Botany, genetics and ethnobotany: a crossed investigation on the elusive tapir's diet in French Guiana

Anatomical, Histological and Histochemical Observations of the Eyelids and Orbital Glands in the Lowland Tapir (Tapirus terrestris Linnaeus, 1785) (Perissodactyla: Ceratomorpha)

The lowland tapir is one of four species belonging to the Tapiridae family of the Ceratomorpha suborder, similar to Rhinocerotidae. This study describes anatomy with morphometry, histology (hematoxylin and eosin, Masson-Goldner trichrome, Movat pentachrome, mucicarmine, picro-Mallory trichrome) and histochemistry (PAS, AB pH 1.0, AB pH 2.5; AB pH2.5/PAS and HDI) of the upper and lower eyelids, and superficial gland of the third eyelid with the third eyelid, deep gland of the third eyelid, and lacrimal gland. The aim of the work is to show the features of the above-mentioned structures typical only for Tapiridae, as well as to show the presence of similarities and differences between the families forming the order Perissodactyla. The eyelashes on the upper eyelid were long, while those of the lower eyelid were short and much less prominent. In the upper and lower eyelid sebaceous glands, a characteristic simple alveolar gland producing a mucus-like secretion and poorly developed tarsal glands were observed. The marginal zone of the posterior surface of the eyelids was covered by stratified columnar epithelium with 18-21 layers of nucleated cells, while the bulbar zone of these surfaces was covered by cubic multilayer epithelium with 6-11 non-keratinized layers of cells and with sparse goblet cells. In only lower eyelids, numerous lymphoid nodules, diffuse lymphocytes and high endothelial venules were observed. The superficial gland was an acinar complex which secreted mucous and contained plasma cells within the interlobular and interlobular connective tissue. The upper and lower branches of the third eyelid were the shape of a bent "caudal fin" and were composed of hyaline cartilage, and they contained conjunctiva associated lymphoid tissue (CALT). The deep gland was also an acinar complex producing a serous character and having numerous diffuse lymphocytes. The lacrimal gland was an acinar complex producing seromucous secretions and had numerous plasma cells located in the glandular interstitium. The results of our research indicate that the features of the anatomy of the eyelids and orbital region in the lowland tapir are also typical of the family Tapiridae, but also have features common to the families Equidae and Rhinocerotidae. We confirm the presence of poorly developed tarsal glands in both eyelids as well as presence of a palpebral part of the lacrimal gland in the upper eyelid, which is typical only to Tapirus terrestris.

Comparative Histology and Histochemistry of the Parotid Gland and Mandibular Gland in the Lowland Tapir (Tapirus terrestris Perissodactyla) and Aardvark (Orycteropus afer Tubulidentata)

In terrestrial mammals, the parotid and mandibular glands secrete different types of saliva into the oral cavity. Both glands were obtained from two female lowland tapirs (Tapirus terrestris) and one female aardvark (Orycteropus afer) from the Wroclaw Zoological Garden (Poland) and examined by light microscopy (hematoxylin and eosin, mucicarmine, periodic acid-Schiff, Alcian blue pH 1.0, Alcian blue pH 2.5, Alcian blue pH 2.5/PAS, and Hale's dialysed iron). Both the parotid glands observed in the lowland tapir and aardvark were compound alveolar serous secretory units, and in both species, the secretion was composed of neutral and acidic mucopolysaccharides (sialo and sulfated mucins). However, in both the lowland tapir and aardvark, a histological examination found the stroma of the mandibular gland was divided into very large lobes by poorly marked connective tissue. While many interlobar and striated ducts were found in the aardvark, very few were found in the lowland tapir. The mandibular gland was a branched tubular (mucous secretion) type in the lowland tapir, but it was a branched tubuloalveolar (mucous-serous) type in the aardvark. In all tested glands, the secretion was composed of neutral mucopolysaccharides, acid-sulfated mucosubstances, and sialomucins.

Roads Disrupt Frugivory and Seed Removal in Tropical Animal-Dispersed Plants in French Guiana

