Lost in the swamp: Drypetes corrugata, a threatened new species from Central Africa, and its two sister species, D. chevalieri and D. tessmanniana (Putranjivaceae)

The emergence of more refined chronologies for climate change and archaeology in prehistoric Africa, and for the evolution of human mitochondrial DNA (mtDNA), now make it feasible to test more sophisticated models of early modern human dispersals suggested by mtDNA distributions. Here we have generated 42 novel whole-mtDNA genomes belonging to haplogroup L0, the most divergent clade in the maternal line of descent, and analysed them alongside the growing database of African lineages belonging to L0’s sister clade, L1’6. We propose that the last common ancestor of modern human mtDNAs (carried by “mitochondrial Eve”) possibly arose in central Africa ~180 ka, at a time of low population size. By ~130 ka two distinct groups of anatomically modern humans co-existed in Africa: broadly, the ancestors of many modern-day Khoe and San populations in the south and a second central/eastern African group that includes the ancestors of most extant worldwide populations. Early modern human dispersals correlate with climate changes, particularly the tropical African “megadroughts” of MIS 5 (marine isotope stage 5, 135–75 ka) which paradoxically may have facilitated expansions in central and eastern Africa, ultimately triggering the dispersal out of Africa of people carrying haplogroup L3 ~60 ka. Two south to east migrations are discernible within haplogroup LO. One, between 120 and 75 ka, represents the first unambiguous long-range modern human dispersal detected by mtDNA and might have allowed the dispersal of several markers of modernity. A second one, within the last 20 ka signalled by L0d, may have been responsible for the spread of southern click-consonant languages to eastern Africa, contrary to the view that these eastern examples constitute relicts of an ancient, much wider distribution.

Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter- and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome-wide single-nucleotide polymorphism data, we demonstrated that species-level divergence coincides temporally and geographically with a period of large-scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.

La présente thèse s’intéresse aux moteurs de la régénération des forêts denses humides tropicales d’Afrique, plus particulièrement au rôle joué par la banque de graines du sol dans cette régénération. Plus spécifiquement, l’étude vise à : évaluer l’abondance et la composition floristique de la banque de graines du sol de deux types de forêt reposant sur des sols différents ; quantifier l’abondance de la banque de graines du sol d’une essence commerciale importante, le tali (Erythrophleum suaveolens) et étudier les facteurs intervenant dans la levée de dormance de ses graines ; évaluer la capacité du système d’imagerie hyperspectrale proche infrarouge à discriminer des graines de deux espèces sœurs, E. suaveolens et E. ivorense. Les résultats montrent que la densité et la composition floristique de la banque de graines du sol varient significativement selon les types de forêt et de sol. Les taxons pionniers sont largement majoritaires dans les deux cas, mais sont mieux représentés dans la banque du sol de la forêt à Celtis (vieille forêt secondaire) que dans le sol de la forêt à Manilkara (forêt mature). Tous taxons confondus, la similarité floristique entre la banque de graines du sol et la végétation environnante est relativement faible quel que soit le type forestier. Cependant, cette similarité s’avère nettement plus importante en ne considérant que les taxons pionniers. Seulement trois espèces de bois d’œuvre ont été observées dans la banque du sol : Nauclea diderrichii, Staudtia kamerunensis et Erythrophleum suaveolens. E. suaveolens, le tali, est une des espèces les plus exploitées d’Afrique centrale. L’évaluation de l’abondance des graines de l’espèce au sein des deux types de forêt révèle une densité plus élevée en forêt à Celtis qu’en forêt à Manilkara, où les graines sont quasi inexistantes bien que les densités d’arbres en âge de reproduction ainsi que les structures diamétriques, soient similaires entre sites. Différentes hypothèses ont été émises pour expliquer ce résultat, la plus probable étant liée à la structure de végétation différente entre les sites. Les canopées des individus vivant dans la forêt à Manilkara seraient davantage dominées et fructifieraient moins fréquemment que dans la forêt à Celtis. La longévité des graines étudiées par spectroscopie de masse par accélérateur révèle que ces semences de tali, viables et enfouies dans le sol, seraient âgées d’environ dix ans. Le système d’imagerie hyperspectrale proche infrarouge s’est avéré efficace dans la distinction des graines d’E. suaveolens et E. ivorense, ce qui ouvre d’intéressantes perspectives quant à l’utilisation de cette technique pour étudier la banque de graines du sol.

