Edem A. Eniang

A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using (*)BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for >10Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas.

Food Habits of the Snake Psammophis phillipsi from the Continuous Rain-Forest Region of Southern Nigeria (West Africa)

Abstract The food habits of the snake Psammophis phillipsi were studied in the rain-forest region of southeastern Nigeria, where this is the most common snake species of the area. A total of 120 prey items were recorded from 327 specimens (73 juveniles; 55 gravid females); many gravid females contained prey. Lizards (mainly Agama agama and Mabuya skinks) were the most common prey type for adult snakes, both gravid and nongravid, and for subadults as well; small mammals were the second most common prey type for all snake categories. Insects and small snakes (including conspecifics) were occasionally consumed. Diet composition did not differ significantly between gravid and nongravid specimens, but gravid specimens more frequently contained small mammals and fewer lizards. Ontogenetic dietary change was relatively minor. Prey and predator mass were significantly related in both adults and subadults.

Non-random structure of a guild of geckos in a fragmented, human-altered, African rainforest

We examined the guild structure of geckos at a farmbush–rainforest mosaic area in southern Nigeria, during three independent survey periods (i.e. dry season of 1997, 2001, and 2005). We used several simulation descriptors (C value, V ratio, number of checkerboard species pairs, number of species combinations), generated by Monte Carlo methods, to contrast the actual data matrix with the randomly generated data matrix. We calculated the relative availability and use by species of habitat types and microhabitat types at each of these survey periods and also studied temporal niche aspects. We found that our gecko guild was composed of six species, including native forest specialists as well as native habitat generalists and exotic species linked to human-made habitats. Monte Carlo simulations revealed the occurrence of a structure in the guild under study with regard to habitat type but not with regard to (a) two types of microhabitat uses (i.e. perch height and size of trees) and (b) daily time. The use of simulation analyses also demonstrated that the various species that were similar in terms of habitat use partitioned their microhabitat niche, reducing potential interspecific competition. On the other hand, those species that were clearly separated with regard to habitat type readily frequented the same microhabitats within different habitat types.

Correlation between annual activity patterns of venomous snakes and rural people in the Niger Delta, southern Nigeria

BackgroundVenomous snakes are among the most serious health hazards for rural people in tropical regions of the world. Herein we compare the monthly activity patterns of eight venomous snake species (Elapidae and Viperidae) with those of rural people in the Niger Delta area of southern Nigeria, in order to identify the periods of highest potential risk for persons, and the human group actually at greater risk of snakebite.ResultsWe documented that above-ground activity of all venomous snakes peaked in the wet season, and that high snake activity and high human activity were most highly correlated between April and August. In addition, we documented that women and teenagers were at relatively higher risk of encountering a venomous snake than adult males, despite they are less often in the field than men.ConclusionsOur results suggest that future programs devoted to mitigate the social and health effects of snakebites in the Niger Delta region should involve especially women and teenagers, with ad-hoc education projects if appropriate. We urge that international organizations working on social and health problems in the developing world, such as IRD, DFID, UNDP, should provide advice through specific programs targeted at especially these categories which have been highlighted in comparatively potential higher threat from snakebites than adult men.

Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae)

The savannah and tropical forest biomes of Africa have a long history of expansion and contraction, and the recent and rapid spread of dry savannah habitats has influenced the spatial and temporal diversification of vertebrate taxa across this region. We used a combination of species tree and phylogeographic methods to describe the spatio-temporal changes through time and across space (= species diffusion) in a clade of seven West African lizard species in the Agama agama species group. A Bayesian species tree diffusion approach was used to compare the relative rates at which species ranges changed across the landscape. We found that some species have high diffusion rates characterized by significant movement in their range location and minor changes to their overall range size, whereas other species show little movement in their range centre with an exponential increase in range size. This discrepancy between the rates that range locations shift versus change in their relative area could be linked to populations tracking their preferred habitats through time. A continuous Bayesian phylogeography approach using a relaxed random walk model was used to estimate the timing and rate of population size change and geographic diffusion in A. picticauda, the single species in the group with an extensive African distribution from Mauritania to Ethiopia. The mean dispersal rate of A. picticauda increased dramatically throughout the Pleistocene, and a Bayesian skyride analysis supports exponential population growth over this same time period. A comparison of genetic diversity across different loci and species suggests that A. lebretoni experienced a mitochondrial selective sweep that has caused a deficit of variation at this locus in relation to nuclear loci.

Are mammal communities occurring at a regional scale reliably represented in “hub” bushmeat markets? A case study with Bayelsa State (Niger Delta, Nigeria)

Abstract. Monitoring of bushmeat markets has traditionally been seen as a source of faunistic and ecological data on mammal communities in West Africa. Nonetheless, it is largely unexplored whether datasets coming from monitoring of large “hub” markets in towns can reliably picture the mammal faunas and community compositions at the local level. Here, Swali market in Bayelsa State, Nigeria, that is one of the largest bushmeat markets in the Niger Delta, was monitored for six months in 2013–2014. Data from Swali market were compared with those collected during regular field surveys at five protected forests situated within 15 km radius from the market. A total of 21 mammal species was recorded at Swali versus 29 in the five protected forests. The trade was more intense by wet season. There was a statistically significant linear relationship between mean weight of the sold mammal and its price. A considerable portion of species that occur at the protected forests did not occur in the market samples, including the very rare species and the smallsized species. However, the abundance in the market of the common species was positively related to their apparent field abundance in the forest reserves. Therefore, it is concluded that large-sized bushmeat markets did not depict reliably the whole faunal composition and the community structure of mammals in West Africa, although these types of surveys are sufficient to characterize the abundance distribution of the common species at the regional scale.

