A global meta-analysis on patterns of amphibian and reptile diversity in agroforestry systems

Advances in herpetological research emanating from China.

Abstract. Zakaria N, Allahudin MIH, Ma’ad SNS, Sulaiman AA, Abdullah NA, Zamri MIM, Mamat MA, Deraman MY. 2022. Diversity amphibians and reptiles at Sungai Kerteh mangrove forest, Terengganu, Malaysia. Biodiversitas 23: 5574-5584. Malaysia has various ecosystems, including mangrove forests, that can support a rich number of amphibians and reptiles. However, amphibians and reptiles remain understudied, especially in mangrove forests. The main objective of this study was to determine the diversity of amphibians and reptiles in the mangrove forest of Sungai Kerteh. The sampling was conducted from 19th until 21st August 2019 by using the Visual Encounter Survey (VES) method along 2 km2 area of Sungai Kerteh. A total of 53 individuals were recorded belonging to 12 species (5 amphibian species and 7 reptile species). For amphibians, three families were recorded, with the family Dicroglossidae being the most abundant, with 13 individuals. For reptiles, eight families were recorded with the family Agamidae being the most abundant with 18 individuals. Fejervarya cancrivora (11 individuals; Family Dicroglossidae) was the most abundant amphibian species, while Leiolepis belliana (14 individuals; Family Agamidae) was the most abundant reptile species. There was no significant difference between the diversity of reptiles (H’: 1.6975) and amphibians (H’: 1.2643) (t: -1.6835, p>0.05). This study provides the first checklist of amphibians and reptiles species that will be helpful in identifying existing herpetofauna species and possible endangered or rare species in the Sungai Kerteh mangrove forest, which will help contribute to the conservation efforts of the herpetofauna in this area.

Malaysia is blessed with lush tropical rainforests that harbour an exceptional diversity of amphibians and reptiles. However, compared to other animal groups, amphibians and reptiles have received limited attention in research, despite their ecological significance. With amphibians and reptile species having been declining rapidly due to anthropogenic activities, there is a pressing need to conserve these species and their habitats. Environmentally Sensitive Areas (ESAs) are designated regions that are beneficial due to their critical role in providing essential ecosystem services and serving as repositories of biodiversity. Nonetheless, the classification of ESAs in Malaysia lacks biological elements and only focuses on physical attributes. To enhance the current ESA classification framework by integrating biological components, there is an urgent need to obtain information on diversity and habitat in Malaysia. Therefore, the objectives of this study were twofold: to determine the diversity of amphibians and reptiles in Gunung Belumut Amenity Forest and to conduct a comparative analysis between the herpetofauna assemblages in Gunung Belumut with other forest reserves in Peninsular Malaysia. The survey was carried out between March and June 2022, with additional sampling conducted in February 2023. The Visual Encounter Survey (VES) and pitfall trap methods were employed to survey the herpetofauna species, focusing on both aquatic and terrestrial habitats within the study area. A total of 210 individuals representing 38 species of herpetofauna were recorded, comprising 18 amphibian and 20 reptile species. Amongst the observed species, Limnonectesblythii was the most frequently encountered amphibian, with 59 individuals observed, while the dominant reptile species was Cyrtodactylusconsobrinus, represented by eight individuals. This pioneering study serves as a vital baseline documentation of the amphibian and reptile assemblages in Gunung Belumut Amenity Forest. It provides valuable information for identifying extant herpetofauna species, including those of potential conservation concern or rarity. These findings contribute to ongoing conservation efforts dedicated to the preservation of herpetofauna within the region. By understanding the diversity and distribution patterns of amphibians and reptiles in Gunung Belumut, effective conservation strategies can be developed to protect these species and their habitats.

