Unveiling the Diet of Elusive Rainforest Herbivores in Next Generation Sequencing Era? The Tapir as a Case Study

Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir''s diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.     

Bushmeat Hunting Alters Recruitment of Large-seeded Plant Species in Central Africa

We investigated the effect of local hunting on plant recruitment at the community level in the Ngotto Forest, Central African Republic. It is the first study of this kind in the afrotropics. To compare our results with previous studies conducted in the neotropics, we used the protocol proposed byNuñez-Iturri and Howe. We compared animal relative abundances and seed length, density and diversity of seedlings at two sites with contrasting anthropogenic pressures: one with low hunting pressure (LH) and one with high hunting pressure (HH). Furthermore, we investigated how density and diversity of recruitment vary with seed length in the two sites. Both sites exhibit similar soil, climate and tree species composition, and have never been logged. Large mammals (frugivores and herbivores) were extirpated from HH and relative abundance of medium-sized frugivores drastically decreased in HH compared with LH. In HH, diversity of seedlings was reduced compared with LH, especially for large-seeded plant species dispersed by large game mammals. The approach used in this study shows promising perspectives to investigate the effects of human disturbances on the regeneration of tropical forests. Furthermore, in the afrotropical context of a lack of data on plant–animal ecological relationships, seed length appears to be a good predictor of the strength of the deficit of plant recruitment due to large mammal extirpation because of hunting. Thus, more efforts are needed to study the ecological roles of large-seeded plants in order to better understand the effects of their disappearance on tropical forest resilience.     

Defaunation and fragmentation erode small mammal diversity dimensions in tropical forests

Forest fragmentation and defaunation are considered the main drivers of biodiversity loss, yet the synergistic effects of landscape changes and biotic interactions on assemblage structure have been poorly investigated. Here, we use an extensive dataset of 283 assemblages and 105 species of small mammals to understand how defaunation of medium and large mammals and forest fragmentation change the community composition and diversity of rodents and marsupials in tropical forests of South America. We used structured equation models to investigate the relationship between small mammal species, functional and phylogenetic diversity with forest size, forest cover and the occurrence of medium and large mammals. The best‐fit model showed that defaunation reduced functional diversity, and that species diversity of small mammals increased with forest patch size. Forest cover did not affect functional and phylogenetic diversity. Our results indicate that occurrence of medium and large sized mammals (probably acting as predators, or competitors of small mammals) and forest patch size help to retain species and functional diversity in small mammal communities. Further, the number of species in a small mammal community was critical to the maintenance of phylogenetic diversity, and may have a pronounced influence on the ecological functions played by small mammals. Identifying how phylogenetic and functional diversity change in function of human pressures allows us to better understand the contribution of extant lineages to ecosystem functioning in tropical forests.     

Asian Tapirs Are No Elephants When It Comes To Seed Dispersal

The elimination of the largest herbivores (elephants and rhinoceroses) from many forests in tropical East Asia may have severe consequences for plant species that depend on them for seed dispersal. We assessed the capacity of Malayan tapirs Tapirus indicus—the next largest nonruminant herbivore in the region—as a substitute for the lost megafauna in this role by studying their ability to disperse the seeds of nine fleshy‐fruited plants with seeds 5–97 mm in length. We combined information from feeding trials, germination tests, and field telemetry to assess the effect of tapir consumption on seed viability and to estimate how far the seeds would be dispersed. The tapirs (N=8) ingested few seeds. Seed survival through gut passage was moderately high for small‐seeded plants (e.g., 36.9% for Dillenia indica) but very low for medium‐ (e.g., 7.6% for Tamarindus indica) and large‐seeded (e.g., 2.8% for Artocarpus integer) plants. Mean seed gut passage times were long (63–236 h) and only the smallest seeds germinated afterwards. Using movement data from four wild tapirs in Peninsular Malaysia we estimated mean dispersal distances of 917–1287 m (range=22–3289 m) for small‐seeded plants. Malayan tapirs effectively dispersed small‐seeded plants but acted as seed predators for the large‐seeded plants included in our study, suggesting that they cannot replace larger herbivores in seed dispersal. With the absence of elephants and rhinos many megafaunal‐syndrome plants in tropical East Asia are expected to face severe dispersal limitation problems.     

