Transferability,development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

Biological pathways play an important role in the occurrence, development and recovery of complex diseases, such as cancers, which are multifactorial complex diseases that are generally caused by mutation of multiple genes or dysregulation of pathways. We propose a path-specific effect statistic (PSE) to detect the differential specific paths under two conditions (e.g. case VS. control groups, exposure Vs. nonexposure groups). In observational studies, the path-specific effect can be obtained by separately calculating the average causal effect of each directed edge through adjusting for the parent nodes of nodes in the specific path and multiplying them under each condition. Theoretical proofs and a series of simulations are conducted to validate the path-specific effect statistic. Applications are also performed to evaluate its practical performances. A series of simulation studies show that the Type I error rates of PSE with Permutation tests are more stable at the nominal level 0.05 and can accurately detect the differential specific paths when comparing with other methods. Specifically, the power reveals an increasing trends with the enlargement of path-specific effects and its effect differences under two conditions. Besides, the power of PSE is robust to the variation of parent or child node of the nodes on specific paths. Application to real data of Glioblastoma Multiforme (GBM), we successfully identified 14 positive specific pathways in mTOR pathway contributing to survival time of patients with GBM. All codes for automatic searching specific paths linking two continuous variables and adjusting set as well as PSE statistic can be found in supplementary materials.  The proposed PSE statistic can accurately detect the differential specific pathways contributing to complex disease and thus potentially provides new insights and ways to unlock the black box of disease mechanisms.     

Impacts of harvesting intensity on tree taxonomic diversity,structural diversity,population structure,and stability in a West African mangrove forest

Wetlands Ecology and Management - Understanding the impacts of wood harvesting intensity on the diversity and structure of ecosystems such as mangroves is essential for defining actions for their...     

Plants in traditional home gardens: richness,composition, conservation and implications for native biodiversity in Benin

Home gardens have received increasing attention and have been insistently presented as hotspots for agro-biodiversity over the last decades. However, apart from their exceptional high plant species diversity, there is little quantitative evidence of the effectiveness of plant species conservation in home gardens. This study examined this issue by assessing (i) the size and membership of garden flora and the contribution to the maintenance of the national flora, (ii) how home garden flora connects to the larger ecosystem it belongs to and (iii) the conservation status of plant species at the home garden level. 360 home gardens distributed in three agro-ecological zones and nine phyto-geographical districts in Benin were visited and inventoried. Diversity parameters at different taxonomic levels were calculated. Species accumulation and spatial occupancy, multivariate methods and rarity index were also used for data analysis. Findings showed that the 360 studied home gardens hosted up to 14.21% of plant species and 44.32% of plant families of the national flora. Home garden flora was constantly dominated by exotic plant species but strongly connected to their surrounding ecosystems, being composed of at least 60% of plant species from their phyto-geographical districts. Finally, home garden plant species were mostly rare and threatened at the home garden level. In this study, we acknowledge the contribution of home gardens to the maintenance of plant species diversity at regional and global levels than local level. Based on the observed prevalence of exotic species, HG effectiveness in sustainably conserving native plant species biodiversity remains questionable.     

Species richness,cultural importance,and prioritization of wild spices for conservation in the Sudano-Guinean zone of Benin (West Africa)

Background

Spices have always been used for their flavor-enhancement characteristics and for their medicinal properties. In Benin, scientific research on spices is scarce, despite their importance in the local population’s daily needs. This study investigated the diversity of wild spices and documented the associated traditional knowledge that can be used for their valuation, domestication, and sustainable management in the Sudano-Guinean Zone of Benin.

Methods

Data were collected during field expeditions using semi-structured interviews in ten localities across the three phytodistricts of the zone. Species richness and Shannon’s diversity index were estimated using species accumulation curves. Use report (UR), cultural importance, use value (UV) index, and informant consensus factor (F_ic) were used to assess traditional knowledge on wild species, their local importance, and informants’ agreement among sociolinguistic groups. Priority wild spices were finally identified using an approach combining eight criteria (native status, economic value, ethnobotanical value, global distribution, national distribution, in-situ and ex-situ conservation status, legislation, and threats assessment) in four prioritization methods (point scoring procedure, point scoring procedure with weighting, compound ranking system, and binomial ranking system).

