from Cameroon, but it is distinguished by advertisement call, morphology, and sequences of 16S, cyt b, and RAG1. The new species is yet another amphibian that occurs in the Itombwe Plateau, further solidifying the position of the plateau as an area of conservation concern. The Albertine Rift (AR) is one of the most important sites for conservation in Africa (Plumptre et al., 2007). The AR encompasses much of the western rift valley extending from 30 km north of Lake Albert to the southern tip of Lake Tanganyika, including all habitats within 100 km east of the border of Democratic Republic of the Congo (DRC). Although all the forests are not yet completely explored, the AR is the richest area of montane forest in Africa (Vande weghe, 2004). Approximately 20% of Africa's amphibians are found in the AR, including several species of the treefrog genus Leptopelis, most of which are endemic to the AR (Plumptre et al., 2007). The Plain Treefrog Leptopelis modestus is a relatively small, forest-dwelling arboreal frog described originally from Came-roon (Werner, 1898). The name L. modestus has been attributed to several other populations, including those from eastern DRC, Nigeria, and Kakamega forest in Kenya (Schiøtz, 1975; Kö hler et al., 2006). Laurent (1973) described L. m. fiziensis as a subspecies of L. modestus because of morphological similarities between the two taxa. Schiøtz (1975) later elevated L. fiziensis to full species status and included a new locality (Gombe Stream National Park, Tanzania). Greenbaum et al. (2012) provided an updated geographic distribution for L. fiziensis that included the Itombwe Plateau. One of the populations of L. modestus from Kakamega forest in western Kenya was recently elevated to full species status as L. mackayi (Kö hler et al., 2006). Recently, one of us (EG) collected specimens of Leptopelis at several AR sites in eastern DRC (Fig. 1). These specimens were superficially similar to L. modestus, but differed from Camer-oonian (i.e., topotypic) L. modestus in morphology and advertisement call characteristics. Because of the cryptic morphology of many Central African Leptopelis (e.g., Schiøtz, 1999), comparative DNA analyses were conducted on L. modestus from Cameroon and eastern DRC. Based on these results, we describe the population from eastern DRC as a new species.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
This is actually in "Contemporary Herpetology" the link is here: http://www.cnah.org/ch/ch/2001/4/index.htm
This study lists the amphibian and reptile species of Kibale National Park, Uganda, and discusses the natural history and biogeography of this unique herpetofauna. This herpetofaunal inventory was compiled based upon literature records and collections made during 17 mo fieldwork between 1995 and 1997, and includes 28 anuran, 15 lizard, and 32 snake species. Faunal comparisons with seven other tropical African forests show a high degree similarity between the Kibale herpetofauna and those of central and West Africa.
PICKERSGILL, M. 1995. Afrixalus dabagae Pickersgill 1992 relegated to synonomy. J. Herpetol. Assoc. Afr. 44(2): 58.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including
options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained
alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples
to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to
clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Amietophrynus superciliaris is known to occur in rain forests from West Africa to eastern Democratic Republic of Congo and Gabon. We herein present morphological and molecular data indicating the existence of three distinct taxa. The name A. superciliaris superciliaris is restricted to toads from the western Lower Guinean Forest (eastern Nigeria, Cameroon, Equatorial Guinea, Gabon). We resurrect A. s. chevalieri for the Upper Guinean forest (Sierra Leone, Guinea, Liberia, Ivo-ry Coast, Ghana) and describe a new species occurring in the eastern part of the Lower Guinean Forest (eastern Demo-cratic Republic of Congo). Amietophrynus channingi sp. nov. from eastern Lower Guinean Forest differs from both other taxa by its brownish lateral coloration (reddish-purple in the other taxa). The new species differs morphologically from western Lower Guinean A. s. superciliaris by a less pointed eyelid process, a dark coloured posterior abdominal region and a dark coloured vertebral line (both absent in A. s. superciliaris), the shape of the parotid glands (bulged and rounded at the posterior tip in the new species, slender drop shaped and pointed at the posterior tip in A. s. superciliaris), and ju-venile interorbital markings (V-shaped in the new species, usually interrupted and broken in A. s. superciliaris). Amietophrynus channingi sp. nov. differs from the Upper Guinean A. s. chevalieri by the presence of an eyelid process (absent in A. s. chevalieri), presence of a dark vertebral line and a pair of dark spots on the posterior part of the back (both absent in A. s. chevalieri). The Upper Guinean A. s. chevalieri differs from western Lower Guinean A. s. superciliaris by the absence of an eyelid process, a dark coloured posterior abdominal region (absent in A. s. superciliaris) and lacking a pair of dark spots in the posterior part of the back (present in A. s. superciliaris). The new species differs from both other taxa by 2.2–2.8% in the investigated 16S rRNA gene. West African and western Central African populations differ by only 0.9–1.1% in 16S rRNA, lacking any intra-taxon variation within each clade, and are cautiously regarded as subspecies although the genetic distinction is mirrored by strong morphological differences and distinct geographic distribution which may support its elevation to species status once that more comprehensive data become available. A key to the taxa of the A. superciliaris-species complex is provided.