热带与亚热带森林分子生态学研究

当前 ,植物学家会有更多的方法和手段来从事植物学的研究 ,如分子生物学方法、遗传学的方法、植物生理学的方法、分类学方法等。其中分子生物学方法直接研究植物遗传物质ＤＮＡ ,从根本上揭示了生物体内涵 ,有着极其重要的作用[4 7] 。因此用分子生物学手段进行生态学的研究有着广泛应用前景和重要意义。分子生物学方法既节省时间和资金 ,又比传统方法解决了更多的问题[6 1] 。例如在动物学研究中 ,用少许的毛发就可以分析高山土拨鼠 (ＭａｒｍｏｔａｍａｒｍｏｔａＳｃｉｕｒｉｄａｅ)的交配系统[30 ] ;粪便所带的肠道粘膜细胞ＤＮＡ也可以…     

Termites, Large Herbivores, and Herbaceous Plant Dominance Structure Small Mammal Communities in Savannahs

Large herbivores and termites are important functional groups in African savannahs. Both groups affect small mammals, which are also important determinants for savannah structure and function. Because vegetation on Macrotermes mounds are preferentially grazed by large herbivores, and mounds represent resource-rich distinct habitat patches for small mammals in relatively resource-poor savannahs, termite mounds are ideal sites for studies of how grazing by large mammals and productivity affect communities of small mammals. We conducted an experiment in Lake Mburo National Park, Uganda, with four treatments: large vegetated Macrotermes mounds (with and without large herbivores) and adjacent savannah areas (with and without large herbivores). We replicated the treatment blocks nine times and trapped small mammals regularly over a period of almost 2 years. Small mammal species assemblages differed considerably between mounds and savannah areas. Grazing had a substantial effect on small mammal species assemblages in the resource-poor savannah, but not in the relatively resource-rich termitaria. Small mammal species abundance, biomass, and richness were higher on termite mounds than adjacent savannah areas. Excluding large herbivores caused a major increase in species abundance, biomass, and richness both on savannah and termitaria. Herbaceous plant species evenness was an important determinant of the small mammal community. Small mammal biomass increased with high plant dominance, indicating that a few dominant plant species are important for biomass production of small mammals. Small mammal diversity was not related to any of the treatments, but increased with plant species evenness as well as richness. Fencing increased species dominance in the small mammal community on both savannah and termitaria, probably because competitive patterns shift from inter-guild (that is, between large and small mammals) to intra-guild (that is, between small mammals) when large mammals are excluded. The study highlights the complex interactions among large herbivores, termites, herbaceous plants, and small mammals in African savannahs. When studying the structure and function of small mammal communities it is therefore important to consider several coexisting functional groups.     

Tree diversity promotes generalist herbivore community patterns in a young subtropical forest experiment

Stand diversification is considered a promising management approach to increasing the multifunctionality and ecological stability of forests. However, how tree diversity affects higher trophic levels and their role in regulating forest functioning is not well explored particularly for (sub)tropical regions. We analyzed the effects of tree species richness, community composition, and functional diversity on the abundance, species richness, and beta diversity of important functional groups of herbivores and predators in a large-scale forest biodiversity experiment in south-east China. Tree species richness promoted the abundance, but not the species richness, of the dominant, generalist herbivores (especially, adult leaf chewers), probably through diet mixing effects. In contrast, tree richness did not affect the abundance of more specialized herbivores (larval leaf chewers, sap suckers) or predators (web and hunting spiders), and only increased the species richness of larval chewers. Leaf chemical diversity was unrelated to the arthropod data, and leaf morphological diversity only positively affected oligophagous herbivore and hunting spider abundance. However, richness and abundance of all arthropods showed relationships with community-weighted leaf trait means (CWM). The effects of trait diversity and CWMs probably reflect specific nutritional or habitat requirements. This is supported by the strong effects of tree species composition and CWMs on herbivore and spider beta diversity. Although specialized herbivores are generally assumed to determine herbivore effects in species-rich forests, our study suggests that generalist herbivores can be crucial for trophic interactions. Our results indicate that promoting pest control through stand diversification might require a stronger focus on identifying the best-performing tree species mixtures.     