Ecological interactions are being affected at unprecedented rates by human activities in tropical forests. Yet, the continuity of ecological functions provided by animals, such as seed dispersal, is crucial for forest regeneration and species resilience to anthropogenic pressures. The construction of new roads in tropical forests is one of the main boosters of habitat destruction as it facilitates human access to previously isolated areas and increases defaunation and loss of ecological functions. It, therefore, becomes increasingly urgent to rapidly assess how recently opened roads and associated anthropogenic activities affect ecological processes in natural habitats, so that appropriate management measures to conserve diversity can be taken. In this study, we aimed to evaluate the effects of anthropogenic pressures on the health status of a mature rainforest crossed by a newly opened road in French Guiana. For this, we combined different methods to conduct a rapid assessment of the forest’s health status. Firstly, we evaluated the activity of frugivores using camera traps deployed in four forest patches located near (<1 km) ecological corridors preserved as canopy bridges over the road during the fruiting periods of four animal-dispersed tree species. Secondly, we analyzed the fate of seeds enclosed in animal-dispersed tropical fruits by calculating the proportions of fruits consumed and seeds removed (either dispersed or predated) by frugivores. Results show that the proportion of fruits opened and consumed was lower in the forest areas located near the road than in the control forest, and this difference was more significant for plant species strictly dependent on large-bodied primates for seed dispersal than for species relying on both primates and birds. Camera traps showed the presence of small primates and kinkajous feeding on Virola fruits in the forest impacted by the road, where large primates were absent. It is thus likely that smaller frugivores exert a compensatory effect that maintains ecological functions near the road. Despite efforts made to preserve forest continuity through ecological corridors, anthropogenic pressures associated with road proximity are affecting wildlife and disrupting associated ecological functions crucial for plant regeneration, contributing to further forest degradation.

The distribution and conservation status of Tapirus terrestris in the South American Atlantic Forest

Tapirus terrestris is the largest South American land mammal, with an extensive historical distribution and capable of occupying diverse habitats, and yet its populations have declined across its range. In order to provide baseline data on the conservation status of tapirs in the Atlantic Forest, we conducted a long-term study in one landscape, visited 93 forests, and received 217 expert reports over the 15-year study. We estimate that 2,665–15,992 tapirs remain in 48 confirmed populations, occupying 26,654 km2 of forest or 1.78% of its original range in the biome. Historically, hunting and deforestation were the main causes of decline, but today population isolation is the principal long-term threat. Vortex models indicate that 31.3–68.8% and 70.8–93.8% of the populations are demographically and genetically non-viable over the next 100 years, respectively, and that only 3–14 populations are viable when considering both variables. Habitat use data indicate that tapirs are adaptable to disturbed and secondary forests and will use diverse tree plantations and agricultural lands but hunting and highways keep populations isolated. Reserve staff report tapirs as common/abundant at 62.2% of the sites, and populations as stable and growing in 60% and 36% of the sites, respectively, and there is ample habitat in the biome for a population expansion, but overcoming the causes of isolation will be necessary for this to occur. Lack of adequate funding for protecting reserves is a chronic threat throughout the biome, especially in federal and state/provincial reserves, and increased funding will be necessary to implement effective conservation plans.

The mutualism-antagonism continuum in Neotropical palm-frugivore interactions: from interaction outcomes to ecosystem dynamics

Frugivory, that is feeding on fruits, pulp or seeds by animals, is usually considered a mutualism when interactions involve seed dispersal, and an antagonism when it results in the predation and destruction of seeds. Nevertheless, most frugivory interactions involve both benefits and disadvantages for plants, and the net interaction outcomes thus tend to vary along a continuum from mutualism to antagonism. Quantifying outcome variation is challenging and the ecological contribution of frugivorous animals to plant demography thus remains little explored. This is particularly true for interactions in which animals do not ingest entire fruits, that is in seed‐eating and pulp‐eating. Here, we provide a comprehensive review of Neotropical palm–frugivore interactions, with a focus on how frugivore consumption behaviour (i.e. digestive processing, fruit‐handling ability and caching behaviour) and feeding types (fruit‐eating, pulp‐eating and seed‐eating) influence interaction outcomes at different demographic stages of palms. We compiled a total of 1043 species‐level palm–frugivore interaction records that explicitly captured information on which parts of palm fruits are eaten by animals. These records showed consumption of fruits of 106 Neotropical palm species by 273 vertebrate species, especially birds (50%) and mammals (45%), but also fish (3%) and reptiles (2%). Fruit‐eating involved all four taxonomic vertebrate classes whereas seed‐eating and pulp‐eating were only recorded among birds and mammals. Most fruit‐eating interactions (77%) resulted in positive interaction outcomes for plants (e.g. gut‐passed seeds are viable or seeds are successfully dispersed), regardless of the digestive processing type of vertebrate consumers (seed defecation versus regurgitation). The majority of pulp‐eating interactions (91%) also resulted in positive interaction outcomes, for instance via pulp removal that promoted seed germination or via dispersal of intact palm seeds by external transport, especially if animals have a good fruit‐handling ability (e.g. primates, and some parrots). By contrast, seed‐eating interactions mostly resulted in dual outcomes (60%), where interactions had both negative effects on seed survival and positive outcomes through seed caching and external (non‐digestive) seed dispersal. A detailed synthesis of available field studies with qualitative and quantitative information provided evidence that 12 families and 27 species of mammals and birds are predominantly on the mutualistic side of the continuum whereas five mammalian families, six mammal and one reptile species are on the antagonistic side. The synthesis also revealed that most species can act as partial mutualists, even if they are typically considered antagonists. Our review demonstrates how different consumption behaviours and feeding types of vertebrate fruit consumers can influence seed dispersal and regeneration of palms, and thus ultimately affect the structure and functioning of tropical ecosystems. Variation in feeding types of animal consumers will influence ecosystem dynamics via effects on plant population dynamics and differences in long‐distance seed dispersal, and may subsequently affect ecosystem functions such as carbon storage. The quantification of intra‐ and inter‐specific variation in outcomes of plant–frugivore interactions – and their positive and negative effects on the seed‐to‐seedling transition of animal‐dispersed plants – should be a key research focus to understand better the mutualism–antagonism continuum and its importance for ecosystem dynamics.

