Targeted detection of mammalian species using carrion fly‐derived DNA

DNA analysis from carrion flies (iDNA analysis) has recently been promoted as a powerful tool for cost‐ and time‐efficient monitoring of wildlife. While originally applied to identify any mammalian species present in an area, it should also allow for targeted detection of species and individuals. Using carrion flies captured in the Taï National Park, Côte d'Ivoire, we assessed this possibility by (i) screening carrion fly DNA extracts with nonspecific and species‐specific PCR systems, respectively, targeting mitochondrial DNA (mtDNA) fragments of any mammal or of Jentink's duiker (Cephalophus jentinki), three colobine monkeys (subfamily Colobinae) and sooty mangabey (Cercocebus atys); and (ii) genotyping carrion fly extracts containing sooty mangabey mtDNA. In comparison with the nonspecific PCR assay, the use of specific PCRs increased the frequency of detection of target species up to threefold. Detection rates partially reflected relative abundances of target species in the area. Amplification of seven microsatellite loci from carrion flies positive for sooty mangabey mtDNA yielded an average PCR success of 46%, showing that the identification of individuals is, to some extent, possible. Regression analysis of microsatellite PCR success and mtDNA concentration revealed that, among all carrion flies analysed for this study, 1% contained amounts of mammal mtDNA sufficient to attempt genotyping with potentially high success. We conclude that carrion fly‐derived DNA analysis represents a promising tool for targeted monitoring of mammals in their natural habitat.     

Tropical rainforest flies carrying pathogens form stable associations with social nonhuman primates

Living in groups provides benefits but also incurs costs such as attracting disease vectors. For example, synanthropic flies associate with human settlements, and higher fly densities increase pathogen transmission. We investigated whether such associations also exist in highly mobile nonhuman primate (NHP) Groups. We studied flies in a group of wild sooty mangabeys (Cercocebus atys atys) and three communities of wild chimpanzees (Pan troglodytes verus) in Taï National Park, Côte d'Ivoire. We observed markedly higher fly densities within both mangabey and chimpanzee groups. Using a mark–recapture experiment, we showed that flies stayed with the sooty mangabey group for up to 12 days and for up to 1.3 km. We also tested mangabey‐associated flies for pathogens infecting mangabeys in this ecosystem, Bacillus cereus biovar anthracis (Bcbva), causing sylvatic anthrax, and Treponema pallidum pertenue, causing yaws. Flies contained treponemal (6/103) and Bcbva (7/103) DNA. We cultured Bcbva from all PCR‐positive flies, confirming bacterial viability and suggesting that this bacterium might be transmitted and disseminated by flies. Whole genome sequences of Bcbva isolates revealed a diversity of Bcbva, probably derived from several sources. We conclude that flies actively track mangabeys and carry infectious bacterial pathogens; these associations represent an understudied cost of sociality and potentially expose many social animals to a diversity of pathogens.     

Short‐term changes in the structure of termite assemblages associated with slash‐and‐burn agriculture in Côte d'Ivoire

Termites are major decomposers in tropical regions and play critical roles in many soil‐related processes. Studies conducted in Asia and the Neotropics suggest that habitat modification can strongly affect termite assemblages, but data on termite communities from forests in Africa, especially West Africa, are scarce. Here, we measured the short‐term impact of slash‐and‐burn agriculture on termite assemblages in an agricultural region of central Côte d'Ivoire. We assessed termite diversity and relative abundance in four habitat types: secondary forest, cleared forest, burned forest, and crop fields. The secondary forest had higher species richness compared with the other habitats, but all habitat types had similar assemblage structures. Fungus‐growing termites were the most abundant feeding group in all habitats. Soil feeders were most abundant in secondary forest, intermediately abundant in cleared and burned forests, and almost entirely absent in crop fields. Wood‐feeding species showed clear responses to burning; their abundances decreased after fire. We conclude that slash‐and‐burn agriculture does not appear to severely erode the diversity of termite assemblages. This could be due to the dominance of ecologically versatile fungus growers or to the relatively long time between clearing and burning. However, forest clearing negatively affects soil feeders, with the Apicotermitinae most affected by canopy loss.     