Functional diversity and redundancy of tropical forest mammals over time

Globally, tropical rain forests comprise some of the most diverse and functionally rich ecosystems but are increasingly degraded by human impacts. Protected areas have been shown to conserve species diversity, but their effectiveness at maintaining functional diversity over time is less well known, despite the fact that functional diversity likely reveals more ecological information than taxonomic diversity. By extension, the degree to which species loss decreases functional diversity within protected areas is also unknown; functional redundancy may buffer communities from loss of functional diversity from some local extinctions. Using eight years of camera trap data, we quantified annual functional dispersion of the large mammal community in the Volcán Barva region of Costa Rica and tested for changes in functional dispersion over time in response to environmental and anthropogenic predictors. We quantified functional redundancy based on simulated declines in functional dispersion with species loss. Observed functional dispersion did not change significantly over time and was not associated with measured environmental or anthropogenic predictors. Quantitative modeling of observed functional traits over time did not identify significant changes. We did however find qualitative trends in relative trait proportions, which could be indicative of functional change in the future. We found high functional redundancy, with average simulated functional dispersion declining significantly only after 9 out of 21 large mammal species were lost from the community. We cautiously suggest that protected tropical rain forests can conserve functional diversity over the course of a decade even in heavily fragmented landscapes. Abstract in Spanish is available with online material.     

Recovery of mammal diversity in tropical forests: a functional approach to measuring restoration

Ecological restoration is increasingly applied in tropical forests to mitigate biodiversity loss and recover ecosystem functions. In restoration ecology, functional richness, rather than species richness, often determines community assembly, and measures of functional diversity provide a mechanistic link between diversity and ecological functioning of restored habitat. Vertebrate animals are important for ecosystem functioning. Here, we examine the functional diversity of small‐to‐medium sized mammals to evaluate the diversity and functional recovery of tropical rainforest. We assess how mammal species diversity and composition and functional diversity and composition, vary along a restoration chronosequence from degraded pasture to “old‐growth” tropical rainforest in the Wet Tropics of Australia. Species richness, diversity, evenness, and abundance did not vary, but total mammal biomass and mean species body mass increased with restoration age. Species composition in restoration forests converged on the composition of old‐growth rainforest and diverged from pasture with increasing restoration age. Functional metrics provided a clearer pattern of recovery than traditional species metrics, with most functional metrics significantly increasing with restoration age when taxonomic‐based metrics did not. Functional evenness and dispersion increased significantly with restoration age, suggesting that niche complementarity enhances species' abundances in restored sites. The change in community composition represented a functional shift from invasive, herbivorous, terrestrial habitat generalists and open environment specialists in pasture and young restoration sites, to predominantly endemic, folivorous, arboreal, and fossorial forest species in older restoration sites. This shift has positive implications for conservation and demonstrates the potential of tropical forest restoration to recover rainforest‐like, diverse faunal communities.     

Co-declining mammals and dung beetles: an impending ecological cascade

Biodiversity loss can precipitate extinction cascades and impair ecological processes. These 'downstream' effects will be exacerbated if functionally important taxa are tightly linked with species threatened by extinction or population decline. We review the current evidence that such a scenario is currently playing out in the linked declines of persistently hunted mammal populations and the dung beetles communities (Coleoptera: Scarabaeidae: Scarabaeinae) that depend on them for adult and larval food resources. Through a close evolutionary association, mammal assemblages have played a fundamental role in structuring extant dung beetle communities. Today many game mammal species' populations are severely depleted by subsistence or commercial hunting, especially in tropical forest systems. Multiple lines of evidence from temperate and tropical systems indicate that the regional-scale decline or extirpation of medium and large bodied mammal faunas can severely disrupt the diversity and abundance of dung beetle communities through alterations in the composition and availability of dung resources. These observed community disassemblies have significant short- and long-term implications for the maintenance of key ecosystem processes including nutrient recycling and secondary seed dispersal. Identifying the species- and community-level traits that buffer or exacerbate these species and functional responses is essential if we are to develop a better understanding of the cascading ecological consequences of hunting in tropical forests.     

Integrating ancient patterns and current dynamics of insect-plant interactions: Taxonomic and geographic variation in herbivore specialization

The search for pattern in the ecology and evolutionary biology of insect-plant associations has fascinated biologists for centuries.High levels of tropical (low-latitude) plant and insect diversity relative to poleward latitudes and the disproportionate abundance of host-specialized insect herbivores have been noted.This review addresses several aspects of local insect specialization,host use abilities (and loss of these abilities with specialization), host-associated evolutionary divergence,and ecological ...     

