Influence of farm characteristics and surrounding habitat on amphibian communities in Afrotropical cocoa

In the highly populated and diverse tropics, conservation in relatively pristine habitats is important but clearly inadequate for sustaining the earth biological diversity. Agro-forestry systems such as shade-coffee plantations that incorporate arboreal vegetation are known to be more resilient for biodiversity conservation than other more drastic land transformations. We evaluated amphibian richness and diversity in 15 coffee plantations from three different regimes; organic coffee plantations, NPK coffee plantations and pesticide use coffee plantations in Kodagu District, Western Ghats, India. We treated five sacred groves as control region (CR) and sampled them using a combination of standardized visual and acoustic transect sampling. The sacred groves that were characterized by natural vegetation showed the highest richness and abundance of amphibians among the four regimes. In organic coffee plantations, overall abundance and richness of amphibians was significantly higher compared to NPK coffee plantations. On the other hand, amphibian richness and diversity in pesticide use coffee plantations were significantly lower compared to all other regimes. The results of the study clearly indicated that, the difference in habitat variables in coffee plantations and use of different treatments for pest control had a significant effect on the species richness and abundance of amphibians. This study highlights the great potential of sacred groves and organic coffee plantations as complementary habitat for the conservation of amphibians.

Forests are being converted to agriculture throughout the Afrotropics, driving declines in sensitive rainforest taxa such as understorey birds. The ongoing expansion of cocoa agriculture, a common small‐scale farming commodity, has contributed to the loss of 80% rainforest cover in some African countries. African cocoa farms may provide habitat for biodiversity, yet little is known about their suitability for vertebrate fauna, or the effect of farm management on animal communities. Here, we report the first in‐depth investigation into avian diversity and community composition in African cocoa, by assembling a dataset of 9,566 individual birds caught across 83 sites over 30 years in Southern Cameroon. We compared bird diversity in mature forest and cocoa using measures of alpha, beta and gamma diversity, and we investigated the effect of cocoa farm shade and forest cover on bird communities. Gamma diversity was higher in cocoa than forest, though alpha diversity was similar, indicating a higher dissimilarity (beta diversity) between cocoa farms. Cocoa farms differed from forest in community composition, with a distinctive decrease in relative abundance of insectivores, forest specialists and ant‐followers and an increase in frugivores. Within cocoa farms, we found that farms with high shade cover in forested landscapes resulted in higher relative abundance and richness of sensitive forest species; shady farms contained up to five times the proportion of forest specialists than sunny farms. Synthesis and applications. Sunny African cocoa farms were less able to support sensitive bird guilds compared with shaded farms in forested landscapes. Our findings support the notion that certain ecological and dietary guilds, such as ant‐followers and forest specialists are disproportionately affected by land‐use change. In light of the current push to increase cocoa production in sub‐Saharan Africa, our results provide policymakers opportunities for more wildlife‐friendly cocoa schemes that maximize avian diversity.

Habitat destruction and fragmentation have been identified as possible causes of large-scale amphibian declines. Here, we examine the effects of adjacent land use and water quality on wetland amphibian species richness, abundance, and community composition in 74 Ontario wetlands. Species richness was positively correlated with wetland area, forest cover, and the amount of wetlands on adjacent lands and negatively correlated with road density and nitrogen levels. The land-use effects peak at 2000–3000 m. Amphibian abundance was positively correlated with forest cover, distance to wetlands >20 ha, and amount of marsh habitat and negatively correlated with road density. The effects of adjacent land use were strongest at around 200 m. Land-use and water quality effects varied widely across species, although most species are positively correlated with forest cover and amount of wetlands on adjacent lands and negatively correlated with road density and water quality. These results suggest that the effects of adjacent land use on amphibian communities can extend over comparatively large distances. As such, effective wetland conservation will not be achieved merely through the creation of narrow buffer zones between wetlands and intensive land uses, but rather will require maintaining a heterogeneous regional landscape containing relatively large areas of natural forest and wetlands.