What's the choice for goji: Lycium barbarum L. or L. chinense Mill.?

ETHNOPHARMACOLOGICAL RELEVANCE

For over one millennium, goji berries have been used traditionally as food and medicine in eastern Asia. In recent decades, it has become increasingly popular globally. However, the biocultural development of goji is poorly known. The botanical origin of goji is controversial: in many but not all modern regional or international quality standards, L. barbarum is accepted exclusively as the botanical origin of goji.

AIM OF THE STUDY

Focusing on historical, biogeographical, botanical, phytochemical and pharmacological data, the overarching aim is to understand the biological origin of goji's historical uses, as well as whether the two species can be used interchangeably.

MATERIALS AND METHODS

The taxonomic literature on L. barbarum and L. chinense were analysed, followed by a study of botanical specimens and fieldwork. Historical herbals and gazetteers were employed to define the historical producing areas and medical properties of goji. An identification of the species used in history was carried out. In a final step the phytochemical and pharmacological literature on the species was compared.

RESULTS AND DISCUSSION

Due to their morphological similarity and different accessibility, fruits of both L. barbarum and L. chinense have been used interchangeably as food and medicine at least since 682 CE. While the fruit of L. barbarum was recognized to be superior in quality, the fruit of L. chinense was commonly used as an equivalent because of its easier accessibility. Cultivation of L. barbarum in China since 1960s improved its availability, which likely lead to its exclusive use as source of goji in China. The long-term safe use with no reported major safety concerns supports that these two species both are useful sources for medicinal Lycium.

CONCLUSIONS

Medicinal plants had been used traditionally long before they were named in scientific nomenclature system. Therefore, the understanding of traditional herbal knowledge and the adequate use of those traditional medicines require a reliable identification based on archival records. This study developed an approach for the identification of species used historically, with an integrated analysis of specimens, historical herbals, and national gazetteers. Additionally, their different chemical profiles and pharmacological activities indicate that they should not be used interchangeably. Further scientific evidence is required for their safe and effective use.

Sowing forests: a synthesis of seed dispersal and predation by agoutis and their influence on plant communities

Granivorous rodents have been traditionally regarded as antagonistic seed predators. Agoutis (Dasyprocta spp.), however, have also been recognized as mutualistic dispersers of plants because of their role as scatter-hoarders of seeds, especially for large-seeded species. A closer look shows that such definitions are too simplistic for these Neotropical animals because agoutis can influence plant communities not only through seed dispersal of large seeds but also through predation of small seeds and seedlings, evidencing their dual role. Herein, we summarize the literature on plant-agouti interactions, decompose agouti seed dispersal into its quantitative and qualitative components, and discuss how environmental factors and plant traits determine whether these interactions result in mutualisms or antagonisms. We also look at the role of agoutis in a community context, assessing their effectiveness as substitutes for extinct megafaunal frugivores and comparing their ecological functions to those of other extant dispersers of large seeds. We also discuss how our conclusions can be extended to the single other genus in the Dasyproctidae family (Myoprocta). Finally, we examine agoutis' contribution to carbon stocks and summarize current conservation threats and efforts. We recorded 164 interactions between agoutis and plants, which were widespread across the plant phylogeny, confirming that agoutis are generalist frugivores. Seed mass was a main factor determining seed hoarding probability of plant species and agoutis were found to disperse larger seeds than other large-bodied frugivores. Agoutis positively contributed to carbon storage by preying upon seeds of plants with lower carbon biomass and by dispersing species with higher biomass. This synthesis of plant-agouti interactions shows that ecological services provided by agoutis to plant populations and communities go beyond seed dispersal and predation, and we identify still unanswered questions. We hope to emphasise the importance of agoutis in Neotropical forests.

