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Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa
Abstract and Figures
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.
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... These elements make up roughly 80% of the recorded species, and represent exceptional range extensions in some cases. Apart from previously published records of the SPFE amphibians (Ernst et al. 2014(Ernst et al. , 2015Channing et al. 2016;Jongsma et al. 2018), additional, unpublished records are particularly noteworthy, as they represent enigmatic taxa in need of distributional and taxonomic revision (e.g. Alexteroon hypsiphonus, Ernst et al. in prep., and Leptopelis millsoni, Bell et al. in prep.) or taxa, in which the southernmost distribution lies in the SPFE (e.g. ...
... This species ranges widely from Uíge in the south to Maquela do Zombo in the north. Northern Angolan individuals are part of a cryptic complex of several species (Jongsma et al. 2018). This species has marked sexual size dimorphism, with females larger. ...
... Tadpoles were frequently found in larger pools at the bottom of waterfalls. The population in the SPFE probably represents the southernmost distribution of the species (Jongsma et al. 2018 Leaché et al. (2019) showed that this species, which is widespread throughout West and Central Africa, is a complex. The SPFE population was not known to Leaché et al. and was not included in their study. ...
We systematically assess the herpetofaunal diversity of the Serra do Pingano Forest Ecosystem (SPFE) and additional localities throughout the northern Angolan province of Uíge during four independent Rapid Assessment (RA) field campaigns held between 2013 and 2019. These assessments represent the first systematic surveys of amphibians and reptiles from the province, and thus we provide the first province-wide species list. We collected data on the status and current threats to amphibians and reptiles in the proposed Serra do Pingano Rainforest National Park and were able to document 33 species of reptiles from Uíge province. Of the 33 species recorded from the province, 10 species are exclusively found in the SPFE. Amphibian surveys yielded 47 amphibian species from the province. These include 14 new country records and additional records that may represent undescribed species. This raises the amphibian count for Angola to at least 133 species, which includes 18 species exclusively found within the SPFE. Species-richness estimators indicate that more species should be detected if survey efforts are intensified. The species composition in the SPFE is unique and consists of a high proportion of forest specialists with restricted ranges and species found nowhere else in the country. This emphasizes today's paramount importance of the SPFE, which is threatened by increasing agricultural encroachment and uncontrolled timber extraction and charcoal production. These principal factors need to be controlled and/or abandoned in already impacted areas. Conservation strategies should particularly consider the strict protection of remaining intact forests and both lentic and lotic aquatic systems. They are not only crucial for safeguarding a significant number of species that depend on these habitats for reproduction; they also provide key ecosystem services to the local population. Angola, and Uíge province in particular, is at a crossroads concerning decisions and trade-offs among utilization, conservation, and preservation of its forests and, thus, substantial parts of the country's biodiversity. The establishment of a National Protected Area in the Serra do Pingano Ecosystem is therefore a necessary and urgently needed first step towards protecting Angola's national biodiversity heritage.
... Abbreviations: PF: primary forest; DF: degraded forest; CP: mosaic of coffee and cocoa plantations; RP: rubber plantation; RF: rice field; l: leaf litter; t: arboreal; a: aquatic; f: fossorial; F: closed forest; D: degraded forest; O: open habitat; ? : unclear as species identification was not possible; d: direct development and non-hatching/non-feeding tadpoles; s: tadpoles in stagnant water (ponds, puddles, tree holes); f: tadpoles in flowing water; *: comprises a species complex (see text); **: the two 'sub-species' occur in sympatry in TNP and may actually represent two valid species; ***: an undescribed species compare Jongsma et al. (2018). 28.6 ± 2.1 23.8 ± 1.4 15.0 ± 1.6 7.9 ± 1.3 10.0 ± 0.1 Estimated species richness (Jack-knife 1) 31.6 ± 1.7 26.3 ± 2.5 16.7 ± 1.8 9.0 ± 1.0 10.9 ± 0. The results of the Jaccard's similarity of species assemblages between the five surveyed habitat types are presented in Table 2. ...
... In contrast, A. galamensis (Fig. 4E) is generally found in savanna habitats, survives successfully in modified habitats (Rödel 2000), and has even been reported from urban areas (Kouamé et al. 2015). This taxon is widespread in sub-Saharan Africa (Channing and Rödel 2019), but comprises several cryptic species (Jongsma et al. 2018). We found A. galamensis in a highly polluted area (06°14'12.7''N, ...
... Abbreviations: PF: primary forest; DF: degraded forest; CP: mosaic of coffee and cocoa plantations; RP: rubber plantation; RF: rice field; l: leaf litter; t: arboreal; a: aquatic; f: fossorial; F: closed forest; D: degraded forest; O: open habitat; ? : unclear as species identification was not possible; d: direct development and non-hatching/non-feeding tadpoles; s: tadpoles in stagnant water (ponds, puddles, tree holes); f: tadpoles in flowing water; *: comprises a species complex (see text); **: the two 'sub-species' occur in sympatry in TNP and may actually represent two valid species; ***: an undescribed species compareJongsma et al. (2018). ...
The conversion of tropical rain forests to agricultural systems is a major threat to tropical biodiversity. In West Africa, studies investigating the effects of this habitat conversion on biodiversity are scarce. In this study, we investigated which forest amphibians survive in the agroforestry systems surrounding West Africa's largest area of protected rainforest, the Taï National Park (TNP) in southwestern Côte d'Ivoire. Species richness was assessed in different habitats types, i.e., a mosaic of coffee and cocoa plantations, rubber plantations, and rice fields, and compared to data from primary and degraded forests in TNP. The anuran assemblage composition differed considerably between forest and agroforestry systems, with the latter comprising only a small subset of generalist forest species and species which usually occur in highly degraded forest habitats or even savanna. Thus, the agroforestry systems in western Côte d'Ivoire seem to be unsuitable for the maintenance of the rich local and regional diversity of forest amphibians.
... Past studies have found evidence for lineages endemic to relictual forests within the DG (e.g., Gaubert et al., 2016;Huntley & Voelker, 2016;Voelker et al., 2017). However, despite increasing evidence of endemism within the gap, it appears that the DG may have played a substantial role in the creation and maintenance of genetic diversification between the UGF and LFG across birds, mammals, and even amphibians (Jongsma et al., 2018), regardless of dispersal ability. ...
... For mammals, the Sanaga or Ogooué Rivers are possible genetic barriers for several taxa (e.g.,Anthony et al., 2007;Nicolas, Missoup, Colyn, Cruaud, & Denys, 2012;Nicolas et al., 2011) which, like understorey birds, may show similar avoidance of nonforested habitats. Additionally, recent studies of reptiles and amphibians have yielded complex results regarding riverine barriers as diversification drivers in the GCF (e.g.,Bell et al., 2017;Jongsma et al., 2018;Leaché & Fujita, 2010). Yet overall, focused assessments of Afro-tropical rivers as drivers of diversity are lacking, despite the evidence that rivers may be adding to complex intraregional patterns of diversification. ...
... ing that reptiles(Bell et al., 2017;Greenbaum, Portillo, Jackson, & Kusamba, 2015;Jongsma et al., 2018) and invertebrates(Light, Nessner, Gustafsson, Wise, & Voelker, 2016;Takano et al., 2017) may contain substantial cryptic diversity. Although we acknowledge the known limitations to using pairwise distance averages from mitochondrial genes and that we lack the sampling power to make sweeping conclusions about any one species, the patterns we recovered underscore the urgent need for more extensive future sampling efforts and further exploration of species limits and patterns of diversification across all terrestrial vertebrate groups in Afro-tropical forests.Determining broad speciation patterns and documenting biodiversity across the Afro-tropical forests have impacts beyond an evolutionary framework. ...
Aim
Vertebrate diversity in the Guineo‐Congolian forests (GCF) of Africa is high, yet mechanisms responsible for generating that diversity remain remarkably understudied. These forests have alternatively been viewed as centres of diversification (“cradles”) or more recently, as the opposite (“museums”). Here, we use a comparative dataset of avian and mammalian species to examine genetic diversification patterns across these forests and use these results to explain observed patterns in light of Plio‐Pleistocene climatic change and life‐history.
Location
Africa.
Methods
We analysed patterns of diversification across the GCF using a dataset composed of 629 and 1,048 mitochondrial sequences from 60 avian and 36 mammalian species, respectively. Uncorrected pairwise genetic distances were compared at three distinct geographical levels: west versus east of the Dahomey Gap, among the three major forest blocks, and among seven historical refugial areas. The timing of diversification was assessed for passerines, Rodentia, and Chiroptera.
Results
We found substantial signatures of diversification in all three levels of our geographical comparisons. We recovered substantial disparity in the amount and depth of structure of diversification patterns between low dispersers (understorey birds and rodents) and more capable dispersers (other bird species and bats). Additionally, our chronogram recovered recent speciation and intraspecific diversification across songbird and mammalian lineages.
Main conclusions
The discrete, and often deep, structuring of genetic diversification for both birds and mammals across the GCF revealed strong correlations between historic landscape fragmentation and dispersal ability. Our results revealed a striking amount of unrecognized genetic diversity, which may be suggestive of cryptic species. Given the rate at which these forests are being negatively impacted by human intervention, our general lack of knowledge concerning vertebrate diversity across these forests may very well impact our ability to identify evolutionary processes underlying diversity and enact meaningful conservation efforts in the future.
... Based on pollen core records (Bonnefille & Riollet, 1988;Brenac, 1988;Girese et al., 1994;Maley, 1987Maley, , 1989Maley, , 1991Maley & Brénac, 1987;Maley & Livingstone, 1983;Sowunmi, 1991) and species distribution data (Colyn, 1987(Colyn, , 1991Richards, 1963;Rietkerk et al., 1995;Sosef, 1991), Maley (1996) proposed several Pleistocene rainforest refugia for sub-Saharan Africa that are still considered today (e.g., Bell et al., 2017;Hughes et al., 2017;Huntley et al., 2019;Jongsma et al., 2018;Larson et al., 2016;Penner et al., 2011;Portik et al., 2017; Figure 1). Many of these hypothesized refugia are located in highland areas (e.g., the Cameroon Volcanic Line and the Albertine Rift; Figure 1, refugia 4 and 10, respectively). ...