Abstract: Standardized, effective sampling methods are required to monitor amphibian population trends and community composition. Funnel traps have been used to ostensibly estimate species richness and relative abundance of larval amphibians. We tested whether funnel traps can be used to provide unbiased estimates of amphibian community composition in playa wetlands by comparing seining—dip netting and passive funnel‐trapping results. Plains spadefoots (Spea bombifrons) were more prone to be captured in funnel traps whereas New Mexico spadefoots (S. multiplicata) were less likely captured by funnel traps than by seines and dip nets. In playas funnel traps should be used only for collecting specimens and not for estimating amphibian community composition.

Natural disturbances play a critical role in structuring many ecosystems. In the southeastern United States, fire suppression and exclusion have removed the natural disturbance regime from many ecosystems, including ephemeral wetlands embedded within longleaf pine forests. We sampled aquatic invertebrate and amphibian communities in 21 pine flatwoods wetlands in northwest Florida from 2012 to 2014. Our objectives were to quantify amphibian and invertebrate community structure, identify differences in amphibian communities across an environmental gradient, and identify how invertebrate communities responded to wetland habitat characteristics. Amphibian communities were more diverse in wetlands with longer hydroperiods but were similar across wetlands with different vegetation structures. To examine the effects of wetland characteristics on aquatic invertebrate communities, we created a set of a priori models relating the abundance of isopods, chironomids, and damselflies to wetland characteristics. The best-approximating models indicated that isopods and damselflies were more abundant in wetlands that were not fire-suppressed. Similarly, total invertebrate abundance was higher in sections of wetlands with low canopy cover when compared to sections of the same wetlands with high canopy cover. Restoration of vegetation structure in wetlands that have experienced long-term fire suppression and wetlands that support longer hydroperiods should be a management priority.

The relevance of cocoa agroforestry is widely discussed in debates on sustainability transition in cocoa, especially in the context of ending hunger and poverty among cocoa farmers. Whereas this has led to multiple cocoa agroforestry investments by NGOs, governments, and cocoa and chocolate companies in West and Central Africa, a notable gap exists in the literature on how these interventions respond to the needs of cocoa farmers who are typically framed as the primary target of equity in cocoa sustainability discussions. This paper contributes to bridging this gap by analyzing equity in implementing various cocoa agroforestry projects by different actors in Ghana’s Juabeso-Bia Landscape (JBL). I find that the ongoing cocoa agroforestry initiatives may be broadly characterized as renovative or additive in terms of how they (re)shape the various components on cocoa farms. Yet, they are all designed to primarily enhance cocoa productivity even when seasonal food insecurity is one of the most pressing challenges among cocoa farmers in the JBL. The persistent neglect of food in cocoa production risks leaving poverty and hunger in cocoa households unaddressed. Additionally, it increases cocoa households' predisposition to forest conversion, making current forms of cocoa agroforestry an indirect driver of deforestation in the landscape. To transform the current situation, policymakers and scholars must reflexively integrate household food security in designing cocoa agroforestry, prioritizing farmers’ involvement in dynamic agroforestry technologies that contribute directly to local food access over time. This contrasts the current policy and practice of cocoa agroforestry, focused on maintaining a prescribed number of shade trees on new or existing cocoa farms but highly likely to engender significantly greater inequity in the cocoa sector.

Studies of the diversity and natural history of amphibians are extremely important and contribute with the knowledge about the patterns of geographical distribution and biology of the species, outlining the factors that influence this distribution, and contributing to the development of conservation projects of them. This study aimed to identify the richness, abundance, spatial and temporal distribution of amphibians in the Bauru region, state of São Paulo, Brazil, and compare the species composition with others regions in the São Paulo state located in the Cerrado and Atlantic Forest. Eight locations were sampled between the years 2009 and 2012. Thirty-seven amphibian species were recorded, which represents 15.61% of the species in the state of São Paulo. In comparison to other regions of the state, Bauru resemble with the north-western region of the state and with the Assis Ecological Station in species composition. The community of amphibians in the studied region is regulated to morphoclimatic conditions, environmental heterogeneity and the conservation of natural resources, which directly reflect on the composition, abundance and species’ spatial and temporal distribution of the amphibians in this region. The richness of amphibians of the Bauru region is significant for the state of São Paulo and contributes with the maintenance of environments with conditions for the occurrence of Proceratophrys moratoi, which is considered in threat of extinction. This study contributed with the filling gap on the amphibian knowledge of the state of São Paulo.