Ticks and rickettsial exposure in lowland tapirs (Tapirus terrestris) of three Brazilian biomes

This study evaluated ticks and rickettsial exposure in 220 free-ranging lowland tapirs, Tapirus terrestris, from 2006 to 2018 in selected areas of three major biomes of Brazil - Atlantic Forest, Pantanal, and Cerrado. Overall, a total of 5970 tick specimens representing the following nine species were collected from tapirs: Amblyomma brasiliense, Amblyomma coelebs, Amblyomma dubitatum, Amblyomma ovale, Amblyomma parvum, Amblyomma sculptum, Amblyomma triste, Haemaphysalis juxtakochi, and Rhipicephalus microplus. Amblyomma sculptum was the most prevalent and abundant tick species in all three biomes; however, mean intensity values for A. sculptum were significantly lower in Atlantic Forest than in the Pantanal or Cerrado, and at the same time, statistically similar among tapirs from Pantanal and Cerrado. Contrastingly, mean intensity values for A. coelebs were significantly higher in the Atlantic Forest than in the other biomes. The remaining tick species were collected in lower numbers, or were exclusive for one biome, e.g., A. brasiliense and H. juxtakochi only in the Atlantic Forest. A total of 177 blood sera (123 individuals plus 54 recaptures) were collected from tapirs and tested for the presence of reactive antibodies to six Rickettsia species by immunofluorescence assay. Overall, 69% (9/13), 49% (62/126), and 66% (25/38) tapir sera from Atlantic Forest, Pantanal and Cerrado, respectively, were seroreactive to at least one Rickettsia species, with no significant difference between the three areas. Although many tapir sera reacted simultaneously to ≥2 Rickettsia species, Rickettsia parkeri elicited highest % seroprevalence and endpoint titers, and was incriminated as the possible agent involved in a homologous reaction in tapirs from the three biomes, where A. ovale was previously found infected by R. parkeri. In fact, seroconversion to R. parkeri was demonstrated in five tapirs that were captured at least twice during the study. This study demonstrated that tapirs were found to be constantly infested by several tick species in the Atlantic Forest, Pantanal and Cerrado biomes; however, the richness of tick infestations was concordant to the tick species known to be established in each biome. Under natural conditions, lowland tapirs were shown to be exposed to tick-borne spotted fever group rickettsiae.

Microstructure of the Surface of the Tongue and Histochemical Study of the Lingual Glands of the Lowland Tapir (Tapirus terrestris Linnaeus, 1758) (Perissodactyla: Tapiridae)

Simple Summary

This is a detailed study of the surface morphology of the tongue and the lingual glands of the lowland tapir (Tapirus terrestris), which expands the understanding of the adaptation of this species to habitats. The histological and ultrastructural analysis of the lingual papillae and lingual glands revealed the presence of two types of mechanical papillae, namely the filiform and conical papillae, while papillae with taste buds (including the fungiform papillae, vallate papillae, and foliate papillae) formed the second, less numerous group. The filiform papillae differed from those of Equidae or Rhinocerotidae. The presence of nine vallate papillae, localized in groups of two surrounded by a ring, or individually, was unique for the examined female tapir. In addition, the vallate papillae contained irregular pseudopapillae on their surface. The foliate papillae contained several sulci between each folia. The presence of sparse taste buds in the side wall of the vallate papillae and foliate papillae is unique for the tapir. Compared to other Perissodactyla, the number of taste buds in the tapir is limited, although the features of its tongue surface make it possible to distinguish this species from representatives of Equidae or Rhinocerotidae.

Abstract

Although the anatomy of the gastrointestinal tract has been characterized in the lowland tapir (Tapirus terrestris), the exact anatomy of its tongue has not been studied. Samples of the lingual papillae and lingual glands were collected from the tongue of an adult female lowland tapir. The microscopic analysis of the structure of the lingual papillae and the histochemical analysis of the secretion of the lingual glands were analyzed. The tongue of the tapir is divided into the apex, body with a distinct lingual prominence, and the root. Its ventral surface is smooth. The most numerous of the mechanical papillae were the filiform papillae, while numerous conical papillae with a sharp apex or more rounded papillae were present in the root of the tongue. There were also nine vallate papillae and pair of foliate papillae. The foliate papillae contained several folds parted by 12–14 grooves. The mucous secretion produced by the lingual glands was more obvious than the serous secretion. The features of the dorsal surface of the tongue as well as the shape and number of the lingual papillae on the surface of the tongue of the examined female tapir differ compared to Equidae or Rhinocerotidae, the other two representatives of Perissodactyla. However, further study is necessary for the synapomorpy of the tapir’s tongue.