The genus Haumania (Marantaceae) consists of three described species of perennial climbers endemic to the tropical lowland rainforest in Central Africa. To unravel their phylogenetic relationship to each other, we used variation among DNA sequences of two nuclear ribosomal (nr) and four plastid (p) markers in five to seven accessions per species sampled across their respective distribution range. Maximum parsimony and Bayesian analyses were applied. All datasets and analyses corroborated the monophyly of the genus. Within the genus, individuals of the species H. danckelmaniana and H. leonardiana were each monophyletic. Individuals of H. liebrechtsiana, however, were paraphyletic. They clustered into two distinct geographic clades (Gabon and Democratic Republic of Congo), with the Gabonese clade being most closely related to the individuals of H. danckelmaniana. The latter might be due to introgression in areas of distributional overlap between these two species, as shown in earlier phylogeographic studies. A recent hybridisation event between H. danckelmaniana and H. liebrechtsiana is documented here in a single individual by incongruence in the nr and p dataset. Overall, the study provides support for H. leonardiana being sister to all other species of this genus. To confirm the absence of hybridisation in H. leonardiana further sampling is proposed in the respective areas of distributional overlap with its sister species.

Mycobacterium ulcerans (MU), the causative agent of Buruli ulcer, is present in a wide spectrum of environments, including terrestrial and aquatic ecosystems in tropical regions. The most promising studies on the epidemiological risk of this disease suggest that some ecological settings may favor infection of animals with MU including human. A species' needs and impacts on resources and the environment, i.e., its ecological niche, may influence its susceptibility to be infected by this microbial form. For example, some Naucoridae may dive in fresh waters to prey upon infected animals and thus may get infected with MU. However, these studies have rarely considered that inference on the ecological settings favoring infection and transmission may be confounded because host carrier sister species have similar ecological niches, and potentially the same host-microbe interactions. Hence, a relationship between the ecological niche of Naucoridae and its infection with MU may be due to a symbiotic relationship between the host and the pathogen, rather than its ecological niche. To account for this confounding effect, we investigated the relationships between surrogates of the ecological niche of water bug species and their susceptibility to MU, by performing phylogenetic comparative analyses on a large dataset of 11 families of water bugs collected in 10 different sites across Cameroon, central Africa. Our results indicate that MU circulates and infects a couple of host taxa, i.e., Belostomatidae, Naucoridae, living both in the aquatic vegetation and as predators inside the trophic network and sister species of water bugs have indeed similar host-microbe interactions with MU.

Dental eruption provides markers of growth and is one component of a chimpanzee's physical development. Dental markers help characterize transitions between life stages, e.g., infant to juvenile. Most of what we know about the timing of development in chimpanzees derives from Pan troglodytes. Much less is known about the sister species, Pan paniscus, with few in captivity and a restricted wild range in central Africa. Here we report on the dental eruption timing for female captive P. paniscus (n = 5) from the Milwaukee and San Diego Zoos whose ages are known and range from birth to age 8.54 years. Some observations were recorded in zoo records on the gingiva during life; others were made at death on the gingiva and on the skeleton. At birth, P. paniscus infants have no teeth emerged. By 0.83 years, all but the deciduous second molars (dm(2) ) (when both upper and lower dentitions are referenced collectively, no super or subscript notation is used) and canines (dc) are emerged. For permanent teeth, results show a sequence polymorphism for an early P4 eruption, not previously described for P. paniscus. Comparisons between P. paniscus and P. troglodytes document absolute timing differences of emergence in upper second incisors (I(2) ), and upper and lower canines (C) and third molars (M3). The genus Pan encompasses variability in growth not previously recognized. These preliminary data suggest that physical growth in captive P. paniscus may be accelerated, a general pattern found in captive P. troglodytes.