Aim The species-rich family of true toads (Anura: Bufonidae) has been the focus of several earlier studies investigating the biogeography of geographically widespread taxa. Herein, we employ newly developed Bayesian divergence estimate methods to investigate the biogeographical history of this group. Resulting age estimates are used to test several key temporal hypotheses including that the origin of the bufonid clade pre-dates Gondwanan vicariance (~105 million years ago, Ma). Area cladograms are also invoked to investigate the geographical origin of the family.
We present a commented catalogue of the type specimens of the Afro-Malagasy frog family Hyperoliidae at the herpetological collection of the Museum für Naturkunde Berlin (ZMB). In current publications and databases, many names based on ZMB primary types are listed as synonyms of other species, the types often declared as lost. Consequently, the respective names are often no longer considered in current taxonomic work. We traced 146 nominal taxa of the family Hyperoliidae in the ZMB collection of which currently 130 are presented by primary types (88 holotypes, 10 lectotypes and 32 taxa based on syntype series); 50 of these taxa are currently considered as valid. Primary types of nine taxa could not be located during our inventory of the collection holdings. Seven taxa are exclusively represented by secondary types (paratypes). Many of these types comprise taxa where types have been thought to be lost. As a further service to the community, we provide important details about collectors and their travel routes, as well as respective documents stored in the collection of the Department of Historical Research at ZMB. This should make it easier to potentially compare the ZMB types in future taxonomic revisions.
Secondary sympatry among sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter‐ and intra‐specific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome‐wide single‐nucleotide polymorphism data, we demonstrated that species‐level divergence coincides temporally and geographically with a period of large‐scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation among the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact among these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.
Batesian mimicry is a phenomenon in nature whereby a non-toxic animal emulates a noxious one, seeking to deter predators by deception. This type of mimicry occurs in many animals, with numerous documented examples of invertebrates, harmless squamates, and even birds that mimic venomous snakes. However, no observations of anurans mimicking venomous snakes have been reported. Based on comparative data from colour pattern, morphology, geographic distribution and behaviour, we propose that the Congolese Giant Toad (Sclerophrys channingi), endemic to Democratic Republic of Congo, is a Batesian mimic of the geographically widespread Gaboon Viper (Bitis gabonica). Although the colour pattern similarity between these taxa is not an exact match, aposematism and precise imitation are not required for Batesian mimicry to be effective, especially when the model (B. gabonica) is dangerously venomous and carefully avoided by other vertebrates. Given the morphological similarity between S. channingi and two other African toad species (S. brauni and S. superciliaris) that are sympatric with B. gabonica and its sister taxon (B. rhinoceros), similar examples of Batesian mimicry are likely.
Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate that our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across micro- and macroevolutionary timescales. [Afrobatrachia; Anura; color evolution; diversification; macroevolution; sexual selection.].
The Albertine Rift region of Africa is one of the most biodiverse areas on the planet, with more threatened and endemic vertebrates than elsewhere on the continent. Many of the endemic species are confined to montane forest or alpine areas. We assessed impacts of loss of habitat to agriculture and predicted impacts from niche modelling of climate change to the endemic species of the Albertine Rift. Modelling species distributions for 162 endemic terrestrial vertebrates and plants, we estimated the average percentage of habitat already lost to agriculture at 38% across all species. However, of the remaining suitable habitat the average percentage protected is currently 46%, greatly increased by the recent establishment of Itombwe, Kabobo and Ngandja Reserves in eastern Democratic Republic of Congo from 30%. Species ranges in 2080 were estimated using climate models and predicted to lead to an average loss of an additional 75% of remaining suitable habitat across all species. An estimated 34 endemic species were predicted to lose >90% of their current remaining suitable habitat. The percentage of the total suitable habitat protected in parks or reserves increases under future climate change to 56% because as ranges contract more of the remaining area occurs within existing protected areas. This indicates that the protected area coverage is reasonably well located for future climate change. Based on these data we estimate that 46% of the endemic species we assessed would qualify for threatened status on the global Red List.