Chewing, dental morphology and wear in tapirs (Tapirus spp.) and a comparison of free-ranging and captive specimens

Feeding practice in herbivorous mammals can impact their dental wear, due to excessive or irregular abrasion. Previous studies indicated that browsing species display more wear when kept in zoos compared to natural habitats. Comparable analyses in tapirs do not exist, as their dental anatomy and chewing kinematics are assumed to prevent the use of macroscopic wear proxies such as mesowear. We aimed at describing tapir chewing, dental anatomy and wear, to develop a system allowing comparison of free-ranging and captive specimens even in the absence of known age. Video analyses suggest that in contrast to other perissodactyls, tapirs have an orthal (and no lateral) chewing movement. Analysing cheek teeth from 74 museum specimens, we quantified dental anatomy, determined the sequence of dental wear along the tooth row, and established several morphometric measures of wear. In doing so, we showcase that tapir maxillary teeth distinctively change their morphology during wear, developing a height differential between less worn buccal and more worn lingual cusps, and that quantitative wear corresponds to the eruption sequence. We demonstrate that mesowear scoring shows a stable signal during initial wear stages but results in a rather high mesowear score compared to other browsing herbivores. Zoo specimens had lesser or equal mesowear scores as specimens from the wild; additionally, for the same level of third molar wear, premolars and other molars of zoo specimens showed similar or less wear compared specimens from the wild. While this might be due to the traditional use of non-roughage diet items in zoo tapirs, these results indicate that in contrast to the situation in other browsers, excessive tooth wear appears to be no relevant concern in ex situ tapir management.

trnL outperforms rbcL as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins (Cebus capucinus, Primates)

DNA metabarcoding is a powerful tool for assessing the diets of wild animals, but there is no clear consensus on which proposed plant barcoding marker is most suitable for dietary analysis. This study compares two DNA plant barcoding markers that are commonly used for dietary analyses from degraded DNA, rbcL and trnL, to detailed dietary observations of wild white-faced capuchins (Cebus capucinus). Observational dietary data and fecal samples (n = 170) were collected for one year from a group of individually recognizable monkeys at La Suerte Biological Field Station, Costa Rica. DNA was extracted and portions of the rbcL and trnL chloroplast were amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed using obitools. Of the two barcoding markers tested, trnL yielded greater numbers of sequences with equal sequencing effort, higher resolution taxonomic identifications (albeit with a larger reference database), and identified a greater number of families also found in the observed diet. There was no relationship between observed capuchin feeding behavior and dietary composition based on either sequence occurrence or relative abundance of sequences using rbcL as a marker. However, dietary composition based on the relative abundance of trnL sequences was significantly positively associated with the observed percentage of feeding and foraging time capuchins' spent on each plant species. Additionally, in 35% of cases, the relative abundance of trnL sequences assigned to particular plant families in fecal samples was highly positively correlated with time spent consuming plants from those same families. Our results indicate that trnL is a more robust DNA metabarcoding marker for plant dietary analysis and may potentially be used to quantitatively assess differences in diet within or between species.

Effects of seasonality and habitat on the browsing and frugivory preferences of Tapirus terrestris in north-western Amazonia

Herbivore foraging is influenced by spatial and seasonal changes in the production of leaves and fruits. To understand how herbivores respond to these changes, it is necessary to identify their habitat preferences and how they use the vegetation available. In the Neotropical region, one of the largest terrestrial herbivores is the lowland tapir (Tapirus terrestris), a species important for its dual role as browser and seed disperser. The objective of this study was to determine the species and plant components (leaves, fruits) utilized by T. terrestris in different time periods and habitats, in relation to changes in food availability in the north-western Amazon. Tapir diet was established through identification of browsing signs and faecal analysis, from data collected in the field during the months of March, April, August and September of 2015. Plant species availability for browsing was sampled in ten 2 × 50-m transects and fruit productivity was estimated in linear transects (~9 km). We found that T. terrestris mostly consumed vegetative parts, i.e. fibre (70–90%), and to a lesser extent fruits (10–30%). Food consumption was selective and concentrated in habitats with higher availability of preferred plants. When fruit intake increased, selectivity in browsing became more intense and limited to preferred species. This information, coupled with our findings about seasonal differences in browsing vs. frugivory patterns, provides valuable knowledge for understanding how environmental heterogeneity may influence the foraging ecology of the lowland tapir.

Empty forest or empty rivers? A century of commercial hunting in Amazonia

The Amazon basin is the largest and most species-rich tropical forest and river system in the world, playing a pivotal role in global climate regulation and harboring hundreds of traditional and indigenous cultures. It is a matter of intense debate whether the ecosystem is threatened by hunting practices, whereby an "empty forest" loses critical ecological functions. Strikingly, no previous study has examined Amazonian ecosystem resilience through the perspective of the massive 20th century international trade in furs and skins. We present the first historical account of the scale and impacts of this trade and show that whereas aquatic species suffered basin-wide population collapse, terrestrial species did not. We link this differential resilience to the persistence of adequate spatial refuges for terrestrial species, enabling populations to be sustained through source-sink dynamics, contrasting with unremitting hunting pressure on more accessible aquatic habitats. Our findings attest the high vulnerability of aquatic fauna to unregulated hunting, particularly during years of severe drought. We propose that the relative resilience of terrestrial species suggests a marked opportunity for managing, rather than criminalizing, contemporary traditional subsistence hunting in Amazonia, through both the engagement of local people in community-based comanagement programs and science-led conservation governance.