In tropical regions, many studies have focused on how vegetation and ecosystem processes recover following the abandonment of anthropogenic activities, but less attention has been given to the recovery patterns of vertebrates. Here we conduct a meta‐analysis (n = 147 studies) of amphibian, reptile, bird and mammal recovery during tropical secondary forest succession (i.e. natural regeneration). For each taxonomic group, we compared changes in species richness and compositional similarity during natural secondary succession to reference forests (mature or old growth forest). In addition, we evaluated the response of forest specialists and the change in bird and mammal functional groups during natural secondary succession in the tropical moist forest biome. Overall, species richness of all groups reached levels of the reference forests during natural secondary succession, but this was not the case for species compositional similarity. The delay in recovery of forest specialists may be the reason for the delay in recovery of species compositional similarity. Overall, vertebrate recovery increased with successional stage, but other potential predictors of diversity recovery, such as, the geographical setting (amphibian and reptile species compositional similarity recovered more rapidly on islands), rainfall (mammal species richness and compositional similarity recovered faster in regions of low rainfall), and the landscape context (amphibian, reptile and mammal species compositional similarity recovered faster in regions with more forest patches) influenced vertebrate recovery. These results demonstrate the important role of secondary forests in providing habitat for many vertebrates, but the slow recovery of species compositional similarity, forest specialists and some functional groups (e.g. insectivorous birds) highlighted the challenge of secondary forest persistence, and strongly argues for the continued protection of old growth/mature forest as habitat for forest specialists and as sources for secondary forest sites.

Increasingly, conserved forests have become disturbed areas due to activities such as agriculture and livestock grazing. Landscape transformation leads to changes in biodiversity. Therefore, in this study, we compared the diversity of amphibians and reptiles in conserved areas (pine forest, oak-pine forest, and pine-oak forest) and disturbed areas in the Mixteca Oaxaqueña, southern Mexico. Fieldwork was conducted between July 2016 and June 2017, covering both the rainy and dry seasons. A total of eight amphibian species included in 5 families and 6 genera and 28 reptile species were recorded, distributed across 11 families and 21 genera. The pine-oak forest and the disturbed area exhibited the highest species richness of herpetofaunal, with 22 species each (4 amphibians and 18 reptiles), and were the most similar to each other with 14 species in common. Twelve amphibian and reptile species are classified in some risk category according to national and international standards. Twelve amphibian and reptile species are classified in some risk category according to national and international standards. The minimal difference in diversity observed in disturbed areas compared to that in pine forest and pine-oak forest suggests that the impact of changes in vegetation cover on amphibian and reptile diversity is relatively minor and not severe. However, the presence of 22 species in the disturbed areas (nine species considered in the risk category by Mexican environmental legislation) highlights the importance of implementing restoration strategies and monitoring the species that persist in disturbed areas. This study represents a significant contribution to the knowledge of amphibians and reptiles in both conserved and disturbed areas in the Mixteca Oaxaqueña, a region with limited available information on this biological group.

The conversion of natural systems into farms and agroecosystems is the main cause of biodiversity loss. In human-dominated landscapes, understanding the interactions between agroforestry systems and adjacent natural vegetation is fundamental to developing sustainable agricultural systems. Species can move between these two systems with natural systems providing the regional pool of species that shape the agricultural values and conservation value of the agroforestry systems. We investigated the influence of neighboring natural habitats on traditional agroforestry systems in the buffer zone of Pendjari Biosphere Reserve in Benin to understand the contribution of regional processes on the quality of agroforestry systems. We expected that agroforestry parklands adjacent to natural vegetation with high species diversity will also have higher plant species diversity. We found no similarity in plant species composition between agroforestry systems and adjacent natural habitats. A small proportion of species in adjacent natural habitats were found in agroforestry systems. The proportion of shared species was not significantly influenced by plant diversity in adjacent natural habitats or the distance from the agroforestry systems to the natural adjacent habitat. However, plant diversity in agroforestry systems was strongly associated with site ethnobotanical values indicating that farmers act as a supplemental but severe environmental filter of the regional species pool. Our study suggests that promoting the plantation of plants with high ethnobotanical use-value is a potentially viable strategy for sustainable agriculture and ecological restoration in Biosphere reserves.