BOOK REVIEWS

Book reviewed in this Article: Wielgorskaya, Tatiana. 1995. Dictionary of generic names of Seed Plants . Pignatti, Sandro (ed.) 1995. Ecologia vegetale . Kreutz, C.A.J. 1995. Orobanche. Die Sommerwurzarten Europas / The European broomrape species. Ein Bestimmungsbuch / A field guide . Lindacher, Robert et al. 1995. PHANART. Datenbank der Gefässpflanzen Mitteleuropas. Erklärung der Kennzahlen, Aufbau und Inhalt . Stevens, Peter F. 1994. The Development of Biological Systematics: Antoine-Laurent de Jussieu, Nature and the Natural System . Sukopp, H., Numata, M. & Huber, A. (eds.) 1995. Urban ecology as the basis of urban planning . Miehe, Sabine & Georg. 1994. Ericaceous Forests and Heathlands in the Bale Mountains of South Ethiopia. Ecology and Man's Impact . Anhuf, Dieter. 1994. Zeitlicher Vegetations- und Klimawandel in Côte d'Ivoire . Wohlfarth-Bottermann, Martin. 1994. Anthropogene Veränderungen der Vegetationsbedeckung in Côte d'Ivoire seit der Kolonialisierung .     

The Spread of African Cassava Mosaic Virus into and within Cassava Fields

Only a small proportion of Bemisia tabaci collected in totally infected cassava fields at a site in Côte d'lvoire transmitted African cassava mosaic virus (ACMV) to test plants. Nevertheless, the monthly increase in disease incidence in an experimental planting was directly related to numbers of adult whiteflies counted on plants 6 weeks earlier. In plots at different spacings, the greatest incidence of ACMV expressed as a percentage of the total stand occurred at the lowest plant density. Much speread into the spacing trial and into two other experimental plantings occurred from outside sources and followed downwind gradients. By contrast, spread from ACMV-infected sources within plantings was limited. It occurred in all directions but over distances of only a few metres. These contrasting patterns of spread are attributed to the differentbehavior of B. tabaci above and within the crop canopy. It is concluded that contamination of cassava fields in the coastal forest area of Côte d'Ivoire is due mainly to rapid spread from outside sources which leads to internal foci that contribute to some further, although limited, spread. These findings are discussed in relation to possible control strategies based on the release of healthy cuttings, dense planting and subsequent roguing. Such measures are unlikely to be effectve in the coastal forest region of Côte d'Ivoire and adjacent countriesunless varieties are grown with greater resistance to infection than those currently used.     

Detection and differentiation of the coconut lethal yellowing phytoplasma in coconut‐growing villages of Grand‐Lahou,Côte d'Ivoire

Surveys for the Côte d'Ivoire lethal yellowing (CILY) phytoplasma were conducted in eight severely CILY‐affected villages of Grand‐Lahou in 2015. Leaves, inflorescences and trunk borings were collected from coconut palms showing CILY symptoms and from symptomless trees. Total DNA was extracted from these samples and tested by nested polymerase chain reaction/RFLP and sequence analysis of the 16S rRNA, ribosomal protein (rp) and the translocation protein (secA) genes. The CILY phytoplasma was detected in 82.9% of the symptom‐bearing palms collected from all the surveyed villages and from all the plant parts. Trunk borings were recommended as the most suitable plant tissue type for sampling. Results indicate that the CILY phytoplasma may have a westward spread to other coconut‐growing areas of Grand‐Lahou. CILY phytoplasma strains infecting coconut palms in the western region of Grand‐Lahou exhibited unique single nucleotide polymorphisms on the rp sequence compared to the strains from the eastern region. Moreover, single nucleotide polymorphisms on the SecA sequence distinguished the CILY phytoplasma from the Cape St. Paul Wilt Disease phytoplasma in Ghana, and the Lethal Yellowing phytoplasma in Mozambique.     

Carrion fly‐derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well‐known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal‐specific (16S) and vertebrate‐specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax , and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.     

Composition and Intraspecific Chemical Variability of Leaf Essential Oil of Laggera pterodonta from Côte d'Ivoire