Populations, pools, and peccaries: simulating the impact of ecosystem engineers on rainforest frogs

Peccary wallows and footprints are important breeding pools for rainforest frogs. We performed a resource supplementation experiment with artificial pools, simulating peccary actions, in a population of the poison frog Allobates femoralis. The population almost doubled resulting from increased local reproduction, but not from immigration. These findings demonstrate the importance of “ecosystem engineers,” such as peccaries, for other species, the frogs. Our results also indicate that human engineering may help to protect amphibian populations.

“Ecosystem engineering” describes habitat alteration by an organism that affects another organism; such nontrophic interactions between organisms are a current focus in ecological research. Our study quantifies the actual impact an ecosystem engineer can have on another species by using a previously identified model system—peccaries and rainforest frogs. In a 4-year experiment, we simulated the impact of peccaries on a population of Allobates femoralis (Dendrobatidae) by installing an array of artificial pools to mimic a forest patch modified by peccaries. The data were analyzed using a gradual before-after control-impact (gBACI) model. Following the supplementation, population size almost doubled as a result of increased autochthonous recruitment driven by a higher per-capita reproduction of males and a higher proportion of reproducing females. The effect was evenly distributed across the population. The differential response of males and females reflects the reproductive behavior of A. femoralis, as only the males use the aquatic sites for tadpole deposition. Our study shows that management and conservation must consider nontrophic relationships and that human “ecosystem engineering” can play a vital role in efforts against the “global amphibian decline.”

Local and scientific knowledge for assessing the use of fallows and mature forest by large mammals in SE Brazil: identifying singularities in folkecology

BACKGROUND

Local ecological knowledge (LEK) has been discussed in terms of its similarities to and its potential to complement normative scientific knowledge. In this study, we compared the knowledge of a Brazilian quilombola population regarding the habitat use and life habits of large mammals with in situ recordings of the species. We also tested the hypothesis that quilombola LEK has a special focus on the anthropogenic portion of the landscape.

METHODS

The habitats investigated were anthropogenic secondary forests and mature forests in the southeastern Atlantic coast of Brazil. We conducted the faunal survey using the camera-trap method. The sampling effort consisted of deploying 1,217 cameras/day in the mature forests and 1,189 cameras/day in the secondary forests. Statistical comparisons regarding the habitat use of the species were based on the randomization procedure. We interviewed 36 men who were more than 40 years old in the three communities studied. Informal, semi-structured and structured interviews were used. Two variables were considered in the LEK analyses: level of internal agreement and level of convergence with the scientific data.

RESULTS

The camera trap sampling resulted in a total of 981 records. Animals such as opossums, tayras, armadillos and deer showed a non-selective pattern in the use of habitats. In contrast, the coati was more common in mature forests. We found that nearly 40% of the interviewees' responses converged with the scientific data on the use of habitats. However, the LEK on the species' life habits was highly convergent with the scientific data. The hypothesis that secondary forests would have a greater relevance for local knowledge was validated for four of the five analyzed species.

CONCLUSIONS

We suggest two principal considerations of ecological and ethnoecological interest: (1) In the Atlantic Forest of the Ribeira Valley, the secondary forests resulting from shifting cultivation were as attractive to the species as the mature forests; (2) The LEK has a special focus on the more anthropogenic portion of the landscape studied. Finally, we argue that this environmental focus in LEK is part of what makes it different from scientific knowledge and unique in its approach toward local environments.

Estimates of density and sustainable harvest of the lowland tapir Tapirus terrestris in the Amazon of French Guiana using a Bayesian spatially explicit capture–recapture model

The Amazonian moist forest, which covers most of French Guiana, is one of the core habitats for the lowland tapir Tapirus terrestris. Tapirs are hunted in French Guiana, although a law introduced in 2011 restricts hunting to one animal per person per hunting trip. We carried out camera-trap surveys in the Nouragues Nature Reserve for 4 years, with the goal of estimating tapir densities in undisturbed conditions and determining sustainable harvest levels for tapirs in French Guiana. We analysed our data with a Bayesian spatially explicit capture–recapture model, with parameter sharing across surveys to improve estimates, and used the model to calculate derived parameters such as maximum sustainable harvest levels. Density estimates for all four surveys were similar and the model indicated a difference in encounter rates for the two camera models used but no difference in encounter rates or home range sizes for males and females or between years. Based on the calculated density of 0.32 tapir km−2 we estimated sustainable harvest levels at 0.009 tapir km−2. Comparing this value to hunting surveys from 11 sites between 1999 and 2006, we found that hunting levels were unsustainable in at least seven villages. We conclude that even the new restrictive hunting law will not prevent overhunting of tapirs in certain areas and thus stronger regulations are needed. However, because of the remoteness of tapir habitat in many parts of French Guiana tapirs are not immediately threatened in the country as a whole.