... Rivers alone have been shown to be important barriers for some species of primates (Mitchell et al., 2015;Telfer et al., 2003), shrews (Jacquet et al., 2015), and frogs (Charles et al., 2018;Penner et al., 2011Penner et al., , 2019Wieczorek et al., 2000;Zimkus et al., 2010), but do not appear to represent an important barrier for many plant species Debout et al., 2011;Hardy et al., 2013;Ley et al., 2014; F I G U R E 1 Locations of major rivers and hypothesized refugia (labeled 1-10) in West and Central Africa, adapted from Maley (1996Maley ( ) et al., 2010. Refugia are suggested to have played an important role in the diversification of rodents (Bohoussou et al., 2015;Nicolas et al., 2011Nicolas et al., , 2012, primates (Clifford et al., 2004;Haus et al., 2013;Tosi, 2008), frogs (Bell et al., 2017;Jongsma et al., 2018), lizards (Allen et al., 2019;Leaché et al., 2017), birds (Fjeldså & Bowie, 2008), pangolins (Gaubert et al., 2016), and rainforest plants (Born et al., 2011;Budde et al., 2013;Daïnou et al., 2010;Dauby et al., 2010;Duminil et al., 2015;Faye et al., 2016;Gomez et al., 2009;Hardy et al., 2013;Ley et al., 2014Ley et al., , 2016Lowe et al., 2010). In some cases, divergence patterns match both refugial and riverine predictions (Anthony et al., 2007;Barej et al., 2011;Bohoussou et al., 2015;Gonder et al., 2011;Jacquet et al., 2014;Jongsma et al., 2018;Leaché & Fujita, 2010;Leaché et al., 2019;Marks, 2010;Portik et al., 2017), suggesting that both may have played roles simultaneously-or in combination-in evolutionary diversification. ...
... Refugia are suggested to have played an important role in the diversification of rodents (Bohoussou et al., 2015;Nicolas et al., 2011Nicolas et al., , 2012, primates (Clifford et al., 2004;Haus et al., 2013;Tosi, 2008), frogs (Bell et al., 2017;Jongsma et al., 2018), lizards (Allen et al., 2019;Leaché et al., 2017), birds (Fjeldså & Bowie, 2008), pangolins (Gaubert et al., 2016), and rainforest plants (Born et al., 2011;Budde et al., 2013;Daïnou et al., 2010;Dauby et al., 2010;Duminil et al., 2015;Faye et al., 2016;Gomez et al., 2009;Hardy et al., 2013;Ley et al., 2014Ley et al., , 2016Lowe et al., 2010). In some cases, divergence patterns match both refugial and riverine predictions (Anthony et al., 2007;Barej et al., 2011;Bohoussou et al., 2015;Gonder et al., 2011;Jacquet et al., 2014;Jongsma et al., 2018;Leaché & Fujita, 2010;Leaché et al., 2019;Marks, 2010;Portik et al., 2017), suggesting that both may have played roles simultaneously-or in combination-in evolutionary diversification. However, because of the spatial overlap of refugia with montane and riverine systems (Hofer et al., 1999(Hofer et al., , 2000, and the sparse pollen core and fossil records for the tropics (Colinvaux et al., 1996;Maley & Brenac, 1998), distinguishing between these three hypotheses has been difficult, especially when relying on phylogeographic data alone. ...
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.
... Groups that remain not fully understood such as Phrynobatrachus (Zimkus et al. 2010), Xenopus (Furman et al. 2015) and Amnirana (Jongsma et al. 2018), all have species widespread in Africa with type localities from Angola, and the resolution of their taxonomy depends on detailed studies in Angola. ...
... During the 2011 expedition to Lagoa Carumbo, a large white-lipped frog was morphologically assigned to the Amnirana lepus group (Branch and Conradie 2015). This assigment has been confirmed in a phylogeny of the genus (Jongsma et al. 2018), and further studies are underway to address the taxonomical status of the Angolan population (Conradie pers. comm.). ...
... Tomopterna cryptotis (Boulenger, 1907) Monard (1937), Ruas (1996) Rough Sand Frog Tomopterna tuberculosa (Boulenger, 1882) Bocage (1895), Monard (1937), Ruas (1996), Baptista et al (2018, unpub (1895), Monard (1937), Ruas (1996) and Jongsma et al. (2018) (continued) ...
Angolan amphibians have been studied since the mid-nineteenth century by explorers and scientists from all over the western world, and collections have been deposited in around 20 museums and institutions in Europe, Northern America, and Africa. A significant interruption of this study occurred during Angola’s liberation struggle and civil war for nearly four decades and, as a consequence, knowledge about the country’s biodiversity became outdated with critical gaps. Since 2009, a new era in Angolan biodiversity studies started as expeditions scattered in southwestern, northeastern, southeastern, and northwestern Angola lead to exciting discoveries, including new records for the country, descriptions of new species, range extensions and taxonomical updates. Currently 111 amphibian species are listed for the country (of which 21 are endemic), but this number is an underestimate and the various unresolved taxonomical issues challenge the study of every other aspect of this group. The Angolan amphibian fauna remains one of the most poorly known in Africa and much still has to be done in order to understand its diversity, evolution and conservation needs. An overview of existing knowledge of Angolan amphibians is presented, including an updated checklist for the country, comments on problematic groups, endemic species, biogeography, recent findings, and priority research topics.
... Amnirana (Jongsma et al., 2018), têm todos eles espécies disseminadas em África com localidades -tipo localizadas em Angola, e a resolução de sua taxonomia depende de estudos detalhados neste país. ...
... A endémica rã -arborícola -de -anchieta, Leptopelis anchietae, e a rã -arborícola--da -floresta -do -congulo, Leptopelis jordani, foram redescobertas na escarpa de Angola (Branch & Conradie, 2015). Esta atribuição foi confirmada numa filogenia do género (Jongsma et al., 2018), estando em curso outros estudos sobre o estatuto taxonómico da população angolana (Conradie, comunicação pessoal ...
... Amnirana albolabris (Hallowell, 1856) Jongsma et al., 2018 Rã -de -lábios -brancos--de -darling ...
Os anfíbios de Angola têm sido estudados desde os meados do século xix por exploradores e cientistas de todo o Ocidente, com colecções depositadas em cerca de 20 museus e instituições da Europa, América do Norte e África. Este estudo sofreu uma interrupção significativa durante as quase quatro décadas da luta de libertação e guerra civil de Angola e, como consequência, o conhecimento sobre a biodiversidade do país tornou‑se obsoleto, com lacunas críticas. Em 2009 começou uma nova era nos estudos da biodiversidade angolana, com expedições no Sudoeste, Nordeste, Sueste e Noroeste de Angola, e levando a descobertas empolgantes, como novos registos para o país, descrições de novas espécies, aumento de áreas de distribuição e actualizações taxonómicas. Actualmente, encontram‑se registadas 111 espécies de anfíbios neste país (das quais 21 são endémicas), mas este número é uma subestimativa e as diversas questões taxonómicas ainda não resolvidas desafiam o estudo de todos os outros aspectos relativos a este grupo. A fauna de anfíbios de Angola continua a ser uma das mais mal conhecidas de África e ainda há muito por fazer para compreender a sua diversidade, evolução e necessidades de conservação. Este capítulo apresenta uma panorâmica geral do conhecimento existente relativo aos anfíbios de Angola, incluindo uma lista de espécies actualizada, comentários sobre grupos problemáticos, espécies endémicas, biogeografia, descobertas recentes e tópicos de investigação prioritários.
... Based on pollen core records (Bonnefille & Riollet, 1988;Brenac, 1988;Girese et al., 1994;Maley, 1987Maley, , 1989Maley, , 1991Maley & Brénac, 1987;Maley & Livingstone, 1983;Sowunmi, 1991) and species distribution data (Colyn, 1987(Colyn, , 1991Richards, 1963;Rietkerk et al., 1995;Sosef, 1991), Maley (1996) proposed several Pleistocene rainforest refugia for sub-Saharan Africa that are still considered today (e.g., Bell et al., 2017;Hughes et al., 2017;Huntley et al., 2019;Jongsma et al., 2018;Larson et al., 2016;Penner et al., 2011;Portik et al., 2017; Figure 1). Many of these hypothesized refugia are located in highland areas (e.g., the Cameroon Volcanic Line and the Albertine Rift; Figure 1, refugia 4 and 10, respectively). ...
... Rivers alone have been shown to be important barriers for some species of primates (Mitchell et al., 2015;Telfer et al., 2003), shrews (Jacquet et al., 2015), and frogs (Charles et al., 2018;Penner et al., 2011Penner et al., , 2019Wieczorek et al., 2000;Zimkus et al., 2010), but do not appear to represent an important barrier for many plant species Debout et al., 2011;Hardy et al., 2013;Ley et al., 2014; F I G U R E 1 Locations of major rivers and hypothesized refugia (labeled 1-10) in West and Central Africa, adapted from Maley (1996Maley ( ) et al., 2010. Refugia are suggested to have played an important role in the diversification of rodents (Bohoussou et al., 2015;Nicolas et al., 2011Nicolas et al., , 2012, primates (Clifford et al., 2004;Haus et al., 2013;Tosi, 2008), frogs (Bell et al., 2017;Jongsma et al., 2018), lizards (Allen et al., 2019;Leaché et al., 2017), birds (Fjeldså & Bowie, 2008), pangolins (Gaubert et al., 2016), and rainforest plants (Born et al., 2011;Budde et al., 2013;Daïnou et al., 2010;Dauby et al., 2010;Duminil et al., 2015;Faye et al., 2016;Gomez et al., 2009;Hardy et al., 2013;Ley et al., 2014Ley et al., , 2016Lowe et al., 2010). In some cases, divergence patterns match both refugial and riverine predictions (Anthony et al., 2007;Barej et al., 2011;Bohoussou et al., 2015;Gonder et al., 2011;Jacquet et al., 2014;Jongsma et al., 2018;Leaché & Fujita, 2010;Leaché et al., 2019;Marks, 2010;Portik et al., 2017), suggesting that both may have played roles simultaneously-or in combination-in evolutionary diversification. ...
... Refugia are suggested to have played an important role in the diversification of rodents (Bohoussou et al., 2015;Nicolas et al., 2011Nicolas et al., , 2012, primates (Clifford et al., 2004;Haus et al., 2013;Tosi, 2008), frogs (Bell et al., 2017;Jongsma et al., 2018), lizards (Allen et al., 2019;Leaché et al., 2017), birds (Fjeldså & Bowie, 2008), pangolins (Gaubert et al., 2016), and rainforest plants (Born et al., 2011;Budde et al., 2013;Daïnou et al., 2010;Dauby et al., 2010;Duminil et al., 2015;Faye et al., 2016;Gomez et al., 2009;Hardy et al., 2013;Ley et al., 2014Ley et al., , 2016Lowe et al., 2010). In some cases, divergence patterns match both refugial and riverine predictions (Anthony et al., 2007;Barej et al., 2011;Bohoussou et al., 2015;Gonder et al., 2011;Jacquet et al., 2014;Jongsma et al., 2018;Leaché & Fujita, 2010;Leaché et al., 2019;Marks, 2010;Portik et al., 2017), suggesting that both may have played roles simultaneously-or in combination-in evolutionary diversification. However, because of the spatial overlap of refugia with montane and riverine systems (Hofer et al., 1999(Hofer et al., , 2000, and the sparse pollen core and fossil records for the tropics (Colinvaux et al., 1996;Maley & Brenac, 1998), distinguishing between these three hypotheses has been difficult, especially when relying on phylogeographic data alone. ...