Effects of logging on the ecological strategy spectrum of a tropical montane rain forest

Agroforestry is part of the package of good agricultural practices (GAPs) referred to as a reference to basic environmental and operational conditions necessary for the safe, healthy, and sustainable production of cocoa. Furthermore, cocoa agroforestry is one of the most effective nature-based solutions to address global change including land degradation, nutrient depletion, climate change, biodiversity loss, food and nutrition insecurity, and rural poverty and current cocoa supply chain issues. This study was carried out in South-Western Côte d’Ivoire through a household survey to assess the willingness of cocoa farmers to adopt cocoa agroforestry, a key step towards achieving sustainability in the cocoa supply chain markedly threatened by all types of biophysical and socio-economic challenges. In total, 910 cocoa households were randomly selected and individually interviewed using a structured questionnaire. Findings revealed that from the overwhelming proportion of farmers practicing full-sun cocoa farming with little or no companion trees associated, 50.2 to 82.1% were willing to plant and to keep fewer than 20 trees per ha in their farms for more than 20 years after planting. The most preferred trees provide a range of ecosystem services, including timber and food production, as well as shade regulation. More than half of the interviewed households considered keeping in their trees in their plantations for more than 20 years subject to the existence of a formal contract to protect their rights and tree ownership. This opinion is significantly affected by age, gender, access to seedlings of companion trees and financial resources. A bold step forward towards transitioning to cocoa agroforestry and thereby agroecological intensification lies in (i) solving the issue of land tenure and tree ownership by raising awareness about the new forest code and, particularly, the understanding of cocoa agroforestry, (ii) highlighting the added value of trees in cocoa lands, and (iii) facilitating access to improved cocoa companion tree materials and incentives. Trends emerged from this six-year-old study about potential obstacles likely to impede the adoption of agroforestry by cocoa farmers meet the conclusions of several studies recently rolled out in the same region for a sustainable cocoa sector, thereby confirming that not only the relevance of this work but also its contribution to paving the way for the promotion of agroecological transition in cocoa farming.

Fire is a frequent feature of African grasslands because agriculture is often used as a management tool in conservation areas. Richness, diversity, and abundance of amphibians were compared in four areas of montane grassland subjected to different fire regimes in Nyika National Park (Malawi, southeastern Africa). The surveys were performed using drift fences and pitfall traps randomly set in four areas (12 sites) subjected to the following fire regimes: (A) no fire for at least 15 years; (B) no fire for at least 10 years; (C) no fire for at least 6 years; and (D) annually burned. We also measured the vegetation cover and vegetation height. We collected 370 amphibians from 17 species and six families during 50 days sampling period. The lowest value of abundance was found in areas C and D. The amphibian species Hyperolius marmoratus and H. nasutus were most abundant in the control area A. Arthroleptis xenodactyloides, Amietophrynus gutturalis and Am. maculatus were found in all areas. There was a strong correlation between vegetation height and species richness. Vegetation structure, which is affected by fire, appears to be a key factor impacting amphibian assemblages in montane grasslands.