Estimation of browse biomass of Ficus thonningii, an indigenous multipurpose fodder tree in northern Ethiopia

Ficus thonningii is a multipurpose browse tree in northern Ethiopia. Despite its importance, techniques for quantifying its browsable biomass have not been developed. To develop best-estimation equations, the dendrometric parameters total height (H), crown height (CH), crown diameter (CD), diameter at stump height (DSH), diameter at breast height (DBH), crown depth (CDp), crown area (CA) and crown volume (CV) were measured from 12 sampled trees comprising three age ranges. Leaves and edible twigs of the sampled trees were clipped, oven dried, weighed and recorded as dry weight (DW). Regression analysis and a multicollinearity test were employed to remove non-significant predictors of DW. Results showed that only CV, CA, CD, CDp and DSH showed a strong correlation with DW. There was high collinearity between CD and CA, CD and CV, and CA and CV. However, CV and DSH had a higher correlation with DW than their counterparts, which suggested their use in the model. Therefore, the best allometric equation was: DW = 0.8470*CV - 0.2202*DSH - 1.5315 (R 2 = 0.99). This equation estimated that F. thonningii produces a very high amount of browsable biomass at all ages compared to common fodder species. The model can be used to plan the browsing rate and understand the ecological role of the species.

Diet of a guild of geckos in a fragmented, human-altered African rainforest : short communication

Abstract The ecology of gekkonids occurring in African forests is poorly known. In this paper, we analyse the feeding habits of a guild of sympatric geckos at a forest‐plantation mosaic area in south‐eastern Nigeria. Faeces were collected on handling from Hemidactylus brookii, H. fasciatus, H. intestinalis, H. mabouia, H. echinus, and Lygodactylus conraui. All species proved to be dietary generalists, with diets based almost entirely on arthropods. However, food niche overlap values between pairs of species were relatively low and Monte Carlo simulations (with RA2 and RA3 algorithms) showed that the overlap values between H. fasciatus and H. intestinalis were significantly higher than those observed for other pairs of species. Monte‐Carlo simulations on co‐occurrence estimators (C‐score, V‐ratio, and number of species combinations) revealed that the gecko guild was not competitively structured along the trophic niche dimension.

Surveys of mammal communities in a system of five forest reserves suggest an ongoing biotic homogenization process for the Niger Delta (Nigeria)

Community composition and an index of relative abundance were analyzed for mammals (excluding most rodents, shrews and bats) of five forest reserves in the Niger Delta (Southern Nigeria). Twenty-nine species were recorded, 86.2% of them being found in all protected areas. Although most of the species were already known from the study area, there were unexpected patterns concerning the duikers. Indeed, the presence of only one species (Philantomba walteri) (CH Smith, 1827) was confirmed, whereas at least five additional duiker species were reported for the study area by earlier authorities. Another duiker species (Cephalophus niger Gray, 1846) was recorded once during the present surveys and is not known whether it represents a stabilized presence in the Niger Delta. The empirical Abundance Index suggested that only three species were very rare (Trichechus senegalensis (Link, 1795), C. niger, and Pan troglodytes (Blumenbach, 1775)). Diversity-dominance diagrams showed that the evenness profiles were similar across study areas. Linear distance (Km) between the barycenters of forest reserves was significantly positively correlated with relative community composition dissimilarity. Overall, a biotic homogenization process for the mammal communities of the five forest reserves was observed, likely as an outcome of the high deforestation of the last 50 years.

Life in the tropical suburbs: Food type partitioning among sympatric African house snakes of the genus Lamprophis (Colubridae)

The food niche partitioning of four species of house snakes (Lamprophis fuliginosus, L. olivaceus, L. lineatus, and L. virgatus) was studied in suburban areas of south‐eastern Nigeria, West Africa. Snakes were captured in the field, and their stomach contents were obtained by forced‐squeezing of the ingested bolus. Pseudo‐community analysis and Monte Carlo simulations, by two different algorithms, were used to investigate whether the community under study was randomly assembled along the trophic niche axis. Four hundred and thirty snake individuals were captured: 52 out of 133 L. fuliginosus (32.1%), 31 of 126 (24.6%) L. lineatus, 30 of 108 (27.8%) L. virgatus, and 20 of 63 (31.7%) L. olivaceus had identifiable food contents in the stomach. Lamprophis fuliginosus appeared as the more generalist species, L. lineatus showed some preference for lizards and frogs, L. virgatus for small mammals (rodents and shrews), and L. olivaceus for nestling birds and small mammals. However, null models showed that the community organization was random along the food niche axis by both the randomization algorithms used in this paper. Thus, we concluded that these four snake species do not partition either the quality or the number of the available resources.