Colleagues: thank you for your interest in this work. A preprint for this paper was generated by accident and it requires major revisions before it will be published. Of course I will update the project when the paper is in press, but until then I will be declining requests for this preprint. Thank you for your understanding.
... It is not yet clear where the zoogeographic barrier between the West and Central African fauna exactly runs: at the Cross River, the Niger Delta, or the Dahomey Gap. Nor has it been clarified what exact processes are responsible for the separation of fauna and flora, and what is the time scale during which taxa in both areas evolved (see Penner et al. 2011;Jongsma et al. 2018 and studies cited therein). The geographic scale, processes and time most likely varies between taxa (see Bell et al. 2017 for Central African examples). ...
... Indeed, many studies, mostly recent, either have discovered related but distinct species in both forest blocs or have shown that "widespread" taxa actually comprise cryptic species complexes, including species that either occur in West or Central African rainforests. Examples of recent discoveries of species pairs within amphibians are Sclerophrys taiensis and S. tuberosus (Bufonidae; Rödel and Ernst 2000); Acanthixalus sonjae and A. spinosus (Hyperoliidae; Rödel et al. 2003); Cardioglossa occidentalis and C. leucomystax (Arthroleptidae; Blackburn et al. 2008); and Amnirana "albolabris-West" and Amnirana albolabris (Ranidae; Jongsma et al. 2018). Among reptiles different species in West and Central Africa have been discovered in the crocodile genera Mecistops and Osteolaemus (Crocodylidae; Shirley et al. 2014); the turtles Pelusios cupulatta and P. gabonensis (Pelomedusidae; Rhodin et al. 2017); the cobras Naja guineensis and N. melanoleuca (Elapidae; Wüster et al. 2018); and the vipers Atheris hirsuta and A. squamigera (Viperidae; Ernst and Rödel 2002). ...
We describe a new stiletto snake, Atractaspis , from western Liberia and southeastern Guinea. The new species shares with morphologically similar western African Atractaspis species, A.reticulata and A.corpulenta , the fusion of the 2 nd infralabial with the inframaxillary. From A.corpulenta the 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 in A.corpulenta ). The new species differs from most A.reticulata by 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 female A.reticulata . The new Atractaspis likely 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.
... Several new undescribed species are known to occur within Equatorial Guinea (De la Riva 1994; Jongsma et al. 2018). Thus, an increase in the number of described species is to be expected in the near future. ...
... Africa". Perret (1977) restricted the type locality to "Gabon" and Jongsma et al. (2018) deduced that it is "north of the Ogooué River in Gabon". ...
Equatorial Guinea is a small west-central African tropical country situated in the Gulf of Guinea. It has a main insular area comprising the volcanic land-bridge island Bioko, the oceanic island Annobón, and a continental part known as Río Muni, which accounts for most of the country’s land area and borders on Cameroon to the north and Gabon to the east and south. Only a few and mostly old publications have dealt specifically with the amphibians of Equatorial Guinea, and an accurate and updated catalogue is lacking. Based on fieldwork, a compilation of literature, and the examination of two important Spanish scientific collections, we present a comprehensive catalogue of the amphibian fauna for Equatorial Guinea. We report 80 species belonging to 32 genera, 13 families and two orders. Of these 80 species, 14 are present only on Bioko, 36 are known only in Río Muni, and 30 occur in both regions. No amphibians are currently known from Annobón. There is a very low level of endemism, with only one species endemic to Bioko. This may be due to the country’s small size, to the relatively uniform landscape (lowland rainforest) of Río Muni, and to the recent connections between Bioko and the continent. Our work revealed several new species and country records and highlighted problems in the taxonomic status of many amphibian populations that need to be addressed. As further field andtaxonomic work is carried out, we expect new species records for the country that will assuredly enrich this catalog.
... However, these populations remain both undescribed and untested using phylogenetic analyses. While many similarly distributed Afrotropical forest-restricted frog species have been recognized to contain undescribed diversity (Barej et al., 2014b(Barej et al., , 2015Bell et al., 2017;Blackburn et al., 2010;Jongsma et al., 2018), there are no previous studies suggesting that the two most widespread species (C. alleni and C. crassipes) contain cryptic lineages. ...
... The deep divergence of 12 Ma (95% HPD: 7-17 Myr; Figure 1c) between C. goliath and C. robusta is more surprising. This Miocene divergence is older than that revealed by other recent studies of Central African anurans for which Pliocene and Pleistocene forest expansion and contractions likely played a role in divergences (Bell et al., 2017;Jongsma et al., 2018;Leaché et al., 2019). This suggests either that similar processes might have also played out over deeper timescales in Central Africa or that other factors such as topographic features, including the Sanaga River, might have driven their divergence. ...
Although Conraua goliath is well known as the largest living frog species, the diversity and evolution of the genus Conraua across sub-Saharan Africa remain poorly understood. We present multilocus phylogenetic analyses of the six currently recognized species that provide insights into divergence times, biogeography, body size evolution and undescribed species. An analysis of divergence times demonstrates that crown-group Conraua arose some time during the latest Oligocene to mid-Mio-cene followed by divergence into major lineages in the mid-Miocene that may reflect the fragmentation of widespread tropical forests in Africa that began at this time. We find three pairs of sister species, C. crassipes + C. beccarii, C. alleni + C. derooi and C. goliath + C. robusta, each of which diverged during the Miocene. These relationships reject phylogenetic hypotheses based solely on biogeography as the geographically peripheral C. beccarii from northeastern Africa is nested within western African species and the Central African species do not form a clade. Our species delimitation analyses provide support for undescribed species in C. alleni, C. bec-carii and C. derooi, and possibly C. crassipes, suggesting that the current taxonomy substantially underestimates species diversity. There is no clear directional trend of either increasing or decreasing body size in Conraua and the three largest species do not form a clade. With a robust phylogenetic hypothesis in hand, further field-based studies are needed to understand the evolution of morphology and life history in this charismatic African anuran clade. K E Y W O R D S body size evolution, divergence dating, Goliath Frog, phylogenetics, species delimitation
... Pairwise sequence divergence values (uncorrected net p-distances, pairwise deletion of missing data) were estimated between A. wahlbergii clades for the 16S gene using MEGA v7.0.14 (Kumar et al. 2016). Coarse estimates of the time periods associated with divergence between clades were made by applying a mutation rate of 1% per million years per lineage to the divergence estimates (following Jongsma et al. 2018). These estimates provide a rough estimation of the epoch during which divergences occurred (e.g. ...
Throughout the Miocene, the African landscape underwent broad climatic shifts that profoundly influenced the distribution of fauna and flora. Since the late Miocene, these shifts have created a landscape in southern Africa that is strongly characterised by savanna and arid environments. Forests persist in small fragments, primarily in mountainous or heterogeneous landscapes. Arthroleptis wahlbergii is a small frog endemic to eastern South Africa that has presumed low dispersal ability. Because of its preference for forests, the dynamics of forests since the late Miocene in this region might have promoted diversification within A. wahlbergii. To investigate whether habitat fragmentation might have driven divergences among populations, we carried out species distribution modelling and population level and phylogenetic analyses using two genetic loci (16S, mitochondrial; RAG-1, nuclear) sequenced for 48 individuals from 14 forests across the c. 500 km range of this species. There is substantial population-level structuring within A. wahlbergii, however the structure does not relate to forest types or catchments. We instead propose that the structure is a result of dynamic and idiosyncratic changes in forest connectivity over the Pleistocene. We identified two geographically circumscribed clades, the northern of which corresponds to true A. wahlbergii. The southern clade corresponds to populations from which Arthroleptis wageri FitzSimons, 1930 was described. This has long been considered a synonym of A. wahlbergii, but our molecular phylogenetic and distribution modelling supports recognising A. wageri as a distinct species.
... The herpetological results were summarised by Branch and Conradie (2015). Significant herpetological discoveries included the discovery of at least two new species of frog, one described (Hyperolius raymondi Conradie et al. 2013), and the description of the other (Amnirana sp.) is in preparation ( Jongsma et al. 2018), and also the first record for Angola ...
This review summarises the current status of our knowledge of Angolan reptile diversity, and places it into a historical context of understanding and growth. It is compared and contrasted with known diversity in adjacent regions to allow insight into taxonomic status and biogeographic patterns. Over 67% of Angolan reptiles were described by the end of the nineteenth century. Studies stagnated during the twentieth century but have increased in the last decade. At least 278 reptiles are currently known, but numerous new discoveries have been made during recent surveys, and many novelties await description. Although lizard and snake diversity is currently almost equal, most new discoveries occur in lizards, particularly geckos and lacertids. Poorly known Angolan reptiles and others from adjacent regions that may occur in the country are highlighted. Most endemic Angolan reptiles are lizards and are associated with the escarpment and southwest arid region. Identification of reptile diversity hotspots are resolving but require targeted surveys for their delimitation and to enable protection. These include the Kaokoveld Centre of Endemism, Angolan Escarpment and the Congo forests of the north. The fauna of Angola remains poorly known and under-appreciated, but it is already evident that it forms an important centre of African reptile diversity and endemism.
... Consequently, we propose that mitochondrial divergence between L. crystallinoron and L. brevirostris is intraspecific genetic variation that reflects phylogeographic structure across the Lower Guineo-Congolian Forests. This pattern of phylogeographic structure between Lower Guinean versus Congolian Forest populations is also evident in L. notatus, and more broadly in several studies of Central African forest amphibians (Bell et al. 2017;Portik et al. 2017;Charles et al. 2018;Jongsma et al. 2018). Mitochondrial sequence divergence is a useful, but imperfect tool, for identifying cryptic species diversity. ...