Biological communities are experiencing rapid shifts of composition in Neotropical ecosystems due to several factors causing population declines. However, emerging evidence has provided insights on the adaptive potential of multiple species to respond to illnesses and environmental pressures. In Costa Rica, the decline of amphibian populations is a remarkable example of these changes. Here we provide evidence of variation in the amphibian richness of a premontane forest of San Ramón (Costa Rica) across a ~30 year period. We also quantified changes in the composition and abundance of the leaf-litter frog community occurring in the same premontane forest, by comparing diversity data with a difference of ~18 years. We evaluated the similarity of species richness from 1980s to 2010s based on several sources, and the dissimilarity of species diversity in the site comparing 28 standardized surveys from 1994-1995 and 2011-2012. We compared the relative abundance of some frogs that inhabit the leaf-litter layer between these same periods. Our results show that there is more similarity in amphibian richness between 1980s and 2010s (~ 52 %) than between 1980s and 1990s (~ 40 %). The richness of leaf-litter anurans was ~ 65 % similar between 1990s and 2010s. The diversity of leaf-litter anuran was clearly different between 1994-1995 and 2011-2012, and it was clustered among those periods. We determined that the amphibian community in this premontane forest drastically changed: many species have disappeared, or gradually declined through the decades (e.g. Pristimantis ridens, P. cruentus, Craugastor bransfordii) as in other well studied localities of Costa Rica, while some few species flourished after being almost absent from the site in the 1990s (e.g. Craugastor crassidigitus, Lithobates warszewistchii). Currently dominant species such as C. crassidigitus would be using developed resistance against Bd-fungus as an advantage (apparent competition) in the premontane forest where the disease is more virulent than in lowlands. Our analysis supports the hypothesis of individualized responses of anuran populations under distinct site and elevations. We suggest to continue monitoring the amphibian communities of premontane tropical forests to understand how this ecosystem gradually resist and adapts to this catastrophic time of biodiversity loss.

Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.

Global climate change is significantly altering the large scale distributions of plants and animals. The Earth has warmed by 0.7°C during the last century. The consequences are already apparent in forest ecosystems as species are responding to the changing climate with shifts in their phenology and geographic distributions. The potential for large increases in global mean temperatures (e.g., 4.3 ± 0.7°C) by 2100 has significant implications for forest species and ecosystems. Under these varying climatic conditions, some species may go extinct either locally or regionally, with climate change acting synergistically with other extinction drivers. Tropical Asian forests contain several biodiversity hotspots and species-rich ecoregions. Our understanding of species’ and forest ecosystems’ vulnerability to global climate change in this region is limited. Addressing this problem is a critical task for current tropical Asian ecological research.The overall aim of this PhD thesis is to investigate the current and potential effects of climate change on the geographic distribution and composition of selected plant and mammal species in tropical Asian forests. The selected plants include Sal (Shorea robusta), Garjan (Dipterocarpus turbinatus) and Teak (Tectona grandis). These all are ecologically and economically important timber trees and are distributed widely across South and Southeast Asia. The selected mammals include Asiatic black bear (Ursus thibetanus), Asian elephant (Elephas maximus), Western hoolock gibbon (Hoolock hoolock) and Bengal tiger (Panthera tigris tigris). These threatened large mammals are of high conservation concern and are typically targeted by international conventions. I present a comprehensive review of the previous literature and new predictive models of species distributions that quantify potential climate change impacts on tropical forests. My results show that projected changes in temperature and rainfall extremes are potential threats to the diverse and species-rich forest ecoregions of tropical Asia.I used bio-climatic models and two scenarios of climate change (a moderate and an extreme Representative Concentration Pathway (RCP) scenario) to assess climate change impacts on the continental scale distributions of two threatened Dipterocarp trees Sal and Garjan, and the valuable timber species, Teak. Annual precipitation was the key bioclimatic variable for explaining the current and future distributions of Sal and Garjan. Suitable habitat conditions for Sal will decline by 24% and 34% by 2070 under the RCP4.5 and RCP8.5 scenarios, respectively. In contrast, the consequences of climate change appear less severe for Garjan, with a decline of 17% and 27% under RCP4.5 and RCP8.5, respectively. Changes in annual precipitation, precipitation seasonality and annual mean actual evapotranspiration may result in shifts in the distributions of Teak across tropical Asia. These findings can contribute to conservation planning for the species and their management under future climates.I developed habitat suitability models for the four large threatened mammals (Asiatic black bear, Asian elephant, Western hoolock gibbon and Bengal tiger), across their entire distributions in Asia. The results suggest that changes in annual precipitation, annual mean temperature, precipitation and temperature seasonality, and land use/land cover change could reduce suitable habitat for these large mammals and therefore increase their extinction risks. It can be concluded that increasing climate stress on tropical forests could lead to greater extinction risks of these threatened large mammals.The findings of this thesis provide a fundamental basis for further studies of climate change impacts on species distribution in tropical Asia, and highlight the conservation importance of the plant and animal species in the region. The modelling outputs can be used to categorize the natural habitats of Sal, Garjan and Teak as low to high risk under changing climates to inform conservation planning and forest management. Given the conservation importance of the threatened large mammals for maintaining a healthy forest ecosystem, the findings of the models can be used to categorize the likely suitable habitats under changing climates and preparing proper guidelines to reduce their extinction risks. To ensure wider applicability to conservation planning for species vulnerable to global climate change, the methods and analyses presented here for tropical Asia could be applied to other tropical regions (i.e., in Africa and the Americas), using different species groups and forest types.