Research on the diversity of amphibians and reptiles on the upstream part of Code River had been done in 2012 and 2017. Result on two previous results were found anurans, snakes and lizards but we did not find any freshwater turtles. Method used on the 2012 and 2017 research was conventional using Visual Encounter Survey (VES). Conventional methods such as VES have limitations, which was the inability to detect difficult-to-find animals such as freshwater turtles. Therefore, a new approach was taken to monitor the diversity of amphibians and reptiles especially to detect freshwater turtles in the Code River, namely the environmental DNA (eDNA) method. The purpose of this research were to monitor the diversity of amphibians and reptiles, and to reveals eDNA sampling efficiency compared to VES. An e-DNA metabarcoding process is conducted with universal CO1 primer on the water sample taken from upstream part of Code River. The results obtained were compared to the data from conventional studies held in 2012 and 2017. The results in 2021 found 12 species of amphibians but all of these species did not naturally distribute in Yogyakarta and even in Indonesia. Furthermore, 5 species of snakes were found, with only 1 species of snake naturally occur in Yogyakarta. Subsequently, we found 6 species of lizards whose natural distribution does not exist in Yogyakarta and even in Indonesia. Finally, we obtained 1 species of tortoise whose natural distribution does not exist in Yogyakarta and even in Indonesia. By far, in Indonesia the identification of amphibian and reptile species in rivers using the e-DNA method has shown less accurate results. The inaccuracy may be due to the lack of specificity of the sequence targets and primers for monitoring reptiles and amphibians in rivers. The target sequences used in this study did not have significant differences between species in reptiles and amphibians, so that the herpetofauna that had been recorded in the Code River were not identified using the e-DNA method. Based on this research, conventional sampling is recommended for monitoring herpetofauna in river areas.
 Keywords: Monitoring, Amphibians; Reptiles; Code River, e-DNA

In Mexico, land use changes have significantly impacted the diversity of amphibians and reptiles in a negative way. In light of this, we evaluate the alpha and beta components of the taxonomic diversity of amphibians and reptiles in a heterogeneous landscape in west-central Mexico. Additionally, we provide a checklist of amphibian and reptile species recorded over nine years of observations within the studied landscape and surrounding areas. The land cover/use types with the highest species richness and alpha taxonomic diversity differed between amphibians and reptiles. Overall beta taxonomic diversity was high for both groups, but slightly higher in reptiles. This taxonomic differentiation mainly corresponded to a difference in the turnover component and was greater in pristine habitats compared to disturbed ones. The checklist records 20 species of amphibians (ten of which are endemic) and 48 of reptiles (30 endemics). Additionally, the study expands the known geographical distribution range of one species of frog and three species of snakes. Our findings suggest that heterogeneous landscapes with diverse land cover/use types can provide essential habitats for the conservation of amphibian and reptile species.

Compared with the herpetofauna of the Sunda shelf islands, the diversity of amphibian and reptile genera on Sulawesi is impoverished. The oceanic character of the herpetofauna is the result of the million-year-long geographic isolation of Sulawesi which is separated from surrounding islands by deep ocean trenches. However, despite ambitious investigations by several industrious scientists during the past two centuries, recent fieldwork on Sulawesi and its smaller off-shore islands has revealed that the diversity of amphibians and reptiles has been largely underestimated. Since the last herpetological synopsis was published in 1996, 30 new amphibian and reptile species plus five subspecies have been described or newly recorded for Sulawesi and its satellite islands. In addition, more than 40 species, mainly skinks, have been identified as new to science and await formal description. This represents an increase by more than 35%! In total, about 210+ different species of amphibians and reptiles are currently recognized from the Sulawesi region almost 60% of which are endemics.