The Central African treefrog Leptopelis brevirostris has a characteristically short and vertically truncated snout, a tooth-like process at the centre of the mandible, and unlike most species of Leptopelis, eats terrestrial gastropods. Two morphologically similar species (L. crystallinoron and L. brevipes) have been described in sympatry with L. brevirostris, each on the basis of a single female specimen and then provisionally synonymised with L. brevirostris by subsequent authors. Here we re-examine the holotypes of the three species and collect both genetic (mtDNA and 25 nuDNA loci) and morphological data across the range of L. brevirostris and its sister species L. notatus to test the hypothesis that L. brevirostris is comprised of more than one species. We found that the diagnostic characters for L. crystallinoron (lacking a visible tympanum and having larger vomerine teeth in contact) and L. brevipes (distinctive dorsal colouration) are also present in L. brevirostris and L. notatus. Furthermore, these characters vary among individuals that share the same mitochondrial haplotype and that occur within a single locality, including the type locality of L. crystallinoron. Although all samples from the type locality of L. crystallinoron form a distinct mitochondrial lineage relative to L. brevipes and L. brevirostris, our analysis of 25 nuclear loci does not support this relationship and instead suggests that this mitochondrial divergence reflects phylogeographic structure across the range of L. brevirostris, including samples from the type localities of L. crystallinoron and L. brevipes. By contrast, the mitochondrial divergence between L. notatus and L. brevirostris is strongly supported in the nuDNA dataset. Consequently, we recognise both L. brevipes and L. crystallinoron as synonyms of L. brevirostris. Given the extensive variation in the colour pattern, the tympanic membrane, and the size and shape of the vomerine teeth among L. brevirostris collected from one locality, variation in these traits should be interpreted with caution in taxonomic research on Leptopelis.
... We then used PAUP Ã v. 4.0a169 (Swofford, 2002) to test for a strict molecular clock using likelihood ratio tests under AICc and BIC criterion with HKY þ I þ G as substitution model. Because the results support a clock-like model (null hypothesis cannot be rejected), we set a strict molecular clock with a mutation rate of 0.0069 sites per million years (Macey et al., 1998), which is compatible with that estimated for 16S for different Ranid species (Chen et al., 2013;Jongsma et al., 2018). We set the mutation rate with a uniform distribution, setting bounds to 0.01 and 0.003 to accommodate for heterogeneity in mutation rates among partitions described above. ...
The Atlantic and Amazon rainforests have a shared but unclear past, with intermittent connections resulting from historical climate change. We investigate these connections by studying the phylogeography and climatic niche of the disjunct distributed frog Lithobates palmipes. We sequenced two fragments of mitochondrial DNA from Atlantic Forest
(AtF) and Amazonia (AmF) individuals and evaluated how genetic diversity is distributed in space and whether past demographic changes occurred. Also, we evaluated the existence of past suitable connections between biomes for L. palmipes through ecological niche models (ENM) and tested for niche divergence. The AtF group is nested within the AmF group and closely related to individuals from eastern Amazonia, a pattern recovered in many species that used
northeast connection routes. We found evidence of recurrent use of connections in different directions and time during the Pleistocene, resulting in genetic structure between biomes, with no signal of demographic change and evidence of niche divergence across both genetic groups. ENMs indicated suitable areas connecting forests throughout northeastern Brazil during the Pleistocene. Mitochondrial lineages do not match biomes exactly. One lineage is composed of AtF populations and eastern Amazonia individuals. The other is composed of western Amazonia individuals, suggesting an effect of past climatic heterogeneity within the Amazonia forest. This is the first evidence that this route drove genetic and ecological diversity for amphibians recently, a group with habits and ecological requirements different from other vertebrates that have been shown to use this putative corridor.
... The region of Lagoa Carumbo has been proposed as a National Park after the results of the rapid biodiversity surveys carried out in 2011 (Huntley and Francisco 2015). These surveys resulted in the description of a new species of Reed frog (Hyperolius raymondi, Conradie et al. 2013), the presence of a new species of Golden-backed frog (Hylarana lepus, Jongsma et al. 2018) and the first country record of the Banded water cobra (Naja annulata, Branch and Conradie 2013). With the description of a new endemic species of snake from this region, the profile of this area is raised even further, reinforcing the motion to declare this a protected area. ...
The African natricine genus Limnophis is represented by two species: Limnophis bicolor Günther, 1865 and Limnophis bangweolicus (Mertens, 1936). They are stout-bodied, semi-aquatic snakes that mostly feed on fish and amphibians, and occur from Botswana and Namibia in the south throughout most of Zambia and Angola to the Democratic Republic of the Congo in the north. We gathered new material from the ranges of both species in Angola and Zambia in order to examine their taxonomic status and identify any overlooked diversity. We constructed a phylogenetic tree, based on three mitochondrial genes (16S, cytb, ND4) and one nuclear gene (cmos), which includes the first DNA sequence data for Limnophis. Three well-supported lineages were identified, each representing separate species. The taxonomic status of the two currently recognised species is validated, and we describe a new species of Limnophis from north-eastern Angola. The new species is distinguished from the others by the combination of distinct ventral and lateral head colouration and patterning, differences in head and ventral scalation, and uncorrected pairwise genetic distances to both L. bicolor and L. bangweolicus of 5.4–8.1% in cytb, 6.1–8.4% in ND4 and 2.7–8.3% in 16S.
... Two possible mechanisms that may have both promoted the splitting include fragmentation of an ancestral widespread forest-restricted species, associated with a reduction of forest cover during alternating cycles of climatic change (Couvreur et al. 2021), and / or the lack of gene flow due to the large Volta River separating the Atewa Range from the Togo-Volta Highlands (Wallace 1852, Penner et al. 2011. Speciation related to reduction and fragmentation in forest cover has been suggested in many West and Central African taxa (e.g., frogs: Jongsma et al. 2018, fruit bats: Hassanin et al. 2015, legumes: Duminil et al. 2013. Similarly, divergence across Lake Volta has already been found in other pairs of sister species, such as Hyperolius picturatus and H. baumanni (Portik et al. 2019) [although there exists a potential photographic record of the later species from the Atewa Range], found from Sierra Leone to central Ghana, and from eastern Lake Volta in Ghana to western Togo, respectively ). ...
Forty-nine years after the last description of a slippery frog, we describe a seventh species of the genus Conraua. The new Conraua is endemic to the Atewa Range Forest Reserve, central Ghana, and is described based on genetic, bioacoustics, and morphological evidence. Recent molecular phylogenetic and species delimitation analyses support this population as distinct from nominotypical C. derooi in eastern Ghana and adjacent Togo. The new species is sister to C. derooi, from which it differs ~4% in the DNA sequence for mitochondrial ribosomal 16S. Genetic divergences in 16S to other species of Conraua range from 4–12%. The new species is distinguished morphologically from its congeners, including C. derooi, by the combination of the following characters: medium body size, robust limbs, lateral dermal fringing along edges of fingers, cream ventral color with brown mottling, the presence of a lateral line system, indistinct tympanum, the presence of inner, outer, and middle palmar tubercles, and two subarticular tubercles on fingers III and IV. We compare the advertisement calls of the new species with the calls from C. derooi and find that they differ by duration, frequency modulation, and dominant frequency. We discuss two potential drivers of speciation between C. derooi and the new species, including river barriers and fragmentation of previously more widespread forests in West Africa. Finally, we highlight the importance of the Atewa Range Forest Reserve as a critical conservation area within the Upper Guinean biodiversity hotspot.
... Unfortunately, this is not unique to the B. mossambicus group. Many recent studies on other herpetofauna have stated that large sampling gaps across sub-Saharan Africa may cause misleading biogeographic conclusions (Medina et al. 2016;Jongsma et al. 2018). The central and eastern localities of B. ombelanonga, as well as the latter from either B. adspersus or B. poweri, may be separated by drainage basins; however, with no contemporary sampling across regions spanning hundreds of kilometers, it is difficult to test these broad biogeographic hypotheses. ...
Recent molecular phylogenetic work has found that Breviceps Merrem, 1820 comprises two major clades, one of which, the B. mossambicus group, is widely distributed across southern sub-Saharan Africa. This group is notable for harboring abundant cryptic diversity. Of the four most recently described Breviceps species, three are members of this group, and at least five additional lineages await formal description. Although Breviceps has long been known to occur in Angola, no contemporary material has been collected until recently. The three most widespread taxa, B. adspersus, B. mossambicus, and B. poweri, may all occur in Angola, but accurate species assignment remains challenging given the rampant morphological similarity between these taxa, and, until recently, the lack of genetic resources. Phylogenetic, morphological, and acoustic analyses of recently collected samples from disparate localities within Angola provide evidence for an undescribed species that is sister to B. poweri. The new species can be diagnosed from its sister taxon by lacking pale spots along the flanks, a pale patch above the vent, and a short, dark band below the nares (all present in B. poweri). Additionally, the male advertisement call differs from the three other Breviceps that might occur in Angola in having both a longer interval between consecutive calls and a higher average dominant frequency. We here describe this lineage as a distinct species, currently only known from Angola, and discuss the presence of other Breviceps taxa within Angola.
... Thus, it is possible that L. millsoni occurs on Bioko and has not yet been detected or has been misidentified as L. rufus. Phylogeographic studies of other large-bodied Bioko anurans including forest tree frogs (Bell, McLaughlin, Jongsma, Blackburn, & Stuart, 2019), foam-nesting tree frogs (Leaché et al., 2019), white-lipped frogs (Jongsma et al., 2018), and clawed frogs (Evans et al., 2015) found very little genetic differentiation between island and continental populations. By contrast, phylogeographic studies of smaller-bodied anurans including leaf-folding frogs (Charles et al., 2018) and reed frogs (Bell et al., 2017) found modest genetic differentiation. ...
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.
... Comments: Amnirana sp. 'albolabris-West' is a forestdwelling frog occurring in the Upper Guinean zone, formerly regarded as being conspecific with the real A. albolabris from Central African forests (Jongsma et al. 2018). While its description is being prepared, the occurrence of this species has been even more recently confirmed for Burkina Faso (Ayoro et al. 2020). ...
This article provides the first assessment and commented checklist of the anuran diversity of the Ivorian part of the Mount Nimba Integrated Nature Reserve (MNINR), West Africa. During a period of 81 days from 18 June 2018 to 17 May 2019, covering both the rainy and dry seasons, 53 amphibian species were recorded. Among these species, 30.2% were endemic to either the Upper Guinea forest zone or smaller areas within that biodiversity hotspot. The amphibian fauna of the Ivorian slope of the MNINR is very similar to those of the Guinean side of Mounts Nimba and the Guinean Simandou Range. Based on the current IUCN Red List data, several recorded species are of high conservation concern: the Critically Endangered Nimbaphrynoides occidentalis; the Endangered Hyperolius nimbae; and the Near Threatened Leptopelis macrotis, Leptopelis occidentalis, and Odontobatrachus arndti. Of particular interest among the survey records were the poorly known Ptychadena arnei, P. pujoli, and P. submascareniensis. The records of Ptychadena retropunctata and Arthroleptis crusculum represent first country records for Ivory Coast, while the records of Odontobatrachus arndti and Phrynobatrachus fraterculus are the second records for the country. In contrast to the Guinean and Liberian parts of Mounts Nimba, the Ivorian part had never been mined or explored for mining, nor do such plans currently exist. As a result, the study area still holds intact mountain forests that include rare and unique habitats with exceptional biodiversity, which need to be preserved for future generations. Consequently, conservation strategies should minimize bush-fires in mountain grasslands, e.g., to protect the viviparous toad N. occidentalis. At lower elevations, it is important to encourage local activities concerning reforestation of the previously forested areas and the conservation of the (sacred) village forests.