Tropical weather disturbances are a major influence on coastal wetlands in North America. However, studies of their impact on biotic communities are rare. The abundance and species composition of amphibians and reptiles were investigated within levee, herbaceous marsh, and forested swamp habitats in southeastern Louisiana from 2002 to 2004 and again in 2005 to 2006. During the course of this study, three major hurricanes (Ivan, Katrina, and Rita) affected our study sites. This allowed us to opportunistically document the effect of major storm disturbances by comparing species richness, diversity, community assemblage, and abundance of amphibians and reptiles before and after hurricane events. We also used a previous study conducted in the same area during the late 1980's to assess long- term community composition changes. We documented the highest species richness in the forested swamp habitat (23 species), but the most diverse assemblage was found in marsh habitat (H 95 2.082). Overall, herpetofaunal diversity decreased and evenness increased in each habitat following hurricanes Ivan and Katrina/Rita. Drastic decreases in overall abundance of amphibians occurred, while the effect on reptile abundance varied with habitat. Reduced abundance of reptiles in marsh was recorded over the course of the study, while abundances in adjacent levee habitat increased, suggesting displacement of certain reptiles from the marsh to the levee. Significant saltwater intrusion was recorded in marsh and levee habitats, but not in the forested swamp. The hurricanes altered community composition and increased species evenness within each habitat, potentially affecting long-term community dynamics and species interactions.

Few studies have been conducted on amphibian communities in managed, second-growth Douglas-fir (Pseudotsuga menziesii) forests in the Pacific Northwest. My objectives were to investigate patterns of amphibian species richness, biomass, and abundance, and explore habitat relationships in different age classes of second-growth Douglas-fir forests managed primarily for timber production. I sampled terrestrial amphibian populations occurring in 4 distinct age classes of managed forest in western Washington with pitfall traps from 1992 to 1994. Although these forests were devoid of residual old growth, and all stands were at least in their second rotation, they contained the same assemblage of amphibian species occurring in unmanaged Douglas-fir forests in this region. Terrestrial amphibian communities in managed forests were structured differently than in unmanaged forests, however, with higher proportions of northwestern salamanders (Ambystoma gracile) and western redback salamanders (Plethodon vehiculum), and a much lower proportion of tailed frogs (Ascaphus truei). Contrary to several previous studies, I found no evidence that variation in amphibian abundances was strongly influenced by the amount of coarse woody debris on the forest floor. Further research is needed to elucidate the effects of intensive timber management on coarse woody debris and its role in the persistence of terrestrial amphibian populations in managed forests. Because rotation-age stands (the oldest age class) had the highest amphibian species richness, total biomass, and total abundance, and contained significantly higher abundances of the ensatina (Ensatina eschscholtzii) and red-legged frog (Rana aurora) than all younger age classes, silvicultural strategies that increase the percentage of rotation-age forest conditions within managed landscapes are likely to enhance the long-term habitat quality of intensively managed forest landscapes for terrestrial amphibians.