The family Hexathelidae ranks among the smaller mygalomorph spider families. Most species are endemic to the Australasian region and the family was traditionally considered an example of a Gondwanan lineage. However, recent studies have cast some doubt on the monophyly of the family. Macrothele is the only genus with an out-of-Gondwana distribution. The bulk of the Macrothele diversity is found in South-east Asia, few species are known from central Africa and two species inhabit Europe: Macrothele calpeiana (Walckenaer, 1805) from the Iberian Peninsula and Macrothele cretica Kulczynski, 1903 endemic to Crete. Here we investigate the origins of the European Macrothele species by means of a multi-locus phylogenetic approach and by inferring the time frame of the diversification of the genus using Bayesian relaxed clock methods. We also provide further insights into the phylogenetic status of the family Hexathelidae. Our results indicate that the diversification of Macrothele traces back to the period of the Gondwana break-up and its present-day distribution most likely reflects the subsequent tectonic plate movements. The two European species were not recovered as sister taxa, suggesting that Macrothele colonised the Mediterranean region twice independently. The polyphyly of the family Hexathelidae is further confirmed and the subfamily Atracinae is identified as the conflicting lineage.

AimThis study aims to reconstruct the evolutionary history of the Crocidura poensis species complex and to identify factors driving diversification within it. We tested whether: (a) there is a pattern of allopatric differentiation coincident with the location of hypothesized Pleistocene forest refugia, (b) sister taxa are separated by broad rivers, (c) sister taxa occupy adjacent but distinct habitat.LocationSub‐Saharan African forests and adjacent savanna.TaxonShrews.MethodsAnalyses were based on 247 specimens collected from across the distribution of the species complex. We reconstructed the phylogeny (Bayesian and maximum likelihood methods) and assessed historical biogeography of this taxonomic group using a combination of mitochondrial and nuclear markers. We mapped the genetic diversity and estimated the divergence times by a relaxed clock model. Informed by multilocus species delimitation methods, we discussed possible taxonomic implications.ResultsThis complex is composed of nine major genetic lineages (proposed species). The earliest split within this complex occurred after 2.0–2.4 Ma, which corresponds to a period of increased aridity and/or extreme environmental variability. Most other divergence events occurred after the Early‐Middle Pleistocene Transition (1.2–0.8 Ma). Divergent selection across ecological gradients could explain diversification within the West African lineage. In Central Africa, the observed phylogeographic pattern fits the Pleistocene refuge hypothesis and supports the existence of multiple small rather than a few large forest refugia during glacial maxima. Large rivers, like the Congo and Sanaga Rivers, are important barriers to gene flow for several lineages but probably were not the primary cause of differentiation.Main conclusionsBoth geographic isolation in distinct forest refugia and divergent selection along ecological gradients could explain Pleistocene diversification within this complex.

Rice yellow mottle virus (RYMV) of the genus Sobemovirus is the main virus infecting rice (Oryza sativa) in Africa. First reported in Kenya (East Africa), RYMV was later found in most countries of East and West Africa where rice is grown, and in Madagascar in the Indian Ocean. In Central Africa however, the disease had never been reported in rice fields. Ninety-eight field samples with typical yellow mottle symptoms from cultivated rice and two wild rice species (Oryza longistaminata and O. barthii) were collected in the Soudano-Sahelian zones, in the north of Cameroon and the south of Chad (Central Africa) in September 2000. RYMV was detected by ELISA with polyclonal antisera (1) in all samples. All virus isolates were also mechanically transmitted to rice cv. BG 90-2, which is highly susceptible to RYMV. Tests with monoclonal antibodies showed that most isolates from Central Africa were of the SI serotype, which is widespread in the Soudano-Sahelian zones of West Africa (1). The coat protein gene of 7 isolates was amplified by RT-PCR and the expected 720 bp fragment was obtained. Resulting sequences (AJ306735, AJ317949, AJ317950, AJ317951, AJ317952, AJ317953, AJ317954) shared over 95% sequence identity. They were compared to a set of sequences of RYMV isolates from cultivated rice of different geographical origins (2). Phylogenetic analyses by maximum parsimony (PAUP 4) showed that isolates from Central Africa belonged to a monophyletic group, a sister group of West African isolates from the Soudano-Sahelian zones, further supporting the geographic basis of RYMV diversity (2). RYMV incidence was generally less than 10% but reached 20% in some irrigated plots in the two countries.