... -Th e genus Amnirana has been recently revised by Jongsma et al. (2018). Based on molecular data this study restricts the name Amnirana albolabris (Hallowell, 1856) Lamotte & Xavier (1981), mentioned that few specimens can be found in the sub-Saharan areas of West Africa. ...
... A large-scale genetic examination of amphibian diversity in Mauritania is warranted because the country is located in a biogeographic crossroad between the Palaearctic and Afrotropic biogeographic realms, and between the Sahara and the Sahel ecoregions. In addition, cryptic diversity has been described within amphibians from sub-Saharan Africa that are known to occur in Mauritania or in the southern bordering countries (Vences et al. 2004;Zimkus et al. 2010;Zimkus and Larson 2011;Zimkus and Gvoždík 2013;Wasonga and Channing 2013;Barej et al. 2014;Deichman et al. 2017;Jongsma et al. 2018). These factors suggest that species diversity could be higher than previously reported (Padial et al. 2013). ...
Our study seeks to: (1) reduce biodiversity knowledge gaps in amphibians from desert and arid regions; (2) quantify species diversity and detect potential cryptic diversity; (3) identify environmental correlates of amphibian richness distribution, and (4) identify diversity hotspots. DNA barcoding and spatial modelling were integrated to map observed and predicted amphibian richness in Mauritania, Africa. We built two DNA barcoding libraries using one mitochondrial (COI) and one nuclear marker (RAG1). Taxon richness was calculated using species delimitation methods. A generalised linear model was employed to identify environmental correlates of amphibian richness and the distribution of diversity hotspots was predicted. We found a total of 16 anuran taxa with Afrotropic affinities, and two genera and four species were added for the amphibian list of Mauritania. Potential cryptic diversity was detected in Hoplobatrachus occipitalis. Amphibian richness was positively correlated with proximity to savannah, gravel floodplains, and with presence of seasonal wetlands, and negatively with proximity to dunes. Major diversity hotspots were predicted in southern Mauritania. Barcoding methods for both genetic markers successfully identified the taxonomic identity of specimens, also uncovering cryptic diversity in the amphibians of the Sahara-Sahel ecoregions. Amphibian richness in Mauritania increases southwards and it is mostly concentrated in areas under pressure due to habitat conversion, lacking legal protection. The combination of DNA barcoding with spatial modelling can be easily applied to any desert system to address pressing needs for research on biodiversity distribution.
... Differences in amphibian diversities between our study sites and these areas in Cameroon might be a result of long-term extensive surveys in the surveyed sites in Cameroon as well as the use of other sampling techniques, for example pitfall traps and dip nets in their sampling and also historically, the areas are known as 'hotspot of amphibian diversity'. It is thus apparent that continuous field sampling in AFR and IFE, including the use of different sampling techniques, might recover some additional species.Our study, in accordance with preceding studies(Jongsma et al., 2018;Nneji et al., 2019a;Portik et al., 2017), provided evidence of biogeographic ties between our study areas and the LGC forest in the form of co-occurrences of species due to shared environmental conditions. We foundA. ...
Despite recent anthropogenic interference, south‐eastern (SE) Nigeria historically hosts a myriad of pristine forest habitats that could sustain diverse amphibian assemblages. Currently, land conversion of primary forests through human activities has led to modified habitats, such as agricultural fields and secondary forest. This calls for biodiversity documentation and initiation of conservation plans. However, the dearth of herpetological studies has limited knowledge of the amphibian species richness and distribution patterns in some forest ecosystems of SE Nigeria. Thus, we surveyed two less‐explored intact forests in SE Nigeria—Afi Forest Reserve (AFR) and Ikpan forest ecosystem (IFE)—to document the patterns of amphibian diversity and distribution. Specimens were searched for opportunistically using visual and acoustic survey methods. Literature searches were conducted to document additional species that were not encountered. Using the observational records and arrays of diversity indices, the patterns of species richness and abundance across habitat types were evaluated. The result of our study revealed the presence of 30 and 31 amphibian species from AFR and IFE, respectively. Our field collections included two unidentified species (Sclerophrys sp. and Hyperolius sp.) from AFR and one (Phrynobatrachus sp.) from IFE. Analyses revealed high species diversity and richness in forest and swamps compared with the agricultural field and savannah. Given the increased human activities and the antecedent threats to forest ecosystems of SE Nigeria, we offer recommendations for the initiation of conservation plans for these two surveyed localities.
... The Gap is a natural forest-savanna mosaic habitat in Ghana,Togo, Benin, and Nigeria that separates the Upper Guinean and Lower Guinean rainforests of West Africa. Numerous examples of West African, forest-specialist vertebrates that are limited by the Gap are known (e.g., Booth 1958;Kingdon 1989;Jongsma et al. 2018), and the Gap also seems to be an effective barrier against the amphibian chytrid fungus in West Africa (Penner et al. 2013;Zimkus et al. 2020). The Gap expanded and contracted periodically during recent geological history, but it has mainly been studied through floral and climate models, and the precise boundary within the Gap that separates vertebrate species is unknown and likely to be taxon-specific (De-menou et al. 2016;Couvreur et al. 2021). ...
The genus Toxicodryas, historically included with the renowned Australasian cat-eyed snakes of the colubrid genus Boiga, currently includes two widespread species (T. blandingii and T. pulverulenta) in western, central, and eastern Africa. We leverage findings from a recent phylogenomic and historical demographic analysis of this genus (based on 2848-4471 Rad-seq loci from across the genome), with robust sampling from throughout the ranges of both species, to define two additional taxonomic units, with species boundaries corresponding to river barriers. Additional morphometric data from scores of examined museum specimens and literature records bolster the recognition of these two new cryptic species. We hypothesize that T. blandingii occurs west of the confluence of the Congo and Ubangi rivers, whereas a cryptic new species that is found east of this biogeographic barrier has significantly higher numbers of ventral scale counts in both sexes, additional significant differences in several scale counts, and lower venom toxicity. Toxicodryas pulverulenta occurs west of the Niger Delta in West Africa, whereas a cryptic new species that is found east of this biogeographic barrier has significantly higher numbers of subcaudal scale counts in both sexes. A review of published information regarding morphological variation, ecology, natural history, habitat, and venom is summarized for these four Toxicodryas species.
High‐throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The “vanishing refuge” diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to becoming generalists also present in non‐forest habitats. Complex arrangements of geographical barriers (hydrology and topography) and ecological gradients between forest and non‐forest habitats may have further influenced the region's biodiversity, but elucidation of general diversification processes has been limited by lack of suitable data. Here, we explicitly test alternative diversification modes in the coastal forests using genome‐wide single nucleotide polymorphisms, mtDNA, spatial and environmental data for three forest (Arthroleptis xenodactyloides, Leptopelis flavomaculatus and Afrixalus sylvaticus) and four generalist (Afrixalus fornasini, A. delicatus, Leptopelis concolor, L. argenteus) amphibians. Multiple analyses provide insight about divergence times, spatial population structure, dispersal barriers, environmental stability and demographic history. We reveal highly congruent intra‐specific diversity and population structure across taxa, with most divergences occurring during the late Pliocene and Pleistocene. Although stability models support the existence of some forest refugia, dispersal barriers and demographic models point toward idiosyncratic diversification modes across taxa. We identify a consistent role for riverine barriers in the diversification of generalist taxa, but mechanisms of diversification are more complex for forest taxa and potentially include topographical barriers, forest refugia and ecological gradients. Our work demonstrates the complexity of diversification processes in this region, which vary between forest and generalist taxa, but also for ecologically similar species with shared population boundaries. This article is protected by copyright. All rights reserved.
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 lizard Holaspisguentheri . 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 as Odontobatrachusnatator and Conrauaalleni . 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.
Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrog Chiromantis rufescens. Guinean and Congolian rain forests, West and Central Africa. Chiromantis rufescens. We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples of C. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial. Population structure within C. rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history of C. rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradients.
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.
We sampled amphibians and reptiles using rapid assessment techniques in primary forest and forest-savannah mosaic habitat in Lékoumou Department, Republic of Congo, near the Batéké Plateau, as part of an environmental impact assessment for a mining project. We detected 38 amphibian and 36 reptile species. Amphibian species included 38 frogs representing 14 genera and 10 families. Reptile species included 23 snakes (representing 18 genera and six families), 11 lizards (representing 8 genera and five families) and two turtles (representing two genera and two families). Five frogs (Foulassi Screeching Frog, Arthroleptis adelphus, Rio Benito Long-fingered Frog, Cardioglossa gracilis, Ongot Long-fingered Frog, Cardioglossa gratiosa, Bates' River Frog, Phrynobatrachus batesii, and Uzungwe Grassland/Ridged Frog, Ptychadena uzungwensis), two snakes (Steinhaus' Worm Snake, Afrotyphlops steinhausi, and Underwood's Tree Snake, Dipsadoboa underwoodi), and two lizards (Kamdem Toham's Half-toed Gecko, Hemidactylus kamdemtohami, and Reichenow's Skink, Lacertaspis reichenowi) represented the first confirmed records for the Republic of Congo. The snake Bothrolycus ater (Loreal-pitted Snake) was previously known from only a few specimens; we present here the first photograph of this species found alive. This study represents the herpetological component of a broader biodiversity survey carried out as an early step toward the goal of establishing Ogooué-Leketi National Park as a protected area. Resumé.-Nous avons échantillonné les amphibiens et les reptiles dans un format d'évaluation rapide, en forêt primaire et en mosaïque forêt-savane dans le département Lékoumou de la République du Congo, près du plateau Batéké, dans le cadre d'une étude d'impact environnemental pour un projet minier. Nous avons trouvé 38 espèces d'amphibiens et 36 espèces de reptiles. Les espèces d'amphibiens comprenaient des représentants de 14 genres et de 10 familles. Les espèces de reptiles comprenaient 23 serpents (représentant 18 genres et six familles), 11 lézards (représentant huit genres et cinq familles) et deux chéloniens (représentant deux familles). Dix espèces représentent les premiers rapports confirmés pour la République du Congo, dont cinq grenouilles (Arthroleptis adelphus, Cardioglossa gracilis, Cardioglossa gratiosa, Phrynobatrachus batesii et Ptychadena uzungwensis), deux serpents (Afrotyphlops steinhausi et Dipsadoboa underwoodi) et deux lézards (Hemidactylus kamdemtohami et Lacertaspis reichenowi). Le serpent Bothrolycus ater, bien que précédemment connu de la République du Congo n'est connu que de quelques spécimens de musée et nous présentons ici la première photo de cette espèce vivante. Cette étude herpétologique fait partie d'une plus grande enquête sur la biodiversité réalisée comme première étape vers l'établissement du parc national Ogooué-Leketi comme aire protégée.