Frugivory and seed dispersal by tapirs: an insight on their ecological role

Tapirs are one of the last extant megafauna species that survived the Pleistocene extinctions. Given their size and digestive system characteristics, tapirs might be the last potential seed disperser of plant species that were previously dispersed by other large mammal species that are now extinct. We compiled evidence from 39 published scientific studies showing that tapirs have a key role as seed dispersers and seed predators. Tapirs play an important role either through seed predation or by facilitating the recruitment of seeds over long distances, therefore influencing the diversity of plant species in the ecosystem. Neotropical tapirs might have a unique role as long-distance seed dispersers of large seeds (<20 mm) because they are capable of depositing viable large seeds in favorable places for germination that even large-bodied primates cannot disperse. Given the high diversity of seed species found in tapir diet, more information is needed on the identification of seed traits that allow the survival of seeds in the tapir's gut. Moreover, further studies are necessary on the role of tapirs as seed dispersers and predators; in particular considering spatial patterns of dispersed seeds, seed viability, effect of dung, and seed density in tapir latrines, and the effect of deposition sites on germination and seedling survival. Because all tapir species are highly threatened, it is paramount to identify gaps in our knowledge on the ecological role of tapirs and, in particular, on critical and endangered plant-tapir interactions to avoid possible trophic cascading effects on ecosystem function.

Diet of lowland tapir (Tapirus terrestris) in El Rey National Park, Salta, Argentina

Lowland tapir (Tapirus terrestris) is the largest herbivore in the Neotropics and, in Argentina, it inhabits a variety of habitats from 100 to 2100 m asl. Lowland tapirs importantly influence their habitat structure because they are selective browsers, seed predators and long-distance seed dispersers. However, increased knowledge of tapir ecology is necessary to support the conservation and management of the species in natural and human-modified environments. Between Jun 2002 and Dec 2008 we assessed the tapir's diet in El Rey National Park, Salta, northwestern Argentina. We collected fresh feces and recorded browsing signs, and we recorded direct observations of tapirs while they were feeding. We analyzed 88 feces samples that had been dried and subsequently weighed. Feces were dominated by fibers and leaves (84.09%), while fruit parts represented a small proportion of the weight (15.91%). During the dry months, a greater percentage of seeds were found in the feces, mainly due to the availability of 3 species of Fabaceae fruits. We recorded a total of 57 plant species from 26 families. Tapirs are adapted to extreme habitats, switching their diet from frugivory to herbivory when fruits are scarce. Considering this, forest remnants and even secondary growth fields should be protected from deforestation.

Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms

Predation is often difficult to observe or quantify for species that are rare, very small, aquatic or nocturnal. The assessment of such species' diet can be conducted using molecular methods that target prey DNA remaining in predators' guts and faeces. These techniques do not require high taxonomic expertise, are applicable to soft-bodied prey and allow for identification at the species level. However, for generalist predators, the presence of mixed prey DNA in guts and faeces can be a major impediment as it requires development of specific primers for each potential prey species for standard (Sanger) sequencing. Therefore, next generation sequencing methods have recently been applied to such situations. In this study, we used 454-pyrosequencing to analyse the diet of Powelliphantaaugusta, a carnivorous landsnail endemic to New Zealand and critically endangered after most of its natural habitat has been lost to opencast mining. This species was suspected to feed mainly on earthworms. Although earthworm tissue was not detectable in snail faeces, earthworm DNA was still present in sufficient quantity to conduct molecular analyses. Based on faecal samples collected from 46 landsnails, our analysis provided a complete map of the earthworm-based diet of P. augusta. Predated species appear to be earthworms that live in the leaf litter or earthworms that come to the soil surface at night to feed on the leaf litter. This indicates that P. augusta may not be selective and probably predates any earthworm encountered in the leaf litter. These findings are crucial for selecting future translocation areas for this highly endangered species. The molecular diet analysis protocol used here is particularly appropriate to study the diet of generalist predators that feed on liquid or soft-bodied prey. Because it is non-harmful and non-disturbing for the studied animals, it is also applicable to any species of conservation interest.

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.