Taxonomic recommendations for British birds: second report

Out-of-Africa again: A phylogenetic hypothesis of the genus Charaxes (Lepidoptera: Nymphalidae) based on five gene regions

Only five species of the genus Tetraconcha Karsch, 1890 have been previously known; they inhabit tropical forests of central and western Africa. Generally, specimens belonging to this genus are scarcely represented in museum collections, probably due to the difficulty in finding them, but also for the fragility of their body and legs. During some recent expeditions in the Central African Republic and Ivory Coast it was possible to put together an abundant amount of specimens. This allowed the present author to revise the genus and to find valid characters to distinguish different species. On the whole, ten new species were discovered and the total number now amounts to fifteen species. Interestingly, in the Dzanga-N’Doki National Park (Central African Republic) seven sister species, previously unknown, live together with T. smaragdina; it was possible to separate them by the shape and number of teeth of the stridulatory file under the left tegmen, and later other taxonomical characters were provided. This may be considered a case of evolutionary radiation; that is, Tetraconcha species in the Dzanga-N’Doki National Park evolved traits that primarily linked to sound communication. This radiation very probably occurred randomly, possibly driven by genetic drift.

Squirrel reservoirs of monkeypox virus are sister species separated by the Sanaga River (Cameroon), as are the two main viral clades.

A molecular phylogeny of Equatorial African Lacertidae, with the description of a new genus and species from eastern Democratic Republic of the Congo

Aim African freshwater fishes serve as important biogeographical indicators of geomorphological and hydrological history across the continent. However, research focusing on the phylogeny, biogeography and diversification of African fishes, particularly in central Africa, is relatively scarce. Here, we evaluate three geological hypotheses regarding the formation of the contemporary Congo basin: (1) the dominance of the Ogooué and Kouilou rivers along the western continental margin during the Cretaceous, (2) an eastward‐flowing Congo‐Zambezian system forming the Rufiji Delta during the Paleogene and (3) river basin capture resulting in the formation of the Lower Congo River during the Pliocene. To do this, we reconstructed the phylogeny of featherfin tetras of the genus Bryconaethiops using their mitochondrial genomes, estimated diversification chronology, and detected biogeographic transitions in Central Africa. Location Afrotropical rivers of Nilo‐Sudan, Lower Guinea, Congo and Malagarasi‐Tanganyika. Time Period Oligocene, Neogene and Quaternary. Taxon Bryconaethiops (Teleostei: Characiformes: Alestidae). Methods Analysis of a molecular matrix of complete mitochondrial genomes comprising 13 protein‐coding genes totaling 14,869 bp for 36 Bryconaethiops and related alestid taxa. Phylogenetic analyses included maximum likelihood, Bayesian fossil calibration, and parametric biogeographic reconstructions. Support for generic monophyly was evaluated using internal and external anatomy with microcomputed tomography (μCT) and conventional morphometric/meristic analyses. Data from museum specimens provided updated distributional ranges for each Bryconaethiops species. Results Time‐calibrated phylogenetic and biogeographic analyses suggest initial diversification of Bryconaethiops occurred in Lower Guinea during the Oligocene ( ca. 25 Ma), followed by transitions to the Nilo‐Sudan and Middle Congo regions during the Early Miocene ( ca. 19–17 Ma). Three distinct Pleistocene dispersal events to the Lower Congo ( ca. 0.7–0.05 Ma) and three to the Upper Congo and Malagarasi of Tanganyika ( ca. 1.5–0.1 Ma) were detected. Morphological analysis reveals four generic synapomorphies associated with modification of the upper and lower jaws, dentition and elongation of dorsal‐fin lepidotrichia, in addition to evidence for revalidation of B. mocquardianus (Thominot, 1886) from Atlantic coastal rivers of the eastern Gulf of Guinea. Main Conclusions Genetic and biogeographical analysis of Bryconaethiops supports the hypothesis that an expansive, centrally situated lowland proto‐Congo was captured by the modern Lower Congo during the Plio‐Pleistocene. Sympatric occurrences of sister taxa point to a complex scenario of allopatric speciation followed by secondary contact and/or resource partitioning across the Congo basin.