The chemical composition of 44 leaf oil samples of Laggera pterodonta (DC.) Sch.Bip. ex Oliv. (Asteraceae) from Côte d'Ivoire was investigated, using combination of chromatographic (GC‐FID) and spectroscopic (GC/MS, ¹³C‐NMR) techniques. Two oil samples chosen according to their chromatographic profiles were submitted to column chromatography and all fractions of CC were analyzed by GC‐FID, GC/MS and ¹³C‐NMR. In total, 83 components accounting for 96.5 to 99.4 % of the whole chemical composition were identified. Significant variations were observed within terpene classes: monoterpene hydrocarbons (0.4–22.7 %), oxygenated monoterpenes (32.9–54.9 %), sesquiterpene hydrocarbons (18.6–38.3 %) and oxygenated sesquiterpenes (3.5–38.4 %). Thus, the 44 compositions were subjected to hierarchical cluster analysis (HCA) and principal component analysis (PCA). Two groups were differentiated according to their composition. All the samples contained 2,5‐dimethoxy‐p‐cymene, α‐humulene and (E)‐β‐caryophyllene among the main components. Other components were present at appreciable contents and allowed differentiation of two groups: sabinene and germacrene D for Group I; 10‐epi‐γ‐eudesmol and eudesm‐7(11)‐en‐4α‐ol for Group II. All the samples collected in Eastern Côte d'Ivoire constituted Group I, while samples collected in the Central area of the country constituted Group II.     

BOOK REVIEWS

Book Reviewed in this article: Anhuf, Dieter. 1997. Satellitenbildgestützte Vegetationklassifikation der Côte d'Ivoire. Mannheimer Geographische Arbeiten 45. ix + 190 pp. ISBN Price: Anhuf, Dieter (ed.). Forschungen im französischsprachigen Ausland. Mannheimer Geographische Arbeiten 43. 179 pp. ISBN Price:     

Long‐term Changes in Fruit Phenology in a West African Lowland Tropical Rain Forest are Not Explained by Rainfall

Decreases in rainfall have been proposed to have a negative impact on tropical rain forests, and West Africa is currently experiencing a decline in rainfall at the multi‐decadal scale. Here, we present analyses of a long‐term dataset on the plant fruiting status from individuals of 44 species of the tropical rain forest of Taï National Park, Côte d'Ivoire. This study includes records of 1401 individuals collected at monthly intervals for over 12 yr, 984 of which survived throughout the entire study period. The aims of this study were to: (1) quantitate inter‐annual trends in species and forest scale fruit presence; and (2) test the importance of rainfall in explaining inter‐annual fruit presence variability. Long‐term upward trends in the expected proportion of individuals with fruits were found for the majority of species, while no significant downward trends were detected, driving a significant upward trend at the community level. Peak production months of the upward trending species were not associated with the dry or wet season. Significant rainfall correlations with the total proportion of individuals showing fruit were generally negative, with only five species showing significant positive correlations. Taken together, these results suggest that the observed inter‐annual trends and variability of fruit abundance are currently not associated with rainfall. We discuss several parsimonious and complex alternative explanations.     

Inventory and abundance of mealybug species in immature and mature cocoa farms in Côte d'Ivoire

From 2013 to 2018, surveys were conducted in counties not previously surveyed in order to determine species of mealybugs present in the cocoa orchard in Côte d'Ivoire as well as their abundance according to the age of cocoa trees. Immature and mature cocoa trees were inspected to hand‐height in 5 and 29 counties infected with Cacao swollen shoot virus (CSSV). In each cocoa farm, mealybugs were searched for on fruits, leaves, flowers, twigs and trunks. Mealybug species were identified, and colonies were counted. Five mealybug species were identified on immature cocoa trees: Ferrisia virgata, Formicococcus njalensis, Planococcus citri, Planococcus kenyae and Pseudococcus longispinus. In addition to these species, four species, Dysmicoccus brevipes, Maconellicoccus hirsutus, Phenacoccus hargreavesi and Pseudococcus jackbeardsleyi were identified on mature cocoa trees. On immature cocoa trees, Fo. Njalensis, Pl. citri and Ps. longispinus comprised were, respectively, 35%, 33% and 19% of colonies, respectively. On mature cocoa trees, Fo. Njalensis and Pl. citri comprised 63.2% and 21.0%, and others species 15.8%. Nevertheless, the abundance of mealybug species varied according to the age of cocoa trees. The preferred organs of mealybugs were pods (74.1%) followed by twigs (13.4%) and flowers (7.4%). Previously, the mealybug Paracoccus burnerae (Brain) was found on Theobroma cacao, which is the first record for this species in Côte d'Ivoire and on this host‐plant.     