A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range

In tropical regions, most primary ecosystems have been replaced by mosaic landscapes in which species must cope with a large shift in the distribution of their habitat and associated food resources. Primates are particularly vulnerable to habitat modifications. Most species persist in small fragments surrounded by complex human-mediated matrices whose structure and connectivity may strongly influence their dispersal and feeding behavior. Behavioral plasticity appears to be a crucial parameter governing the ability of organisms to exploit the resources offered by new matrix habitats and thus to persist in fragmented habitats. In this study, we were interested in the dietary plasticity of the golden-crowned sifaka (Propithecus tattersalli), an endangered species of lemur, found only in the Daraina region in north-eastern Madagascar. We used a DNA-based approach combining the barcoding concept and Illumina next-generation sequencing to (i) describe the species diet across its entire range and (ii) evaluate the influence of landscape heterogeneity on diet diversity and composition. Faeces from 96 individuals were sampled across the entire species range and their contents were analyzed using the trnL metabarcoding approach. In parallel, we built a large DNA reference database based on a checklist of the plant species of the Daraina region. Our results suggest that golden-crowned sifakas exhibit remarkable dietary diversity with at least 130 plant species belonging to 80 genera and 49 different families. We highlighted an influence of both habitat type and openness on diet composition suggesting a high flexibility of foraging strategies. Moreover, we observed the presence of numerous cultivated and naturalized plants in the faeces of groups living in forest edge areas. Overall, our findings support our initial expectation that P. tattersalli is able to cope with the current level of alteration of the landscape and confirm our previous results on the distribution and the dispersal ability of this species.

Functional redundancy and complementarities of seed dispersal by the last neotropical megafrugivores

BACKGROUND

Functional redundancy has been debated largely in ecology and conservation, yet we lack detailed empirical studies on the roles of functionally similar species in ecosystem function. Large bodied frugivores may disperse similar plant species and have strong impact on plant recruitment in tropical forests. The two largest frugivores in the neotropics, tapirs (Tapirus terrestris) and muriquis (Brachyteles arachnoides) are potential candidates for functional redundancy on seed dispersal effectiveness. Here we provide a comparison of the quantitative, qualitative and spatial effects on seed dispersal by these megafrugivores in a continuous Brazilian Atlantic forest.

METHODOLOGY/PRINCIPAL FINDINGS

We found a low overlap of plant species dispersed by both muriquis and tapirs. A group of 35 muriquis occupied an area of 850 ha and dispersed 5 times more plant species, and 13 times more seeds than 22 tapirs living in the same area. Muriquis dispersed 2.4 times more seeds in any random position than tapirs. This can be explained mainly because seed deposition by muriquis leaves less empty space than tapirs. However, tapirs are able to disperse larger seeds than muriquis and move them into sites not reached by primates, such as large forest gaps, open areas and fragments nearby. Based on published information we found 302 plant species that are dispersed by at least one of these megafrugivores in the Brazilian Atlantic forest.

CONCLUSIONS/SIGNIFICANCE

Our study showed that both megafrugivores play complementary rather than redundant roles as seed dispersers. Although tapirs disperse fewer seeds and species than muriquis, they disperse larger-seeded species and in places not used by primates. The selective extinction of these megafrugivores will change the spatial seed rain they generate and may have negative effects on the recruitment of several plant species, particularly those with large seeds that have muriquis and tapirs as the last living seed dispersers.

Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances

While the morphological identification of prey remains in predators' faeces is the most commonly used method to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase chain reaction-based methods are increasingly used to detect prey DNA in the predator food bolus and have proven efficient, delivering highly accurate results. When studying complex diet samples, the extraction of total DNA is a critical step, as polymerase chain reaction (PCR) inhibitors may be co-extracted. Another critical step involves a careful selection of suitable group-specific primer sets that should only amplify DNA from the targeted prey taxon. In this study, the food boluses of five Rattus rattus and seven Rattus exulans were analysed using both morphological and molecular methods. We tested a panel of 31 PCR primer pairs targeting bird, invertebrate and plant sequences; four of them were selected to be used as group-specific primer pairs in PCR protocols. The performances of four DNA extraction protocols (QIAamp(®) DNA stool mini kit, DNeasy(®) mericon food kit and two of cetyltrimethylammonium bromide-based methods) were compared using four variables: DNA concentration, A(260) /A(280) absorbance ratio, food compartment analysed (stomach or faecal contents) and total number of prey-specific PCR amplification per sample. Our results clearly indicate that the A(260) /A(280) absorbance ratio, which varies between extraction protocols, is positively correlated to the number of PCR amplifications of each prey taxon. We recommend using the DNeasy(®) mericon food kit (QIAGEN), which yielded results very similar to those achieved with the morphological approach.