The rate of deforestation of primary tropical forests due to agricultural expansion is higher in Southeast Asia compared to all other world's tropical regions. Deforestation in tropical forests is a major threat for global biodiversity, because estimated 50-90 % of the world's species are living in tropical forests. Therefore, human dominated landscapes and forested land-use systems such as agroforestry become increasingly important as a storage reservoir of global biodiversity. Biodiversity is related to ecosystem functioning, with complementarity in resource use as a major mechanism. Pollination is essential for plant-derived ecosystem services such as food production, and pollinators are one of the major functional groups for human well-being. Agroforestry systems often include coffee (Coffea sp. L.) and cacao (Theobroma cacao L.) as important cash crops, traditionally crown under a canopy of shade trees and with fruit set depending on pollination. Because of the variety of planted shade and fruit trees, agroforestry systems resemble primary forests more than any other agricultural habitat type and have great but little explored potential to offer substitute habitats for many tropical forest species. My aim was to evaluate the importance of agricultural systems for conservation of trap-nesting Hymenoptera and the pollinator community. I analyzed a land-use gradient in a tropical forested landscape, from primary forests, agroforestry systems differing in diversity of the shade trees and openland such as grassland and fallow land. I assessed the relative importance of different strata for species richness with trap nests, which offer standardized nesting resources for different guilds of above-ground nesting Hymenoptera and their antagonists. Furthermore, I linked pollinator richness to habitat modification and final crop yield and analyzed species-specific differences in resource use. I also assessed the contribution of agroforestry system for the maintenance of high densities of a pest predating wasp species over the course of one year. This study took place in Central Sulawesi (Indonesia) in the surrounding of the village Toro at the margin of a primary tropical forest (Lore Lindu National Park). The results show that total bee species richness in the herb layer increased with increasing land-use intensity and was highest in openland. However, species richness estimation and additive partitioning of biodiversity revealed higher overall bee species richness, presumably due to high management diversity, in agroforestry systems compared to primary forests and openland. Agroforestry systems offer higher floral diversity in the understorey, due to the richer herb layer and cash crops, than primary forests and provide more nesting sites for cavity-nesting bee species than openland. The canopy in primary forests was far more important for trap-nesting bee and wasp richness than the understorey. This pattern reversed with intensification in agroforestry systems where highest richness was found in the understorey. Food resource availability and microclimatic conditions appeared to make the canopy in primary forests a more suitable habitat for most species and might cause underestimation of species richness when only lower strata are sampled. In addition, agroforestry habitats showed high beta diversity due to high land-use diversity and between-plot community dissimilarity, showing that agricultural management can be crucial for conservation plannings on a landscape scale. I used standardized pumpkin plantations in different habitat types to test the effect of pollinator diversity on crop yield. Bee pollinators showed species specific differences in flower visiting traits, such as height, time and body size-related flower visiting behaviour. I provide the first empirical evidence of the relation between spatiotemporal and behavioural complementarity in resource use of a pollinator community causing increased crop yield. Furthermore, I show that the native bee community can sustain pollination services in absence of managed honey bees. Using the highly abundant wasp species Rhynchium haemorrhoidale (F.) (Eumenidae, Hymenoptera), I show that agroforestry systems can maintain high insect densities of a pest predator, even under intense land-use management. Tropical regions experience lower climatic fluctuations between the seasons compared to temperate zones. However, R. haemorrhoidale undergoes seasonal changes in density and body size, due to a complex combination of potential reasons (e.g. climate, food supply, parasitism) independent of habitat type. In conclusion, agroforestry systems can play a crucial role in the conservation of the understorey pollinator communities and densities of pest predators, whereas the importance of the canopy for species richness is increasing with decreasing land-use intensity and is highest in primary forests. Furthermore, I show that the ecosystem service of pollination and crop yield strongly depends on the bees' functional diversity. Low-intensity land-use and a complex shade-tree canopy appear to increase local and regional Hymenoptera richness and to sustain important ecosystem services, showing the necessity to include such agricultural systems in landscape-wide conservation programs.

Land use and biodiversity patterns of the herpetofauna: The role of olive groves

Lestari ND, Suprayogo D, Rachmansyah A. 2018. Local biodiversity conservation in Sigi, Central Sulawesi, Indonesia: Analysis of the effect of elevation, land accessibility, and farmers’ income and perception on vegetation diversity in agroforestry systems. Biodiversitas 19: 283-291. The objectives of the research were to evaluate the level of landscape vegetation diversity in agroforestry systems and to determine the effect of elevation, accessibility, and farmer's income and perception on vegetation diversity in agroforestry systems. The research was conducted in Sigi District, Central Sulawesi, Indonesia. The method used was the Multidisciplinary Landscape Assessment approach. The research sites were located in 3 districts and 6 representative villages i.e. Padende and Sibedi in the lower landscape (23-75 m asl.), Balane and Doda in the middle landscape (148-504 m asl.), Dombu and Ongulero in the upper landscape (1163-1404 m asl.), with 5 replications in each village. The total area of the six villages was 3772.13 ha that consisted of 1217.13 ha of agroforestry systems (32.3%). The research covered a population of 392 households who had landed with agroforestry systems. A total of 30 agroforestry farmers and their land (minimum 0.25 ha, homogeneous land system) were selected as samples. Research activities like observation, survey, and analysis were divided into two aspects, namely biophysical and socioeconomic aspects. The results revealed that at landscape level agroforestry systems had relatively high plant species diversity (H'= 3.1) and needed to be optimized to enhance its role as buffering zone for biodiversity conservation and for supporting sustainable livelihood. Efforts to improve vegetation diversity must be adjusted to habitat conditions (elevation and soil health), where vegetation can grow and produce well. The regional development such as accessibility improvement is still needed and it will not threaten the vegetation diversity as long as there is a harmony between human activities and the environment. An increase in the level of income with a positive perception of farmers on the benefits of vegetation diversity in the future will have a main role in vegetation diversity conservation as fundamental asset in sustainable development.

