A hotspot revisited - a biogeographical analysis of West African amphibians

Phylogenetic relationships within western African Torrent Toads (Anura: Bufonidae: Werneria) with focus on the taxonomic status of Werneria preussi and Atelopus africanus

Bufo preussi Matschie, 1893 from Mt. Cameroon was the first African Torrent toad to be described, soon followed by Atelopus africanus Werner, 1898 from Bismarkburg in Togo. Shortly after, both species were considered conspecific and, currently, both fall under the name Werneria preussi following taxonomic revisions. The type locality of A. africanus was consequently believed to be an error, especially due to the absence of reports of Werneria individuals in Togo in subsequent years. However, it remained uncertain if this synonymy is justified or if A. africanus may indeed represent a valid but potentially extinct species. To answer this question, we generated the first mitochondrial data (12S, 16S and COI) for name-bearing types of W. preussi and A. africanus using a museomic approach. This was further complemented by mitochondrial and nuclear data of contemporary relatives. Our multi-gene phylogeny inferred from mitochondrial data showed that W. preussi and A. africanus constitute a well-supported monophyletic group, which further includes W. submontana. Together with distance values falling below the commonly used species threshold of 3% for 16S and 6% for COI, this result provides strong evidence for A. africanus being a junior synonym of W. preussi, and the absence of this genus in Togo. It further indicates that W. submontana does not represent a species distinct from W. preussi, but rather a geographic variety differing morphologically from topotypic W. preussi. Due to this morphological differentiation, we propose to consider the W. submontana populations as a distinct subspecies and herein introduce the new name Werneria preussi submontana comb. nov. We further designate a lectotype for W. preussi, in order to increase nomenclatural stability and facilitate future research focusing on African Torrent Toads.

Giant Tree Frog diversification in West and Central Africa: Isolation by physical barriers, climate, and reproductive traits

Secondary sympatry amongst 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 intraspecific 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 amongst 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 amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.

WP, Sterkhova VV, Kusamba C, Rödel M, Penner J, Peterson AT, Brown RM. Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes

The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

Eye behavior predicts susceptibility to visual distraction during internally directed cognition

When we engage in internally directed cognition (e.g., planning or imagination), our eye behavior decouples from external stimuli and couples to internal representations (e.g., internal visualizations of ideas). Here, we investigated whether eye behavior predicts the susceptibility to visual distraction during internally directed cognition. To this end, participants performed a divergent thinking task, which required internally directed attention, and we measured distraction in terms of attention capture by unrelated images. We used multilevel mixed models to predict visual distraction by eye behavior right before distractor onset. In Study 1 (N = 38), visual distraction was predicted by increased saccade and blink rate, and higher pupil dilation. We replicated these findings in Study 2 using the same task, but with less predictable distractor onsets and a larger sample (N = 144). We also explored whether individual differences in susceptibility to visual distraction were related to cognitive ability and task performance. Taken together, variation in eye behavior was found to be a consistent predictor of visual distraction during internally directed cognition. This highlights the relevance of eye parameters as objective indicators of internal versus external attentional focus and distractibility during complex mental tasks.

Comparative phylogeography of West African amphibians and reptiles

Comparative phylogeographic studies often support shared divergence times for co-distributed species with similar life histories and habitat specializations. During the late Holocene, West Africa experienced aridification and the turnover of rain forest habitats into savannas. These fragmented rain forests harbor impressive numbers of endemic and threatened species. In this setting, populations of co-distributed rain forest species are expected to have diverged simultaneously, whereas divergence events for species adapted to savanna and forest-edge habitats should be absent or idiosyncratic. We conducted a Bayesian analysis of shared evolutionary events to test models of population divergence for 20 species of anurans (frogs) and squamates (lizards and snakes) that are distributed across the Dahomey Gap, a climate change-induced savanna barrier responsible for fragmenting previously contiguous rain forests of Ghana into two regions: the Togo-Volta Hills and the Southwestern Forests. A model of asynchronous diversification is supported for anurans and squamates, suggesting that drivers of diversification are not specifically related to ecological and life history associations with habitat types. Instead, the wide variability of genetic divergence histories exhibited by these species suggests that biodiversity in this region has been shaped by diversification events that extend beyond the Holocene. Comparisons of the genealogical divergence index, a measure of the genetic divergence between populations due to the combined effects of genetic isolation and gene flow, illustrate that these populations represent a broad sampling of the speciation continuum.