Results

A total of 14 species, belonging to 12 genera and 9 families, were inventoried. The most prominent families were Zingiberaceae (21.43%), Annonaceae (21.43%), and Rutaceae (14.29%). More than 200 specific uses were reported, with the Tchabè people holding the greatest level of knowledge (70 uses; UR?=?5.70?±?0.33). The culturally most important spices differed among sociolinguistic groups. Most of the informants agree on the use of the species among (F_ic = 0.72–0.98) and across the considered use categories (F_ic = 0.88–0.99). The highest UV were registered for Aframomum alboviolaceum (UV?=?0.93), Lippia multiflora (UV?=?0.76), and Aframomum angustifolium (UV?=?0.18). Overall, people perceived wild spices as declining due to agriculture, grazing, and drought. Five species, A. alboviolaceum, L. multiflora, Monodora tenuifolia, Xylopia aethiopica, and Z. zanthoxyloides, were the most prioritized for conservation.

Conclusions

This study provides information relevant for the implementation of conservation and domestication actions of wild spices in Benin. Priority species could be integrated into traditional agroforestry systems (e.g., home gardens). However, for this to be effective, further research should be undertaken on morphological and genetic diversity and propagation methods of priority wild spices.

     

Functional diversity of home gardens and their agrobiodiversity conservation benefits in Benin,West Africa

Background

Understanding the functional diversity of home gardens and their socio-ecological determinants is essential for mainstreaming these agroforestry practices into agrobiodiversity conservation strategies. This paper analyzed functional diversity of home gardens, identified the socio-ecological drivers of functions assigned to them, and assessed the agrobiodiversity benefits of home gardens functions.

Methods

Using data on occurring species in home garden (HG) and functions assigned to each species by the gardeners, the study combined clustering and discriminant canonical analyses to explore the functional diversity of 360 home gardens in Benin, West Africa. Next, multinomial logistic models and chi-square tests were used to analyze the effect of socio-demographic characteristics of gardeners (age, gender, and education level), agro-ecological zones (humid, sub-humid, and semi-arid), and management regime (single and multiple managers) on the possession of a functional type of home gardens. Generalized linear models were used to assess the effect of the functions of home gardens and the determinant factor on their potential in conserving agrobiodiversity.

Results

Seven functional groups of home gardens, four with specific functions (food, medicinal, or both food and medicinal) and three with multiple functions (more than two main functions), were found. Women owned most of home gardens with primarily food plant production purpose while men owned most of home gardens with primarily medicinal plant production purposes. Finding also showed that multifunctional home gardens had higher plant species diversity. Specifically, crops and crop wild relatives occurred mainly in home gardens with food function while wild plant species were mostly found in home gardens with mainly medicinal function.

Conclusions

Home gardening is driven by functions beyond food production. These functions are mostly related to direct and extractive values of home gardens. Functions of home gardens were gendered, with women mostly involved in home food gardens, and contribute to maintenance of crops and crop wild relatives while men were mostly home medicinal gardeners and contribute to the maintenance of wild plant species in home gardens. Although multiple functional home gardens were related to higher plant diversity, there was no guarantee for long-term maintenance of plant species in home gardens.

     

Persistence in fluctuating environments

Understanding under what conditions interacting populations, whether they be plants, animals, or viral particles, coexist is a question of theoretical and practical importance in population biology. Both biotic interactions and environmental fluctuations are key factors that can facilitate or disrupt coexistence. To better understand this interplay between these deterministic and stochastic forces, we develop a mathematical theory extending the nonlinear theory of permanence for deterministic systems to stochastic difference and differential equations. Our condition for coexistence requires that there is a fixed set of weights associated with the interacting populations and this weighted combination of populations’ invasion rates is positive for any (ergodic) stationary distribution associated with a subcollection of populations. Here, an invasion rate corresponds to an average per-capita growth rate along a stationary distribution. When this condition holds and there is sufficient noise in the system, we show that the populations approach a unique positive stationary distribution. Moreover, we show that our coexistence criterion is robust to small perturbations of the model functions. Using this theory, we illustrate that (i) environmental noise enhances or inhibits coexistence in communities with rock-paper-scissor dynamics depending on correlations between interspecific demographic rates, (ii) stochastic variation in mortality rates has no effect on the coexistence criteria for discrete-time Lotka–Volterra communities, and (iii) random forcing can promote genetic diversity in the presence of exploitative interactions.

One day is fine, the next is black.—The Clash