Edge-induced narrowing of dietary diversity in leaf-cutting ants

Much of the ecological alteration faced by human-modified Neotropical forests can be assigned to edge effects, including the proliferation of some voracious herbivores such as leaf-cutting ants. However, the underlying mechanisms/impacts of tropical forest edge on herbivores performance and their foraging behaviour (e.g. dietary diversity) have rarely been investigated. The goal of this study was, therefore, to determine whether and how the annual diet (i.e. species richness, diversity and the relative proportion of pioneer versus non-pioneer species of plant materials) of Atta cephalotes colonies differs in the forest edge versus the interior zone of a large remnant of Atlantic forest in northeastern Brazil. Among the key results was a strong habitat effect on dietary diversity (explaining ca. 40-50% of the variation), which, in edge colonies, decreased approximately by one fourth compared to interior colonies (inverse of Simpson's index: 3.7±0.84 versus 4.99±0.95). There was a predominance of leaf fragments collected from pioneer species in the diet in both habitat (86% in edge and 80.4% in interior). Edge colonies collected proportionally more fragments from pioneer species than colonies located in the forest interior. Our results are the first to demonstrate an edge-mediated relaxation of dietary restrictions in leaf-cutting ants. These findings render robust support to previous evidence indicating the reduction of bottom-up forces as a key factor explaining both edge-induced hyper-abundance and increased herbivory of leaf-cutting ants in human-modified Neotropical landscapes.     

Diversity and ecology of Radiolaria in modern oceans

Among the many inhabitants of planktonic communities, several lineages have biomineralized intricate skeletons. These have existed for millions of years and include the Radiolaria, a group of marine protists, many of which bear delicate mineral skeletons of different natures. Radiolaria are well known for their paleontological signatures, but little is known about the ecology of modern assemblages. They are found from polar to tropical regions, in the sunlit layers of the ocean down to the deep and cold bathypelagic. They are closely involved in the biogeochemical cycles of silica, carbon and strontium sulfate, carrying important amounts of such elements to the deep ocean. However, relatively little is known on the actual extent of genetic diversity or biogeographic patterns. The rapid emergence and acceptance of molecular approaches have nevertheless led to major advances in our understanding of diversity within and evolutionary relationships between major radiolarian groups. Here, we review the state of knowledge relating to the classification, diversity and ecology of extant radiolarian orders, highlighting the substantial gaps in our understanding of the extent of their contribution to marine biodiversity and their role in marine food webs.     

Four ways towards tropical herbivore megadiversity

Most multicellular species alive are tropical arthropods associated with plants. Hence, the host-specificity of these species, and their diversity at different scales, are keys to understanding the assembly structure of global biodiversity. We present a comprehensive scheme in which tropical herbivore megadiversity can be partitioned into the following components: (A) more host plant species per se , (B) more arthropod species per plant species, (C) higher host specificity of herbivores, or (D) higher species turnover (beta diversity) in the tropics than in the temperate zone. We scrutinize recent studies addressing each component and identify methodological differences among them. We find substantial support for the importance of component A, more tropical host species. A meta-analysis of published results reveals intermediate to high correlations between plant and herbivore diversity, accounting for up to 60% of the variation in insect species richness. Support for other factors is mixed, with studies too scarce and approaches too uneven to allow for quantitative summaries. More research on individual components is unlikely to resolve their relative contribution to overall herbivore diversity. Instead, we call for the adoption of more coherent methods that avoid pitfalls for larger-scale comparisons, for studies assessing different components together rather than singly, and for studies that investigate herbivore beta-diversity (component D) in a more comprehensive perspective.     

Genetic diversity increases insect herbivory on oak saplings

A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Quercus robur) half-sib families. We quantified genetic diversity at the plot level by genotyping all oak saplings and assessed overall damage caused by ectophagous and endophagous herbivores along a gradient of increasing genetic diversity. Damage due to ectophagous herbivores increased with the genetic diversity in oak sapling populations as a result of higher levels of damage in mixtures than in monocultures for all families (complementarity effect) rather than because of the presence of more susceptible oak genotypes in mixtures (selection effect). Assemblages of different oak genotypes would benefit polyphagous herbivores via improved host patch location, spill over among neighbouring saplings and diet mixing. By contrast, genetic diversity was a poor predictor of the abundance of endophagous herbivores, which increased with individual sapling apparency. Plant genetic diversity may not provide sufficient functional contrast to prevent tree sapling colonization by specialist herbivores while enhancing the foraging of generalist herbivores. Long term studies are nevertheless required to test whether the effect of genetic diversity on herbivory change with the ontogeny of trees and local adaptation of specialist herbivores.     