A new stiletto snake (Lamprophiidae, Atractaspidinae, Atractaspis) from Liberia and Guinea, West Africa

We describe a new stiletto snake,Atractaspis, from western Liberia and southeastern Guinea. The new species shares with morphologically similar western AfricanAtractaspisspecies,A.reticulataandA.corpulenta, the fusion of the 2ndinfralabial with the inframaxillary. FromA.corpulentathe new species differs by a more slender body (276–288 ventrals and 19 or 20 dorsal scale rows versus 178–208 ventrals with 23–29 dorsal scale rows), a divided anal plate and divided subcaudal scales (both non-divided inA.corpulenta). The new species differs from mostA.reticulataby having 19 or 20 dorsal scale rows at midbody (versus 21–23, rarely 19), and a lower ventral count (276–288 versus 304–370). The new species thus has a relatively longer tail: snout-vent-length / tail-length in the female holotype (15.7) and paratype (21.5) versus a mean of 23.6 in seven femaleA.reticulata. The newAtractaspislikely is endemic to the western part of the Upper Guinea forest zone and thus adds to the uniqueness of this diverse and threatened biogeographic region.

Herpetological surveys in two proposed protected areas in Liberia, West Africa

In March and April 2018 we surveyed amphibians and reptiles in two Proposed Protected Areas (PPAs) in Liberia. In the Krahn-Bassa Proposed Protected Area (KBPPA) in eastern Liberia 36 species of amphibians and 13 species of reptiles were recorded. In the Foya Proposed Protected Area (FPPA) in western Liberia 39 species of amphibians and 10 species of reptiles were recorded. The encountered herpetological communities in both sites were typical for West African rainforests. However, some species indicated disturbances, in particular at the edges of the study areas, the surrounding villages and plantations, and old artisanal gold mining sites within forests. Of particular conservation interest was the discovery of a high percentage of typical rainforest specialists with ranges restricted to the western part of the Upper Guinea rainforest biodiversity hotspot. Outstanding discoveries in KBPPA were two new species of puddle frogs, and the first country record for the arboreal, parachuting lizardHolaspisguentheri. Remarkable records in FPPA comprise a new species of stiletto snake, a new puddle frog and records of various frog species typically breeding in undisturbed rainforest streams, such asOdontobatrachusnatatorandConrauaalleni. Both study areas comprise an important proportion of the remaining rainforests in the Upper Guinea forest zone. The new discoveries indicate that within this biogeographic area, southeastern and western Liberian rainforest may still hold various undiscovered species and species of conservation concern. Further surveys in KBPPA and FPPA and nearby forests should clarify the distribution and conservation status of the new taxa.

This study also emphasizes that the western part of the Liberian forests comprise at least partly a herpetofauna which differs from that of the East of the country. The recorded threatened amphibian species are all specialized on relatively undisturbed rainforests and they all have only small geographic ranges. The remaining parts of undisturbed or little disturbed forests thus have high importance for the long-term survival of these species. In conclusion the study areas have a high conservation potential and should be urgently protected from any further forest loss degradation and uncontrolled hunting.

Leapfrogging into new territory: How Mascarene ridged frogs diversified across Africa and Madagascar to maintain their ecological niche

The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals. Haplotype networks were reconstructed and species boundaries were investigated using three species-delimitation approaches: Bayesian generalized mixed Yule-coalescent model (bGMYC), the Poisson Tree Process model (PTP) and a cluster algorithm (SpeciesIdentifier). Estimates of similarity in bioclimatic niche were calculated from species-distribution models (maxent) and multivariate statistics (Principal Component Analysis, Discriminant Function Analysis). Ancestral-area reconstructions were performed on the phylogeny using probabilistic approaches implemented in BioGeoBEARS. We detected high levels of genetic differentiation yielding ten distinct lineages or operational taxonomic units, and Central Africa was found to be a diversity hotspot for these frogs. Most speciation events took place throughout the Miocene, including "out-of-Africa" overseas dispersal events to Madagascar in the East and to São Tomé in the West. Bioclimatic niche was remarkably well conserved, with most species tolerating similar temperature and rainfall conditions common to the Central African region. The P. mascareniensis complex provides insights into how bioclimatic niche shaped the current biogeographic patterns with niche conservatism being exhibited by the Central African radiation and niche divergence shaping populations in West Africa and Madagascar. Central Africa, including the Albertine Rift region, has been an important center of diversification for this species complex.

Multiple genetic lineages challenge the monospecific status of the West African endemic frog family Odontobatrachidae

Background

Correct species identification is crucial in different fields of biology, and in conservation. The endemic West African frog family Odontobatrachidae currently contains a single described species, Odontobatrachus natator. From western Guinea to western Côte d'Ivoire it inhabits forests around waterfalls or cascades. Based on more than 130 specimens from 78 localities, covering the entire distribution, we investigated the molecular diversity of these frogs.

