DIETARY ANALYSIS: REPTILES
CROCODILES
Wallace K. M., Leslie A. J. (2008): Diet of the Nile crocodile (Crocodylus niloticus) in the Okavango Delta, Botswana. Journal of Herpetology 42: 361-368.
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The analysis of stomach contents can shed light on patterns of prey availability and foraging habits of a predator; however, recent studies have shown the potential bias in dietary studies resulting from differential digestion rates of various prey items. The stomachs of 286 Nile Crocodiles (17–166 cm snout–vent length) were lavaged over a two-year period. Taking prey residence times into account, the contents were examined for prey eaten within 24 h. Crocodylus niloticus has a similar ontogenetic shift in diet to that of other crocodilians. Yearlings consumed primarily aquatic insecta and arachnida. As crocodile size increased (juveniles), the diet became more diverse including crustacea, amphibia, and fish. The largest size class (subadults) consumed primarily fish. Yearlings fed consistently throughout the year; however a higher proportion of empty stomachs occurred within the juvenile and subadult size classes during the winter months. Seven species of nematodes were found within the stomachs, four of which represent new geographic records.
Laverty T. M., Dobson A. P. (2013): Dietary overlap between black caimans and spectacled caimans in the Peruvian Amazon. Herpetologica 69: 91-101.
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The Black Caiman (Melanosuchus niger) experienced a dramatic population decline in the mid-20th century, becoming extinct or locally rare over most of its range due to habitat destruction and the commercial value of its hide. As the success and re-establishment of the species is now dependent on conservation efforts throughout the Amazon basin, Black Caimans require continuous monitoring despite extensive current legal protection. Although such efforts have mitigated the threat of human harvesting, a key issue facing the species today is ecological competition from sympatric Spectacled Caimans (Caiman crocodilus). In this study, we investigated this inferred competition by detailing the dietary overlap between Black Caimans and Spectacled Caimans in the Pacaya Samiria National Reserve in 2009. Using an adaptation of the hose-Heimlich technique, we collected and then compared the stomach contents of several individuals of each species. We found that although the proportions of prey items in their stomach contents varied seasonally, the dietary overlap between the two species remained high, suggesting intense competition for food resources. In addition to seasonal changes, the diet composition of Black Caimans also shifted ontogenetically. Young Black Caimans primarily ate insects and crustaceans, whereas larger individuals mostly preyed on fish, reducing intraspecific competition between crocodilian adults and young. Our findings suggest that Spectacled Caimans will continue to hinder the recovery of the Black Caiman population.
Brown J. C., Shirley M. H., Yog‐yog A., van Weerd M., Balbas M. G., Tarun B. A., Siler C. D. (2021): Use of diet and body condition assessments as intermediate indicators of translocation success in the Critically Endangered Philippine crocodile (Crocodylus mindorensis). Aquatic Conservation: Marine and Freshwater Ecosystems 31: 2817-2829.
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Intermediate metrics of translocation success are useful for long-lived, slow to mature species where survival and reproduction happen over decades. With fewer than 150 individuals in the wild, the Critically Endangered Philippine crocodile (Crocodylus mindorensis) is one of the most threatened species on Earth. This study presents the first analysis of diet and body condition of wild Philippine crocodiles and headstarted (i.e. captive-reared) individuals released into the wild over the last decade, and uses these results to show how diet and body condition can be pertinent intermediate metrics of translocation success. Analyses of stomach contents revealed 17 different aquatic and terrestrial invertebrate and vertebrate prey species. Interestingly, 70% of Philippine crocodiles showed snails to be the predominent prey type, followed by fish (36.7%), birds (33.3%) and reptiles (33.3%). More than 50% of crocodiles consumed the invasive golden apple snail, a leading agricultural pest. Regardless of crocodile history (wild vs. headstarted) or size class (juvenile vs. adult), no evidence was found for dietary differences in percentage occurrence, percentage composition or prey diversity. Body condition was significantly higher in wild compared with headstarted individuals when analysed together in a pooled group, although neither group differed significantly from the standardized expectation, and headstarted individuals were not significantly different when body condition was derived independently for the two groups. This study provides a working example of how assessing the convergence of diet and body condition between translocated and wild individuals can provide complementary monitoring parameters to demonstrate post-release establishment of translocated crocodylians. The congruent dietary composition and comparable body condition observed in this study suggest that headstarted crocodiles adapt well following release. Crocodylus mindorensis survives in an agricultural landscape and is likely to play an ecologically important role by exploiting invasive species, reinforcing the importance of this species to local communities.
LIZARDS
Angelici F. M., Luiselli L., Rugiero L. (1997): Food habits of the green lizard, Lacerta bilineata, in central Italy and a reliability test of faecal pellet analysis. Italian Journal of Zoology 64: 267-272.
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Food habits of the green lizard (Lacerta bilineata) were studied in some Mediterranean sites of the vicinities of Rome (Latium, central Italy), by means both of stomach dissection of individuals found already dead in the field and faeces analysis of living individuals. The taxonomic diet composition of the lizards was accurately described by both methods, thus demonstrating the reliability of faecal pellet analysis as a non‐cruel method to study lizard diets. However, by using the faeces analysis technique, it is difficult to measure the exact food intake rate (items / unit of time) as well as the size distribution of prey ingested by lizards. There was a remarkable ontogenetic change in the taxonomic diet composition of green lizards: adults essentially consumed beetles and isopods, whereas juveniles fed mainly upon orthopterans, spiders, and Rhynchota. Cannibalism and predation upon small vertebrates (lizards) were very rare events. It is suggested that (i) age‐related differences in microhabitat frequented could explain the dietary differences between young and adult lizards due to different availability of the various prey categories in the various microhabitats, and that (ii) adults and juveniles partition their habitats to reduce intraspecific interference competition.