Occurrence of blood-feeding terrestrial leeches (Haemadipsidae) in a degraded forest ecosystem and their potential as ecological indicators

Blood-feeding invertebrates are emerging model taxa in biodiversity assessments, both as indicators of mammal abundance and also as sources of mammal DNA for identification. Among these, terrestrial leeches arguably offer the greatest promise; they are abundant and widespread in the humid tropics, and their blood meals can be easily assayed to establish diet. Unfortunately, terrestrial leeches are understudied, with little known about their ecology and behavior. Such information is needed to evaluate their utility as ecological indicators and to account for potential sampling biases that might arise from habitat preferences. By combining occupancy modeling and thermal tolerance assays, we determined the factors affecting species occurrence in the related terrestrial brown (Haemadipsa sumatrana) and tiger leech (Haemadipsa picta), both of which are widespread in tropical forests in Southeast Asia. We sampled both species across a degraded forest landscape in Sabah, Borneo, in wet and dry seasons, associating occurrence with habitat-level metrics. We found that, for both species, detection probability increased with canopy height regardless of season. Additionally, increased vegetation heterogeneity had a strong negative influence on brown leech occurrence in the dry season, implying an interaction between vegetation structure and climate. However, we found no difference in physiological thermal tolerance (CT_MAX) between the two species. Finally, using a reduced dataset, we found a small improvement in brown leech model fit when including mammal abundance. Our results suggest that the presence of terrestrial leeches may act as useful ecological indicators of habitat quality and potentially mammalian abundance. Abstract in Indonesia is available with online material.     

Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis

Unisexual vertebrates typically form through hybridization events between sexual species in which reproductive mode transitions occur in the hybrid offspring. This evolutionary history is thought to have important consequences for the ecology of unisexual lineages and their interactions with congeners in natural communities. However, these consequences have proven challenging to study owing to uncertainty about patterns of population genetic diversity in unisexual lineages. Of particular interest is resolving the contribution of historical hybridization events versus post formational mutation to patterns of genetic diversity in nature. Here we use restriction site associated DNA genotyping to evaluate genetic diversity and demographic history in Aspidoscelis laredoensis, a diploid unisexual lizard species from the vicinity of the Rio Grande River in southern Texas and northern Mexico. The sexual progenitor species from which one or more lineages are derived also occur in the Rio Grande Valley region, although patterns of distribution across individual sites are quite variable. Results from population genetic and phylogenetic analyses resolved the major axes of genetic variation in this species and highlight how these match predictions based on historical patterns of hybridization. We also found discordance between results of demographic modelling using different statistical approaches with the genomic data. We discuss these insights within the context of the ecological and evolutionary mechanisms that generate and maintain lineage diversity in unisexual species. As one of the most dynamic, intriguing, and geographically well investigated groups of whiptail lizards, these species hold substantial promise for future studies on the constraints of diversification in unisexual vertebrates.     

The assembly of tropical tree communities – the advances and shortcomings of phylogenetic and functional trait analyses

Tropical tree communities present one of the most challenging systems for studying the processes underlying community assembly. Most community assembly hypotheses consider the relative importance of the ecological similarity of co‐occurring species. Quantifying this similarity is a daunting and potentially impossible task in species‐rich assemblages. During the past decade tropical tree ecologists have increasingly utilized phylogenetic trees and functional traits to estimate the ecological similarity of species in order to test mechanistic community assembly hypotheses. A large amount of work has resulted with many important advances having been made along the way. That said, there are still many outstanding challenges facing those utilizing phylogenetic and functional trait approaches to study community assembly. Here I review the conceptual background, major advances and major remaining challenges in phylogenetic‐ and trait‐based approaches to community ecology with a specific focus on tropical trees. I argue that both approaches tremendously improve our understanding of tropical tree community ecology, but neither approach has fully reached its potential thus far.     

Forward from the crossroads of ecology and evolution

Community genetics is a synthesis of community ecology and evolutionary biology. It examines how genetic variation within a species affects interactions among species to change ecological community structure and diversity. The use of community genetics approaches has greatly expanded in recent years and the evidence for ecological effects of genetic diversity is growing. The goal of current community genetics research is to determine the circumstances in which, and the mechanisms by which community genetic effects occur and is the focus of the papers in this special issue. We bring a new group of researchers into the community genetics fold. Using a mixture of empirical research, literature reviews and theoretical development, we introduce novel concepts and methods that we hope will enable us to develop community genetics into the future.     

Prediction of group patterns in social mammals based on a coalescent model

This study describes a statistical model which assumes that mammal group patterns match with groups of genetic relatives. Given a fixed sample size, recursive algorithms for the exact computation of the probability distribution of the number of groups are provided. The recursive algorithms are then incorporated into a statistical likelihood framework which can be used to detect and quantify departure from the null-model by estimating a clustering parameter. The test is then applied to ecological data from social herbivores and carnivores. Our findings support the hypothesis that genetic relatedness is likely to predict group patterns when large mammals have few or no predators.