Frogs in the genus Amnirana (family Ranidae) are widely distributed across sub-Saharan Africa and present a model system for exploring the relationship between diversification and geography across the continent. Using multiple loci from the mitochondrial (16S) and nuclear genomes (DISP2, FICD, KIAA2013, REV3L), we generated a strongly supported species-level phylogeny that provides insights into the continental biogeography of African species of Amnirana, which form a monophyletic group within the genus. Species delimitation analyses suggest that there may be as many as seven additional species of Amnirana in Africa. The biogeographic history of Amnirana is marked by several dispersal and vicariance events, including dispersal from the Lower Guinean Forest into the Congo Basin. In addition, phylogeographic patterns within two widespread species, A. albolabris and A. galamensis, reveal undescribed cryptic diversity. Populations assigned to A. albolabris in western Africa are more closely related to A. fonensis and require recognition as a distinct species. Our analyses reveal that the Lower and Upper Guinean Forest regions served as important centers of interspecific and intraspecific diversifications for Amnirana.
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. We implemented a multilocus phylogeographic approach to examine diversity within the widely distributed Central African pygmy chameleon, Rhampholeon boulengeri. Gene-tree analyses coupled with a comparative coalescent-based species delimitation framework revealed R. boulengeri as a complex of at least six genetically distinct species. The spatiotemporal speciation patterns for these cryptic species conform to general biogeographic hypotheses supporting vicariance as the main factor behind patterns of divergence in the Albertine Rift, a biodiversity hotspot in Central Africa. However, we found that parapatric species and sister species inhabited adjacent habitats, but were found in largely non-overlapping elevational ranges in the Albertine Rift, suggesting that differentiation in elevation was also an important mode of divergence. The phylogeographic patterns recovered for the genus-level phylogeny provide additional evidence for speciation by isolation in forest refugia, and dating estimates indicated that the Miocene was a significant period for this diversification. Our results highlight the importance of investigating cryptic diversity in widespread species to improve understanding of diversification patterns in environmentally diverse regions such as the montane Afrotropics.
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species-specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainland Guineo-Congolian forest and that habitats across the exposed land bridge likely enabled dispersal in some species, but not in others. We did not find evidence that rivers are biogeographic barriers across any of the species complexes. Despite marked differences in the geographic extent of stable climates and temporal estimates of divergence among the species complexes, we recovered a shared pattern of intermittent climatic suitability with recent population connectivity and demographic expansion across the Congo Basin. This pattern supports the hypothesis that genetic exchange across the Congo Basin during humid periods, followed by vicariance during arid periods, has shaped regional diversity. Finally, we identified many distinct lineages among our focal taxa, some of which may reflect incipient or unrecognized species. This article is protected by copyright. All rights reserved.