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 savannah 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 (gdi), 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. This article is protected by copyright. All rights reserved
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.
During nineteenth century, the early descriptions of amphibians often have very imprecise onymotopes (type localities). We have investigated such descriptions for Gabon. We provide some historical informations about the collectors of the specimens and we refine the places of collections.
We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated
methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing
systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The
new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict
gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line.
The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command
line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput
and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
The interplay between range expansion and concomitant diversification is of fundamental interest to evolutionary biologists, particularly when linked to intercontinental dispersal and/or large scale extinctions. The evolutionary history of true frogs has been characterized by circumglobal range expansion. As a lineage that survived the Eocene–Oligocene extinction event (EOEE), the group provides an ideal system to test the prediction that range expansion triggers increased net diversification. We constructed the most densely sampled, time-calibrated phylogeny to date in order to: (i) characterize tempo and patterns of diversification; (ii) assess the impact of the EOEE; and (iii) test the hypothesis that range expansion was followed by increased net diversification. We show that late Eocene colonization of novel biogeographic regions was not affected by the EOEE and surprisingly, global expansion was not followed by increased net diversification. On the contrary, the diversification rate declined or did not shift following geographical expansion. Thus, the diversification history of true frogs contradicts the prevailing expectation that amphibian net diversification accelerated towards the present or increased following range expansion. Rather, our results demonstrate that despite their dynamic biogeographic history, true frogs diversified at a relatively constantly rate, even as they colonized the major land masses of Earth. © 2017 The Author(s) Published by the Royal Society. All rights reserved.
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 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.
This paper gives a historical overview of the African rain forest from its origins, towards, the end of the Cretaceous period. The areas around the Gulf of Guinea, in particular from Ivory Coast to Nigeria and especially Cameroon, Gabon and Congo, appear to have been already occupied at this time by wet tropical forest formations mainly composed of Angiosperms. In the course of the Tertiary period the combined effect of the equator being situated further north than now and the development of the Antarctic ice cap favoured the development of wet tropical conditions over a large part of North Africa. Towards the end of the Tertiary, the equator reached its present position and the northern hemisphere ice caps appeared, and these phenomena resulted in the disappearance of the forest formations spread across the north of Africa, and the concentration of these formations near the equatorial zone around the Gulf of Guinea and in the Congo-Zaire basin. From 800 000 years ago onwards the marked glacial variations at middle and high latitudes in both hemispheres, lowered temperatures in equatorial areas and brought arid climates at times of maximum glacial extension. -Author
A molecular phylogeny of the Afrotropical anuran genus Amietia based on 323 16S sequences indicates that there are 19 species, including four not yet described. No genetic material was available for the nominal A. inyangae. We consider them to represent full species, and define them based on 16S genetic distances, as well as differences in morphology, tadpoles and advertisement call where known. An analysis based on two mitochondrial and two nuclear genes (12S, 16S, 28S and tyrosinase exon 1), from 122 samples, confirmed the phylogenetic relationships suggested by the 16S tree. We recognise and (re-) describe the following species: Amietia angolensis (Bocage, 1866), A. chapini (Noble, 1924), A. delalandii (Duméril & Bibron, 1841), A. desaegeri (Laurent, 1972), A. fuscigula (Duméril & Bibron, 1841), A. hymenopus (Boulenger, 1920), A. inyangae (Poynton, 1966), A. johnstoni (Günther, 1893), A. moyerorum sp. nov., A. nutti (Boulenger, 1896), A. poyntoni Channing & Baptista, 2013, A. ruwenzorica (Laurent, 1972), A. tenuoplicata (Pickersgill, 2007), A. vandijki (Visser & Channing, 1997), A. vertebralis (Hewitt, 1927), and A. wittei (Angel, 1924). Three further candidate species of Larson et al. (2016) await formal naming. We provisionally regard A. amieti (Laurent, 1976) as a junior synonym of A. chapini (Noble, 1924). Amietia lubrica (Pickersgill, 2007) is shown to be a junior synonym of A. nutti, while A. quecketti (Boulenger, 1895) is shown to be a junior synonym of A. delalandii (Duméril & Bibron, 1841), and A. viridireticulata (Pickersgill, 2007) is placed as a junior synonym of A. tenuoplicata (Pickersgill, 2007). On the basis of similarity of 16S sequences, we assign A. sp. 1, A. sp. 3 and A. sp. 6 of Larson et al (2016) to the nomina A. chapini (Noble, 1924), A. desaegeri (Laurent, 1972), and A. nutti (Boulenger, 1896) respectively.
Une nouvelle classification provisoire de la superfamille des Ranoidea, et plus particulierement de la famille des Ranidae et du genre Rana, est proposee. Le genre Rana est ici subdivise, principalement sur la base de criteres phenetiques, en trente-trois groupes, auxquels est ici provisoirement attribue le rang de sous-genres. Le but principal de cette classification provisoire, qui doit etre comprise comme un outil de travail et non pas comme une proposition definitive, est de servir de guide pour de futures etudes sur la phylogenie de cette famille tres vaste et a repartition quasi cosmopolite : cette classification aidera a selectionner des especes representatives de chaque groupe phenetique pour l'etude des etats de caracteres, et a choisir les hors-groupes appropries pour l'etablissement de la polarite des morphoclines de caracteres. Ce n'est que lorsque la phylogenie de la famille dans son ensemble sera resolue qu'il sera possible d'elaborer une classification plus stable, qui s'averera peut-etre tres differente de celle qui est presentee ci-dessous.
Mahenge Mountain is part of the Eastern Arc Mountains in Tanzania. It is bordered by the Kilombero flood plain to the west and forms a continuous mountain block with the Mbarika to the south, lying close to the Udzungwa and Southern Highland Mountain blocks. The amphibian fauna of the forests of Mahenge Mountain has not been investigated until recent fieldwork carried out in the Sali Forest Reserve that has revealed a diverse forest fauna. In this study new records are reported, details of habitats are given and a checklist of the amphibians and reptiles of Mahenge Mountain are provided. In addition, biogeographical analyses were carried out to investigate patterns of spatial turnover in species. This was achieved by calculating the standard similarity index between the amphibian assemblages of the highland Mahenge Mountains (>850 m) and the lowland Kilombero floodplain (<400 m). The results show significant differences (62%) between the two areas, reflecting large altitudinal turnover in species between the widespread lowland fauna and the montane fauna. This is further emphasized by a comparison of transects in lowland Mozambique and highland Zimbabwe, which has a comparable similarity index measure of 54%, impressive when comparing the difference in distance and altitude between the two transects. The reasons for this marked lowland-highland differentiation in Tanzania are poorly understood. Concern is raised for the preservation of this highland endemic fauna in the light of continuing habitat destruction.
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 evolutionary
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 molecular
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 species,
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 histories
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).
We describe two new species of puddle frogs, genus Phrynobatrachus, from the south-western Republic of the Congo. One of them, P. horsti sp. nov., occurs also in neighbouring Gabon and is morphologically most similar to the Cameroonian P. ruthbeateae. It differs from the latter species by smaller males with longer thighs and shanks. The new species comprises various colour morphs but always has less conspicuous black borders between flanks and belly than P. ruthbeateae. The distinct and large black axillary blotch of P. ruthbeateae is either much smaller in P. horsti sp. nov., or broken into numerous irregularly shaped smaller dots. Similarly, a black transversal line at the anterior ventral border of thighs and the black face mask is less distinct and irregularly delimitated in P. horsti sp. nov. when compared to P. ruthbeateae. The mean genetic difference in the sampled region of the 16S rRNA gene between P. horsti sp. nov. and 40 other western African congeners range from 3.66-18.10%. The second new species, P. mayokoensis sp. nov., differs from all other known congeners by the combination of a compact and warty body, the absence of a spiny eyelid tubercle and pedal webbing, a conspicuous black triangle on throat and anterior part of the belly, and a distinct large red blotch on the anteriorproximal surface of the thighs. It exhibited a mean genetic difference in the 16S rRNA to 40 other western African congeners ranging from 1.34-16.98%. The genetically most similar sequence stems from a GenBank entry of a Gabonese frog, determined as P. ogoensis. A comparison of the new species with P. ogoensis syntypes confirmed their specific distinctiveness, most convincingly underlined by the absence of pedal webbing in the new species and the pronounced pedal webbing in P. ogoensis. The GenBank entry thus most likely is based on a misidentification and P. mayokoensis sp. nov. may also occur in neighbouring Gabon. The discovery of the two new frog species is further evidence of the huge gap in our knowledge concerning the species richness in the Guineo-Congolian rainforests.
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.
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.
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 Ivory Coast it inhabits forests around waterfalls or cascades. Based on more than 130 specimens from 78 localities, covering the entire distributional range, we investigated the molecular diversity of these frogs.
Our analyses included mitochondrial and nuclear genes, including 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-Ivory Coast. 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.
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 in highlights the urgent need to protect these frogs, all of which are endemic to small areas within the Upper Guinean biodiversity hotspot.