Plant Species Diversity in the Southern Part of the Taï National Park (Côte d’Ivoire)

Plant species diversity is surveyed in the southern part of the Taï National Park (TNP), Côte d’Ivoire. This park is the largest remaining tract of pristine forest in the West African rainforest biodiversity hotspot. Plant assemblages and environment factors were surveyed in 39 temporary 625-m² plots within three areas. The species list was completed thanks to itinerant prospections. TWINSPAN classification and detrended correspondence analysis were applied to the 39 relevés. We recorded a total of 916 plant species, including 169 West African endemics, that rises the floristic richness of TNP in 1233 species. Most plant species recorded were Guineo-Congolian species (90.9%) among which 8% were ‘Sassandrian species’, i.e. endemics of the extreme southwest Côte d’Ivoire. Eight of these endemics were exclusive of the southern part of TNP. The forest is very species-rich, particularly in Rubiaceae, Leguminosae and Euphorbiaceae. Most of the sampled species (59.5%) were erect phanerophytes with a dbh≤10 cm. We distinguished 7 plant community types, mainly determined by geomorphology and disturbance history. Lowland forests were typical dense evergreen forests with different degrees of maturity related to historical human impact. Inselbergs and swampy depressions provide an original azonal vegetation. We conclude that the southern part of TNP contributes significantly to the regional biodiversity hotspot since it includes the last remnants of primary evergreen rainforest and contains species assemblages from both higher rainfall biomes on moist soils derived from schist parent material and lower rainfall biomes on inselberg slopes and top. As anthropogenic disturbance clearly reduces biodiversity, these last remnants should be integrally protected.     

Mosquito (Diptera: Culicidae) Larval Ecology in Rubber Plantations and Rural Villages in Dabou (Côte d'Ivoire)

In Côte d'Ivoire, rubber cultivation has more than doubled since 2010. These mass agricultural areas require a large workforce with little information on how this environment might impact risk of mosquito-borne diseases. The objective of this study was to assess the larval ecology of mosquitoes in rubber areas of Dabou, Côte d'Ivoire. From January to June 2017, an entomological survey was conducted of mature (MP) and immature (IP) rubber plantations, as well as in villages surrounded by rubber plantations (SV) and remote from rubber plantations (RV). The number and type of potential and positive breeding sites were recorded, and mosquito larval densities and diversity were estimated. Seven genera divided into 31 species including major vector such as Anopheles gambiae s.l. and Aedes aegypti were identified. A total of 1,660 waterbodies were identified with a larvae positivity rate of 63.1%. A majority of waterbodies were identified in SV (N?=?875, 53.4% positivity rate), followed by MP (N?=?422, 81.8% positivity rate), IP (N?=?194, 72.2% positivity rate) and least in RV (N?=?169, 57.4% positivity rate). The most important breeding sites for disease vectors were leaf axils in IP (N?=?108, 77.1%), latex collection cups in MP (N?=?332, 96.2%) and the containers abandoned in the SV (N?=?242, 51.8%) as well as in the RV (N?=?59, 60.8%). All these results allow us to affirm that the cultivation of rubber trees has an impact on the larval ecology by increasing the number of available sites and favoring a high larval density and diversity.

     

Field application of the polymerase chain reaction (PCR) to the detection and characterization of trypanosomes in Glossina longipalpis (Diptera: Glossinidae) in Côte d'Ivoire

The Polymerase Chain Reaction (PCR) technique was used for the identification of natural trypanosome infections in Glossina longipalpis (Diptera: Glossinidae) in Côte d'Ivoire. A total number of 139 flies were examined microscopically for the presence of trypanosomes. Out of them 50 were detected positive and were subsequently prepared for the PCR using primers specific for Trypanosoma (Nannomonas) congolense of Savannah, Riverine-Forest, Kilifi, and Tsavo types, T. (N.) simiae, T. (Duttonella) vivax and Trypanozoon. Almost 90% of the infections detected by the PCR were attributed to Nannomonas, especially T. congolense Savannah and Riverine-Forest types, with many infections in which both of these two types were present T. simiae and T. vivax were also detected in some flies. The sequence specificity of the PCR products was confirmed by hybridization with parasite-type specific DNA probes. Differences between parasitological and PCR results are discussed.     