Woody and non-woody plant species conservation is one of the ecosystem services provided by agroforestry (AF) systems across the agricultural landscapes. Little attention has been paid to assessing the conservation of plant diversity in AF systems. This study was, thus, aimed at investigating plant species diversity, structure, and composition of three AF systems in Gedeo zone of south-eastern rift–valley agricultural landscape of Ethiopia. The study was conducted in three agroforestry systems, namely, enset based, coffee–enset based (C–E based AF), and coffee–fruit trees–enset based (C–Ft–E based AF) agroforestry systems. Twenty farms representative of each AF system were randomly selected, and inventory of the floristic diversity was employed in a 10 m × 10 m sample plot per farm. A total of 52 perennial woody and non-woody plant species belonging to 30 families were recorded. Of all species identified, 33 (63.5%) were native, of which two species, namely Millettia ferruginea (Hochst.) Baker and Erythrina brucei Schweinf., were registered as endemic. The highest proportion of native species was recorded in enset based AF (93.3%), and the least were in C–Ft–E based AF (59%). According to the IUCN Red List and local criteria, 13 species were recorded as being of interest for conservation in all AF systems. The woody species Prunus africana was identified as both vulnerable by IUCN Red List and rare for 25% of species that least occur. The Shannon diversity index and richness showed that C–Ft–E based AF systems were significantly different from the two remaining AF systems. However, the species abundance and evenness did not show significant differences between the three AF systems. In general, retaining such numbers of woody and non-woody perennial plant species richness under the AF systems of the present study underlines their potential for biodiversity conservation.

The Balsas Basin (BB) is a biogeographic province in south-central Mexico that straddles the Mexican Transition Zone and the Neotropical region. We provide a list of the amphibian and reptile species of the BB based on a detailed review and update of recent species lists of its constituent states. The BB is home to 51 native amphibian and 155 native reptile species, which represent 14.7% of the herpetofauna of Mexico. No amphibian and six reptile species are endemic to the BB. Six species of amphibians and seven of reptiles are categorized as being of conservation concern status (vulnerable, endangered, or critically endangered) on the International Union for Conservation of Nature’s (IUCN) Red List. The main threat these species face is habitat loss due to urbanization, agriculture, and pollution. The herpetofauna of the BB shows significant overlap with neighboring provinces. The composition of amphibian species in the BB is closest to that of the Pacific Lowlands, whereas the composition of reptile species is closest to the Sierra Madre del Sur and the Transvolcanic Belt. These findings suggest that while the BB supports significant amphibian and reptile diversity, its conservation importance may be limited due to the low levels of endemism and the relatively small proportion of species at risk.

This article is reprinted with permission from the National Association of Biology Teachers. ***Note: Figures may be missing from this format of the document Abstract: Tomasek et al describe the protocols used in an ongoing research project on amphibian and reptile diversity at Cool Springs Environmental Education Center near New Bern NC. Herpetofaunal surveys have been conducted for the past five years on a 1700-acre site owned by the Weyerhaeuser Corp. Four protocols have been utilized too capture and compile a list of reptiles and amphibians--these protocols can be duplicated to some degree on almost any school site with some small acreage. Article: This article describes the protocols used in an ongoing research project on amphibian and reptile diversity at Cool Springs Environmental Education Center near New Bern, North Carolina. Herpetofaunal surveys have been conducted for the past five years on a 1700-acre site owned by the Weyerhaeuser Corporation. Four protocols have been utilized to capture and compile a list of reptiles and amphibians. These protocols can be duplicated to some degree on almost any school site with some small acreage. Such a study can be conducted with students of almost any age group, providing them with opportunities to conduct inquiry-based scientific research. If you decide to implement a similar study using your school grounds, parents' private property, or perhaps a local public park, students will learn to conduct field surveys and will learn more about habitat types, relationships between habitat and wildlife, niche partitioning, common and scientific names of local amphibians and reptiles, and their migratory patterns. Students will gain experience in making detailed observations, asking questions, and analyzing data. Most importantly, as students learn about the types of wildlife in the area they study, their environmental awareness will be piqued and stretched.