Results

Our analyses included mitochondrial and nuclear genes, with a concatenated alignment of 3527 base pairs. We detected high level of genetic differentiation with five distinct lineages or operational taxonomic units (OTUs). These OTUs were also identified by two different species delimitation approaches, Generalized Mixed Yule Coalescent (GMYC) and cluster algorithm. All OTUs occur in parapatry in the Upper Guinean forests. One OTU, assigned to the “true” Odontobatrachus natator, covers the largest distribution, ranging from the border region of western Sierra Leone-Guinea to eastern Liberia. Two OTUs are restricted to western Guinea (Fouta Djallon and foothills), while two others occur in eastern Guinea and the border region of Guinea-Liberia-Côte d'Ivoire. The OTU representing O. natator consists of two divergent subclades: one restricted to the Freetown Peninsula (Sierra Leone) and the other covering all populations further inland. Environmental niche models indicated that the restricted Freetown Peninsula population is separated by unsuitable habitat from remaining populations.

Conclusion

Geographic isolation of OTUs and molecular differences comparable to species level differentiation in other frog families indicate that O. natator contains cryptic species diversity. Respective distribution patterns most probably resulted from repeated changes of forest cover (contraction and expansion) over evolutionary timescales. The survival within forest refugia that have persisted through multiple drier periods and subsequent dispersal during wetter times may best explain the observed geographic distributions of OTUs. According to the IUCN Red List range criteria each OTU should be classified as “Endangered.” If the Freetown Peninsula “natator” population is recognized as a distinct species it would warrant recognition as “Critically Endangered.” The identification of cryptic lineages highlights the urgent need to protect these frogs, all of which are endemic to small areas within the Upper Guinean biodiversity hotspot.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0346-9) contains supplementary material, which is available to authorized users.

The first endemic West African vertebrate family - a new anuran family highlighting the uniqueness of the Upper Guinean biodiversity hotspot

BACKGROUND

Higher-level systematics in amphibians is relatively stable. However, recent phylogenetic studies of African torrent-frogs have uncovered high divergence in these phenotypically and ecologically similar frogs, in particular between West African torrent-frogs versus Central (Petropedetes) and East African (Arthroleptides and Ericabatrachus) lineages. Because of the considerable molecular divergence, and external morphology of the single West African torrent-frog species a new genus was erected (Odontobatrachus). In this study we aim to clarify the systematic position of West African torrent-frogs (Odontobatrachus). We determine the relationships of torrent-frogs using a multi-locus, nuclear and mitochondrial, dataset and include genera of all African and Asian ranoid families. Using micro-tomographic scanning we examine osteology and external morphological features of West African torrent-frogs to compare them with other ranoids.

RESULTS

Our analyses reveal Petropedetidae (Arthroleptides, Ericabatrachus, Petropedetes) as the sister taxon of the Pyxicephalidae. The phylogenetic position of Odontobatrachus is clearly outside Petropedetidae, and not closely related to any other ranoid family. According to our time-tree estimation Odontobatrachus has been separated from other frog lineages since the Cretaceous (90.1 Ma; confidence interval: 84.2-97.1 Ma). Along with this molecular evidence, osteological and external diagnostic characters recognize West African torrent-frogs as distinct from other ranoids and provide strong support for the necessity of the recognition of a new family of frogs. This is the only endemic vertebrate family occurring in the Upper Guinea biodiversity hotspot.

CONCLUSION

Based on molecular and morphological distinctiveness, the West African torrent-frog Odontobatrachus natator is allocated to a newly described anuran family. The discovery of an endemic vertebrate family in West Africa highlights the Upper Guinean forests as an outstanding, but highly endangered biodiversity hotspot.

Two-stage recovery of amphibian assemblages following selective logging of tropical forests

There is a lack of quantitative information on the effectiveness of selective-logging practices in ameliorating effects of logging on faunal communities. We conducted a large-scale replicated field study in 3 selectively logged moist semideciduous forests in West Africa at varying times after timber extraction to assess post logging effects on amphibian assemblages. Specifically, we assessed whether the diversity, abundance, and assemblage composition of amphibians changed over time for forest-dependent species and those tolerant of forest disturbance. In 2009, we sampled amphibians in 3 forests (total of 48 study plots, each 2 ha) in southwestern Ghana. In each forest, we established plots in undisturbed forest, recently logged forest, and forest logged 10 and 20 years previously. Logging intensity was constant across sites with 3 trees/ha removed. Recently logged forests supported substantially more species than unlogged forests. This was due to an influx of disturbance-tolerant species after logging. Simultaneously Simpson's index decreased, with increased in dominance of a few species. As time since logging increased richness of disturbance-tolerant species decreased until 10 years after logging when their composition was indistinguishable from unlogged forests. Simpson's index increased with time since logging and was indistinguishable from unlogged forest 20 years after logging. Forest specialists decreased after logging and recovered slowly. However, after 20 years amphibian assemblages had returned to a state indistinguishable from that of undisturbed forest in both abundance and composition. These results demonstrate that even with low-intensity logging (≤3 trees/ha) a minimum 20-year rotation of logging is required for effective conservation of amphibian assemblages in moist semideciduous forests. Furthermore, remnant patches of intact forests retained in the landscape and the presence of permanent brooks may aid in the effective recovery of amphibian assemblages.