Factors Influencing Tree Phenology in Taï National Park,Côte d'Ivoire1

Entrained phenology patterns of tropical trees are expected to be sensitive to short‐term fluctuations in typical rainfall and temperature. We examined 47 mo of data on the flowering, fruiting, and new leaf phenology for 797 trees from 38 species in the Taï National Park, Côte d'Ivoire. We determined the timing of the phenology cycles in relation to seasonal rainfall, temperature, and solar radiation. Regression analysis was used to examine how variations in rainfall and temperature influenced deviations in the peaks and troughs of phenology cycles. We also investigated whether populations that fruit during periods of community‐wide fruit scarcity were those populations with relatively long‐ or short‐fruiting duration. Flower, fruit, and leaf‐flushing phenophases all exhibited 12‐mo cycles. The broad peak in flowering began with the northward zenithal passing in April and ended with the southward zenithal passing in September. Fruiting peaks occurred in the long dry season, and leaf flushing peaked in the long dry season but continued into the wet season. Deviations from phenology cycles were largely attributable to short‐term fluctuations in rainfall and/or temperature. Fruiting durations of species were related to the mean diameter at breast height. Species with long‐ and short‐fruiting durations contributed equally to fruit abundance during periods of community‐wide fruit scarcity.     

Impact of Commercial Hunting on Monkey Populations in the Taï region,Côte d'Ivoire1

We studied the impact of hunting on monkey species in the Taï National Park and adjacent forests in Côte d'Ivoire. The average wild meat consumption per capita per year was assessed from market surveys and interviews. We determined that the amount of primate wild meat being extracted in the Taï National Park and surrounding forests was 249 t in 1999. Hunting pressure was the highest on the larger primate species such as red colobus, Procolobus badius, black and white colobus, Colobus polykomos, and the sooty mangabey, Cercocebus torquatus atys. Estimates of population densities were based on line transect surveys. The maximum annual production of each species was calculated using the Robinson and Redford model (1991) and assuming unhunted conditions. Comparing current harvest levels with the maximum sustainable yield suggests that harvest of red colobus monkeys (Procolobus badius) is sustainable, whereas current off‐take of the black and white colobus (Colobus polykomos), the sooty mangabey (Cercocebus atys), diana monkeys (Cercopithecus diana), and Campbell's monkeys (Cercopithecus campbelli) exceeds sustainability by up to three times.     

Characterization of phytoplankton assemblages in a tropical coastal environment using Kohonen self‐organizing map

This study was aimed at understanding the main abiotic environmental factors controlling the distribution patterns of abundance and composition of phytoplankton (size less than 10 μm) assemblages in the coastal waters of south‐eastern Côte d'Ivoire. Data were collected during two cruises, in January (low‐water period) and October (high‐water period) of 2014. A total of 67 species were identified and assigned to Bacillariophyceae (49%), Cyanophyceae (21%), Chlorophyceae (13%), Euglenophyceae (10%), Dinophyceae (4%) and Chrysophyceae (3%). Three biotic zones (I, IIA and IIB) were distinguishable on a Kohonen self‐organizing map after an unsupervised learning process. The diatom genera Eunotia sp., Navicula sp. and Actinoptychus senarius are significantly associated with I, IIA and IIB biotic zones, respectively. A clear seasonal cum salinity trend was apparent in phytoplankton distribution patterns. Turbidity and nitrate levels were the main abiotic factors controlling phytoplankton distribution in I, the upland tidal regions of the lagoon. In regions along the lagoon–sea continuum, phosphate and turbidity exert the most control during the low‐water season (IIA), while total dissolved solids control phytoplankton distribution during the high‐water season (IIB). These are climate‐sensitive parameters whose concentrations depend on prevailing hydroclimatic processes. Therefore, seasonality can have important consequences on phytoplankton community and inadvertently the productivity of these systems.     

A contribution to the study of the avifauna of the Bossematie Forest (Abengorou/Côte d'Ivoire). The future of Bossematie Forest: current status

Yaokokore Beibro, K.H. & Ellenberg, H. 2000. A contribution to the study of the avifauna of the Bossematie Forest (Abengorou/Côte D'Ivoire). The future of Bossematie Forest: current status. Ostrich 71 (1 & 2): 292–294.

The Bossematie forest, eastern Cdte d'Ivoire (3°35'-3°20' longitude west and 6°35'6°20' latitude north), has been heavily exploited in the past and is now being rehabilitated by the SODEFOR (Societe de Developpement des Forêts) and the GTZ (German Technical Co-operation). To estimate the potential for the rehabilitation, the bird fauna was studied during a four year period including the field work of three observers of about 24 person-months. Until now we recorded in the forest and the surroundings 337 species belonging to 203 genera and 58 families. 251 species were present within the forest borders with 133 only observed there and not outside. Five species are considered as near-threatened and four species as vulnerable. To study the ecology of forest species in more detail, an intensive analysis of the communities of different forest stages and treatments was carried out by the first author.