The hypothesis of Pleistocene forest refugia was tested using comparative phylogeography of Scotonycterini, a fruit bat tribe endemic to Africa containing four species: Scotonycteris zenkeri, Casinycteris argynnis, C. campomaanensis, and C. ophiodon. Patterns of genetic structure were assessed using 105 Scotonycterini (including material from three holotypes) collected at 37 localities, and DNA sequences from the mitochondrial cytochrome b gene (1140 nt) and 12 nuclear introns (9641 nt). Phylogenetic trees and molecular dating were inferred by Bayesian methods. Multilocus analyses were performed using supermatrix, SuperTRI, and *BEAST approaches. Mitochondrial analyses reveal strong phylogeographical structure in Scotonycteris, with four divergent haplogroups (4.9–8.7%), from Upper Guinea, Cameroon, western Equatorial Africa, and eastern Democratic Republic of the Congo (DRC). In C. argynnis, we identify two mtDNA haplogroups corresponding to western and eastern Equatorial Africa (1.4–2.1%). In C. ophiodon, the mtDNA haplotypes from Cameroon and Ivory Coast differ by only 1.3%. Nuclear analyses confirm the validity of the recently described C. campomaanensis and indicate that western and eastern populations of C. argynnis are not fully isolated. All mtDNA clusters detected in Scotonycteris are found to be monophyletic based on the nuclear dataset, except in eastern DRC. In the nuclear tree, the clade from western Equatorial Africa is closely related to individuals from eastern DRC, whereas in the mitochondrial tree it appears to be the sister-group of the Cameroon clade. Migrate-n analyses support gene flow from western Equatorial Africa to eastern DRC. Molecular dating indicates that Pleistocene forest refugia have played an important role in shaping the evolution of Scotonycterini, with two phases of allopatric speciation at approximately 2.7 and 1.6 Mya, resulting from isolation in three main forest areas corresponding to Upper Guinea, Cameroon, and Equatorial Africa. Two cryptic species and two subspecies are described herein in the genus Scotonycteris. Female philopatry and male biased dispersal are supported for the smallest taxa, i.e., the three species of Scotonycteris and C. argynnis. The Congo, Ntem, and Sanaga rivers are identified as biogeographic barriers to the dispersal of Scotonycteris during interglacial periods. A greater capacity for long-distance dispersal is inferred for the largest species, C. ophiodon.
Vegetation history in tropical Africa is still to date hardly known and the drivers of population differentiation and speciation processes are little documented. It has often been postulated that population fragmentations following climate changes have played a key role in shaping the geographic distribution patterns of genetic diversity and in driving speciation. Here we analyzed phylogeographic patterns (chloroplast-DNA sequences) within and between eight (sister) species of widespread rainforest herbs and lianas from four genera of Marantaceae (Halopegia, Haumania, Marantochloa, Megaphrynium), searching for concordant patterns across species and concordance with the Pleistocene refuge hypothesis. Using 1146 plastid DNA sequences sampled across African tropical lowland rainforest, particularly in the Lower Guinean (LG) phytogeographic region, we analyzed intra- and interspecific patterns of genetic diversity, endemism and distinctiveness. Intraspecific patterns of haplotype diversity were concordant among most species as well as with the species-level diversity pattern of Marantaceae. Highest values were found in the hilly areas of Cameroon and Gabon. However, the spatial distribution of endemic haplotypes, an indicator for refuge areas in general, was not congruent across species. Each proposed refuge exhibited high values of endemism for one or a few species indicating their potential role as area of retraction for the respective species only. Thus, evolutionary histories seem to be diverse across species. In fact, areas of high diversity might have been both refuge and/or crossing zone of recolonization routes i.e., secondary contact zone. We hypothesize that retraction of species into one or the other refuge happened by chance depending on the species' distribution range at the time of climate deterioration. The idiosyncratic patterns found in Marantaceae species are similar to those found among tropical tree species, especially in southern LG.
We describe a new small Phrynobatrachus species from southern Cameroon. The new species exhibits a combination of unique morphological characters and a distinctive colour pattern consisting of a black lateral face mask, a black throat in males, a white throat with uniform black lower mandibles in females and a white belly in both sexes. Morphologically it is characterized by small size, absence of an eyelid cornicle, presence of black spines on anterior part of vocal sac in males, spines on flanks, presence of discs on toe and finger tips, distinct webbing, absence of nuptial pads on male thumbs and scapular ridges converging in a straight line. Analysis of mitochondrial 16S rRNA revealed that the new species differs from 34 other West and Central African species of the genus by a minimum distance of 4.5% and is most similar to several Phrynobatrachus species which are almost all endemic to the Cameroon volcanic line or parts of it, i.e. P. chukuchuku (4.9%), P. werneri (5.1%), P. steindachneri (5.2%), P. schioetzi (5.6%), P. batesii (5.9%), P. cricogaster (5.5%), P. danko (6.1%), and P. manengoubensis (6.1%), respectively. The new species is most similar to P. batesii, which was described from forests close to the type locality of the new species. Morphologically the new species differs from P. batesii by much smaller size (< 20 mm vs. 25-31 mm), shape of scapular ridges, belly colour, shorter shanks, absence of nuptial pads and presence of gular spines in breeding males.
A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multi species coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The Nearest-Neighbor Interchange (NNI) algorithm was adapted to proposes changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted simulation study to examine the statistical properties of the method using 6 populations (2 sequences each) and a true number of 3 species, with values of divergence times and ancestral populations sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Re-analyses of two datasets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and the prior on population size parameters (θ) on Bayesian species delimitation.
AimIn this study we identified large-scale variation in tree species composition across tropical African forests and determined the underlying environmental and historical factors. LocationTropical forests from Senegal to Mozambique. Methods
Distribution data were gathered for 1175 tree species in 455 sample sites scattered across tropical Africa, including all types of tropical forests (wet, moist, dry, and lowland to moderate elevation montane forests). The value of elevation and 19 climatic variables extracted from the BIOCLIM data set were assigned to each sample site. We determined the variation in species composition using correspondence analysis and identified the environmental correlates. We defined floristic clusters according to species composition and identified the characteristic species using indicator analysis. ResultsWe identified a major floristic discontinuity located at the Albertine rift that separated the dry, moist and wet forests of West and Central Africa (the entire Guineo-Congolian Region) from the upland and coastal forests of East Africa. Except for the Albertine Rift, we found no evidence to support the other proposed floristic discontinuities (Dahomey Gap etc.). We detected two main environmental gradients across tropical African forests. The rainfall gradient was strongly correlated with the variation in tree species composition in West and Central Africa. The elevation/temperature gradient highlighted the major floristic differences within East Africa and between East Africa and the Guineo-Congolian Region, the latter being most probably due to the geological disruption and associated climatic history of the East African uplift. Main conclusionsWe found floristic evidence for three main biogeographical regions across the tropical African forests, and described six floristic clusters with particular environmental conditions within these regions: Coastal and Upland for East Africa, Dry and Wet-Moist for West Africa, and Moist and Wet for Central Africa.
Cycles of Quaternary climate change are assumed to be major drivers of African rainforest dynamics and evolution. However, most hypotheses on past vegetation dynamics relied on palaeobotanical records, an approach lacking spatial resolution, and on current patterns of species diversity and endemism, an approach confounding history and environmental determinism. In this context, a comparative phylogeographic study of rainforest species represents a complementary approach because Pleistocene climate fluctuations may have left interpretable signatures in the patterns of genetic diversity within species. Using 1274 plastid DNA sequences from eight tree species (Afrostyrax kamerunensis, A. lepidophyllus, Erythrophleum suaveolens, Greenwayodendron suaveolens, Milicia excelsa, Santiria trimera, Scorodophloeus zenkeri, Symphonia globulifera) sampled in 50 populations of Atlantic Central Africa (ACA), we averaged divergence across species to produce the first map of the region synthesizing genetic distinctiveness and standardized divergence within and among localities. Significant congruence in divergence was detected mostly among five of the eight species and was stronger in the northern ACA. This pattern is compatible with a scenario of past forest fragmentation and recolonization whereby forests from eastern Cameroon and north-eastern Gabon would have been more affected by past climate change than those of western Cameroon (where one or more refugia would have occurred). By contrast, southern ACA (Gabon) displayed low congruence among species that may reflect less drastic past forest fragmentation or a more complex history of vegetation changes. Finally, we also highlight the potential impact of current environmental barriers on spatial genetic structures.This article is protected by copyright. All rights reserved.
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.
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.
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.
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.
Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5-7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group.
The Crocidura obscurior or West African pygmy shrew complex is endemic to West African
forests from south-eastern Guinea, eastern Liberia, southern Cote d ^ ’Ivoire and southwestern Ghana. We explore the genetic and morphometric diversity of 239 individuals of
the C. obscurior complex from 17 localities across its geographical range. Using genetic data
from three mitochondrial (16S, cytochrome b and COI) and four nuclear markers (BRCA1,
STAT5A, HDAC2 and RIOK3) and skull geometric morphometrics, we show that this
complex is composed of two cryptic and sympatric species, C. obscurior and C. eburnea. We
then test several hypotheses to infer their evolutionary history. The observed phylogeographical pattern based on cytochrome b and COI sequences fits the forest refuge theory:
during arid phases of the Plio-Pleistocene, around 3.5, 2.1, 1 and 0.5 Mya, a small number
of populations survived in isolated forest patches and diverged allopatrically. During wetter
climatic periods, forests expanded, leading to secondary contacts between previously isolated
populations. Our results also suggest the possible contribution of episodes of isolation in subrefuges. Historical variation of the West African hydrographic network could also have contributed to the observed patterns of genetic differentiation. Rivers such as the Volta and
Sassandra may act as past and/or current barriers to gene flow. Although these two species
have sympatric distributions, their phylogeographical histories are somewhat dissimilar due
to small differences in their dispersal abilities and ecological requirements.
A new species of squeaker frog (genus Arthroleptis) is described from Pico Basile on Bioko Island (Equatorial Guinea), which lies just off the coast of Cameroon in the Gulf of Guinea. A previous molecular phylogenetic study indicates that this new species is nested within a species complex—Arthroleptis poecilonotus—that comprises morphologically indistinguishable populations that represent several cryptic species. The new species from Bioko is, however, easily distinguishable from both closely related and geographically proximate Arthroleptis by a combination of its moderately large body size (approximately 25% larger than frogs in the remaining poecilonotus species complex) and unique ventral color pattern. It is further distinguished from all other Arthroleptis by the presence of spines on the crus in large males and from other populations in the poecilonotus species complex by the occasional presence of a supernumerary tubercle at the base of pedal digit II. Statistical analyses of measurement data, including a principal components analysis, demonstrate that the new species from Bioko is both larger and has relatively longer hindlimbs and toes than other populations of the poecilonotus species complex. These analyses also suggest that the poorly known A. brevipes is morphologically diagnosable, but the status of other taxa such as A. bivittatus and A. zimmeri remains unclear. This new Arthroleptis is the only frog that is unequivocally endemic to Bioko Island.