The zoogeographical patterns of the forest faunas of treefrogs (Hype-roliidae and genus Leptopelis) in tropical Africa are analysed. This group is well-suited for such a work since especially the genus Hyperolius shows great diversification and signs of recent spéciations. For the purpose of this analysis, the species are separated into sylvicolous ("high forest") and parasylvicolous ("farmbush"). The forests in this study are tentatively divided into ten forest blocks based on differences in the treefrog fauna, and such differences are analysed. The sylvicolous species of the genus Hyperolius have a distribution pattern with a total separation at species level between forest blocks which may reflect the division of the forest belt through drier periods of late Pleistocene into a number of isolated refugia where moist forest and its fauna have persisted and may have resulted in allopatric spéciation. The genera Afrixalus and Leptopelis show less diversification since the sylvicolous species of these genera are separated into three regions, or groups of forest blocks, with groups of species common for these regions, but with no species common between these regions, and only slightly overlapping in southern Nigeria. These regions are West Africa west of the Dahomey Gap/Nigeria, Central Africa and the Eastern Forests. The parasylvicolous species show a fundamentally different distribution pattern. One group is found in West Africa and in Central Africa along the Atlantic coast but not far inland. Another group is found in Central Africa, including Cameroun and easternmost Nigeria and the forest block along the Atlantic coast. Finally one group is widely distributed in the dry parts of the Eastern Forests. The three groups are separated at species level, but the former two have a considerable area of geographical overlap along the Atlantic coast of Central Africa from Cross river southwards. The distribution of the parasylvicolous fauna does not show well-defined "faunal breaks" similar to the sylvicolous fauna, but species diversification and distinction between vicariant taxa seem to have taken place at different, apparently "random" places, perhaps reflecting the original, linear distribution of this fauna in a narrow forest edge towards the savanna. The ill-delimited orophile treefrog faunas are found in three areas with full separation at species level: Mount Cameroun and the Cameronese ridge; the mountains in Central Africa (Albertine Rift and adjacent highlands); and the Eastern Arc Mountains. A recent proposal that the species structure in the genus Hyperolius can be traced back to Cretaceous is discussed. It is argued that climatic changes in late Pleistocene are sufficient to explain the present species structure.
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing
methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform
(FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid
residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy
of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
Two different heuristics, the progressive method (FFT‐NS‐2) and the iterative refinement method (FFT‐NS‐i), are implemented
in MAFFT. The performances of FFT‐NS‐2 and FFT‐NS‐i were compared with other methods by computer simulations and benchmark
tests; the CPU time of FFT‐NS‐2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT‐NS‐i is over
100 times faster than T‐COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
Recent surveys for the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) in Africa have documented the infectious disease in frogs and caecilians from forested habitats in multiple areas of Central and East Africa. We tested 166 frogs for the presence of Bd from 45 localities representing a diverse array of habitats and elevations (793–2852 m.a.s.l.) in the Albertine Rift (AR) region of eastern Democratic Republic of the Congo during four field seasons from 2008–2011. Fifty-eight of these frogs were positive, for an overall Bd-prevalence of 34.9%. Three genera of frogs (Callixalus, Chrysobatrachus and Nectophryne) are reported to be Bd positive for the first time. Behavioural observations of Bd-positive frogs calling for mates and basking suggest the AR amphibian fauna was not severely affected by chytridiomycosis during the survey. Given the enormous levels of endemism and conservation value of the AR amphibian fauna, additional studies of Bd should focus on the region.
Twenty-eight species, four new to Uganda, inhabit the Impenetrable Forest, including an unknown species of Petropedetes, a genus hitherto not known to occur E of Cameroun. -from Authors
The diversity and extent of forest in the Itombwe Mountains, eastern Congo Democratic Republic (formerly Zaire), are among the most significance in continental Africa. Despite some human impact, this area still harbors a wide range of vegetation types, including forests and grasslands, drylands and wetlands, and mid-altitude to upper-montane habitats. Forests extend from mid-altitude through sub-montane and montane to alpine zones. These first results provide a general description of the Itombwe Mountains as a basis for more detailed investigations. Certain priorities in conservation-development actions are suggested, based mainly on tree species knowledge; this information could influence further decision-making processes and management guidelines for the conservation and sustainable use of Itombwe's natural resources.
Treefrogs of the family Hyperoliidae are distributed in Africa, Madagascar and the Seychelles. In this study, their phylogeny was studied using sequences of fragments of the mitochondrial 16S and 12S rRNA and cytochrome b genes. The molecular data strongly confirmed monophyly of the subfamily Hyperoliinae but indicated that the genus Leptopelis (subfamily Leptopelinae) is more closely related to species of the African family Astylosternidae. The Seychellean genus Tachycnemis was the sister group of the Malagasy Heterixalus in all molecular analyses; this clade was deeply nested within the Hyperoliinae. A re-evaluation of the morphological data did not contradict the sister group relationships of these two genera. The subfamily Tachycneminae is therefore considered as junior synonym of the Hyperoliinae. In addition, the molecular analysis did not reveal justification for a subfamily Kassininae. Biogeographically, the origin of Malagasy hyperoliids may not be well explained by Mesozoic vicariance in the context of Gondwana breakup, as indicated by the low differentiation of Malagasy hyperoliids to their African and Seychellean relatives and by analysis of current distribution patterns.