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 prevailing explanation for the observed distributional patterns and areas of endemism of tropical forest organisms is the Pleistocene refuge hypothesis, which proposes that wide-ranging ancestral taxa were isolated into forest refuges during certain glacial periods, and that this isolation provided them with the opportunity to speciate. John Endler has recently argued that two predictions of the refuge hypothesis-that contact zones between vicars should be between refuges and that contact zones of rapidly reproducing butterflies should be wider than those of more slowly reproducing birds-are not borne out by the evidence. Endler therefore rejects the refuge hypothesis. We show that the data available are far too imprecise to permit any conclusions regarding contact zone widths and that, according to our reanalysis of the African bird data used by Endler, all the contact zones between vicars do indeed occur between refuges, exactly where they are expected. Additional strong support for the refuge hypothesis comes from the existence of many taxa endemic to the particular forest areas which have been postulated as refuges and from fragmented taxa which are still allopatric, never having come into secondary contact.
The phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range - the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group.
While investigating the genetic structure in wild bonobos,1 we realized that the widely accepted scenario positing that the Pleistocene appearance of the Congo River separated the common ancestor of chimpanzees (Pan troglodytes) and bonobos (P. paniscus) into two species is not supported by recent geographical knowledge about the formation of the Congo River. We explored the origin of bonobos using a broader biogeographical perspective by examining local faunas in the central African region. The submarine Congo River sediments and paleotopography of central Africa show that the Congo River has functioned as a geographical barrier for the last 34 million years. This evidence allows us to hypothesize that when the river was first formed, the ancestor of bonobos did not inhabit the current range of the species on the left bank of the Congo River but that, during rare times when the Congo River discharge decreased during the Pleistocene, one or more founder populations of ancestral Pan paniscus crossed the river to its left bank. The proposed scenario for formation of the Congo River and the corridor hypothesis for an ancestral bonobo population is key to understanding the distribution of great apes and their evolution.
AimThis study aims to reconstruct the evolutionary history of the African rodent genus Malacomys and to identify factors driving diversification within this genus.LocationAfrican tropical lowland forest.Methods
Analyses were based on sampling representatives from most of the known geographical range of the genus. We assessed genetic structure and historical biogeography using a combination of mitochondrial and nuclear markers. Morphological differences between lineages were analysed using a geometric morphometric approach.ResultsThree species of Malacomys are recognized within the genus. Two are endemic to West Africa, and one is endemic to Central Africa. Our analyses reveal a strong phylogeographical structure with 13 lineages, most of them allopatric or parapatric. A complex biogeographical history, including dispersal–vicariance events, explains the current genetic structure of Malacomys. Discrete divergence events within the genus are dated to the mid-Pliocene (3.7 Ma, 95% range: 2.4–5.2 Ma) and the Pleistocene (less than 1.9 Ma, with most events less than 1 Ma). Morphological variation is partly congruent with genetic structure and may indicate local adaptations.Main conclusionsClimatic oscillations, which led to periodic fragmentation of the forest habitat, seem to be the major driver of diversification within this genus. Our results support the existence of multiple small, rather than a few large, forest refugia during glacial maxima. Rivers have played a significant role in shaping boundaries of several regional haplogroups, either by promoting diversification or by preventing secondary contact between previously isolated lineages.
ABSTRACT
Aim Phylogeographical signatures of past population fragmentation and demographic change have been reported in several African rain forest trees. These signatures have usually been interpreted in the light of the Pleistocene forest refuge hypothesis, although dating these events has remained impracticable because of inadequate genetic markers. We assess the timing of interspecific and intraspecific genetic differentiation and demographic changes within two rain forest Erythrophleum tree species (Fabaceae: Caesalpinioideae).
Location Tropical forests of Upper Guinea (West Africa) and Lower Guinea (Atlantic Central Africa).
Methods Six single-copy nuclear genes were used to characterize the phylogeographical patterns of the parapatric sister species, Erythrophleum suaveolens (characteristic of semi-deciduous or gallery forests) and Erythrophleum ivorense (characteristic of evergreen forests). The number of gene pools within each species was determined and the timings of their divergence and past demographic changes were estimated using Bayesian-based coalescent approaches.
Results Three geographically separated gene pools were identified within E. suaveolens, and a single gene pool was inferred in E. ivorense. All gene pools show signatures of demographic bottlenecks concomitant with the last glacial period (c. 120–12 ka). Species-tree inferences show that the two species diverged c. 600 ka, whereas the divergence between E. suaveolens gene pools was dated to the late Pleistocene (first divergence c. 120 ka, second c. 60 ka).
Main conclusions (1) Molecular dating of demographic changes of two African tropical forest tree species is consistent with the Pleistocene forest refuge hypothesis. (2) Tree species from Guinean evergreen tropical forests might have been less affected by past climate change than semi-deciduous species. (3) Our phylogeographical data support a recent date (Holocene) of the last opening of the Dahomey Gap.
The genus Atoconeura previously comprised two species; one with five subspecies. Principal Component Analysis of 33 characters of 148 specimens and cladistic analysis of 28 characters revealed six discrete taxa, partly with narrowly overlapping ranges. Subspecies aethiopica, Kenya and pseudeudoxia of biordinata are raised to specific rank; the synonymy of chirinda with biordinata is confirmed; A. luxata sp. n. is described from West Africa. A key to the species is provided and the poorly known behaviour, ecology and biogeography are discussed. The author has not witnessed oviposition; one report suggests that it may be perched, solitary and epiphytic, which is unusual within the family. The species are largely restricted to streams above 1000 m, except A. luxata sp. n. that is only known below that altitude, but always at the foot of highlands. Four species demonstrate a distribution pattern recalling a 'ring species' in highlands, circling Lake Victoria and the dry north of Tanzania. The phylogeny suggests an expansion of the genus from the western lowlands to the eastern highlands, or vice versa, followed by an expansion through the Albertine Rift and Eastern Arc Mts to the Kenyan and ultimately Ethiopian highlands. Especially in the case of a western origin there appears to have been a tendency of the species to occur at increasing altitudes in the course of their evolution.
Oceanic islands accumulate endemic species when new colonists diverge from source populations or by in situ diversification of resident island endemics. The relative importance of dispersal versus in situ speciation in generating diversity on islands varies with a number of archipelago characteristics including island size, age, and remoteness. Here we characterize inter-island dispersal and in situ speciation in frogs endemic to the Gulf of Guinea islands. Using mitochondrial sequence and genome-wide SNP data we demonstrate that dispersal proceeded from the younger island (São Tomé) to the older island (Príncipe) indicating that for organisms that disperse overseas on rafts, dispersal between islands may be determined by ocean currents and not island age. We find that dispersal between the islands is not ongoing, resulting in genotypically distinct but phenotypically similar lineages on the two islands. Finally, we demonstrate that in situ diversification on São Tomé Island likely proceeded in allopatry due to the geographic separation of breeding sites, resulting in phenotypically distinct species. We find evidence of hybridization between the species where their ranges are sympatric and the hybrid zone coincides with a transition from agricultural land to primary forest, indicating that anthropogenic development may have facilitated secondary contact between previously allopatric species. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
The continental highlands of the Cameroon Volcanic Line (CVL) represent biological ‘sky islands’ with high levels of species richness and endemism, providing the ideal opportunity to understand how orogenesis and historical climate change influenced species diversity and distribution in these isolated African highlands. Relationships of puddle frogs (Phrynobatrachus) endemic to the CVL are reconstructed to examine the patterns and timing of puddle frog diversification. Historical distributions were reconstructed using both elevation and geography data. Puddle frogs diversified in the CVL via several dispersal and vicariance events, with most of the locally endemic species distributed across the northern part of the montane forest area in the Bamenda‐Banso Highlands (Bamboutos Mts., Mt. Lefo, Mt. Mbam, Mt. Oku and medium elevation areas connecting these mountains). Two new species, P. jimzimkusi sp. n. and P. njiomock sp. n., are also described based on molecular analyses and morphological examination. We find that these new species are most closely related to one another and P. steindachneri with the ranges of all three species overlapping at Mt. Oku. Phrynobatrachus jimzimkusi sp. n. is distributed in the southern portion of the continental CVL, P. njiomock sp. n. is endemic to Mt. Oku, and P. steindachneri is present in the northeastern part of the montane forest area. Both new species can be distinguished from all other puddle frogs by a combination of morphological characters, including their large size, ventral coloration and secondary sexual characteristics present in males. These results highlight the Bamenda‐Banso Highlands, and specifically emphasize Mt. Oku, as a centre of diversification for puddle frogs, supporting the conservation importance of this region. Our results also provide new insights into the evolutionary processes shaping the CVL ‘sky islands’, demonstrating that lineage diversification in these montane amphibians is significantly older than expected with most species diverging from their closest relative in the Miocene. Whereas climatic changes during the Pliocene and Pleistocene shaped intraspecific diversification, most speciation events were significantly older and cannot be linked to Africa's aridification in response to Pleistocene climate fluctuations.
Torrent frogs of the genus Petropedetes Reichenow, 1874 as currently understood have a disjunct distribution with species endemic to West, Central or East Africa. We herein present a phylogenetic analysis including all but one of the currently described 12 species of the genus. Maximum Likelihood and Bayesian analyses of combined nuclear (rag1, SIA, BDNF) and mitochondrial (16S, 12S, cytb) genes of more than 3500 base pairs, revealed clades corresponding to the three sub-Saharan regions. Molecular results are confirmed by morphological differences. Surprisingly, the three geographic clades do not form a monophyletic group with respect to closely related families Pyxicephalidae and Conrauidae and therefore require taxonomic changes. We resurrect ArthroleptidesNieden, 1911 for the East African taxa. The Central African taxa remain in the genus Petropedetes. The West African members are placed in the new genus Odontobatrachus gen. nov. The phylogenetic position of the new genus remains incertae sedis as it was not assigned to any of the four families included in our analyses. Potential new species have been detected within all three major clades, pointing to a still not fully clarified diversity within African torrent frogs.
We report on a species-rich amphibian community from the Forêt Classée du Pic de Fon, southeastern Guinea. The high diversity of habitat types, ranging from Guinea savannah and Upper Guinean rainforest to montane grassland and forest is reflected by the anuran community composition. We recorded at least 33 species from the two sites investigated and estimate that 50–60 species occur within the mountain range. We discuss lesser known and taxonomically problematic species, and summarize data of the whole amphibian community. Several species might be new to science, including one, Amnirana fonensis n. sp., described in the present paper. This new species is distinct from all other West African congeners on the basis of its very rough skin. Nearly 60% of the species recorded from the Forêt Classée du Pic de Fon are endemic to the Upper Guinean rainforest zone and about half of the recorded species are endemic to the western part of this zone. This qualifies the Simandou Range as a very important biodiversity hotspot facing a number of threats, including the possibility of future open cast mining along the mountain ridge. We briefly discuss possible effects of threats on the amphibian community in particular and on the regional ecosystem in general.