Brown D. S., Jarman S. N., Symondson W. O. (2012): Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms. Molecular Ecology Resources 12: 259-266.
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Little quantitative ecological information exists on the diets of most invertebrate feeding reptiles, particularly nocturnal or elusive species that are difficult to observe. In the UK and elsewhere, reptiles are legally required to be relocated before land development can proceed, but without knowledge of their dietary requirements, the suitability of receptor sites cannot be known. Here, we tested the ability of non‐invasive DNA‐based molecular diagnostics (454 pyrosequencing) to analyse reptile diets, with the specific aims of determining which earthworm species are exploited by slow worms (the legless lizard Anguis fragilis) and whether they feed on the deeper‐living earthworm species that only come to the surface at night. Slow worm faecal samples from four different habitats were analysed using earthworm‐specific PCR primers. We found that 86% of slow worms (N = 80) had eaten earthworms. In lowland heath and marshy/acid grassland, Lumbricus rubellus, a surface‐dwelling epigeic species, dominated slow worm diet. In two other habitats, riverside pasture and calciferous coarse grassland, diet was dominated by deeper‐living anecic and endogeic species. We conclude that all species of earthworm are exploited by these reptiles and lack of specialization allows slow worms to thrive in a wide variety of habitats. Pyrosequencing of prey DNA in faeces showed promise as a practical, rapid and relatively inexpensive means of obtaining detailed and valuable ecological information on the diets of reptiles.
Kartzinel T. R., Pringle R. M. (2015): Molecular detection of invertebrate prey in vertebrate diets: trophic ecology of Caribbean island lizards. Molecular Ecology Resources 15: 903-914.
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Understanding community assembly and population dynamics frequently requires detailed knowledge of food web structure. For many consumers, obtaining precise information about diet composition has traditionally required sacrificing animals or other highly invasive procedures, generating tension between maintaining intact study populations and knowing what they eat. We developed 16S mitochondrial DNA sequencing methods to identify arthropods in the diets of generalist vertebrate predators without requiring a blocking primer. We demonstrate the utility of these methods for a common Caribbean lizard that has been intensively studied in the context of small island food webs: Anolis sagrei (a semi-arboreal ‘trunk-ground’ anole ecomorph). Novel PCR primers were identified in silico and tested in vitro. Illumina sequencing successfully characterized the arthropod component of 168 faecal DNA samples collected during three field trips spanning 12 months, revealing 217 molecular operational taxonomic units (mOTUs) from at least nine arthropod orders (including Araneae, Blattodea, Coleoptera, Hemiptera, Hymenoptera, Isoptera, Lepidoptera and Orthoptera). Three mOTUs (one beetle, one cockroach and one ant) were particularly frequent, occurring in ≥50% of samples, but the majority of mOTUs were infrequent (180, or 83%, occurred in ≤5% of samples). Species accumulation curves showed that dietary richness and composition were similar between size-dimorphic sexes; however, female lizards had greater per-sample dietary richness than males. Overall diet composition (but not richness) was significantly different across seasons, and we found more pronounced interindividual variation in December than in May. These methods will be generally useful in characterizing the diets of diverse insectivorous vertebrates.
Perez-Cembranos A., Leon A., Perez-Mellado V. (2016): Omnivory of an insular lizard: sources of variation in the diet of Podarcis lilfordi (Squamata, Lacertidae). Plos One 11: e0148947.
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Through 17 years and from a sample of 7,790 faecal pellets and 26,346 prey items, we studied the diet of the Balearic lizard Podarcis lilfordi in Aire Island (Menorca, Balearic Islands, Spain). We analysed the diet in terms of prey frequencies, as well as by their volume and biomass contributions. The diet of the Balearic lizard was extremely variable through the years, months and areas under study. The dominance of small clumped prey, particularly ants, was confirmed. However, the main contribution by volume corresponded to beetles, with a relevant role for Diplopoda and terrestrial Isopoda during some months and at particular areas of the island. Several prey items were probably captured at the base of shrubs, under stones or inside rock crevices. Therefore, our estimations of electivity would only be reliable for epigeal and flying prey. The capacity of the Balearic lizard to include marine subsidies in its diet, such as coastal crustaceans, is noteworthy. Also, its consumption of carrion from carcasses of gulls and rabbits and leftovers from human visitors is remarkable. Juvenile conspecifics can also be a sporadic food resource, especially during the second half of summer, whereas the consumption of vegetal matter is constant for each whole year. The shifts of vegetal exploitation among areas of the island and months take place according to availability of different plant species at each area or during a given period. Thus, lizards are able to conduct a thorough monitoring of plant phenology, exploiting a large variety of plant species. Omnivory does not imply the indiscriminate inclusion of any edible food in its diet. Rather, the inclusion of several food items means the adoption of a wide range of foraging behaviours adapted to the exploitation of each food resource.
Pinho C. J., Santos B., Mata V. A., Seguro M., Romeiras M. M., Lopes R. J., Vasconcelos R. (2018): What is the giant wall gecko having for dinner? Conservation genetics for guiding reserve management in Cabo Verde. Genes 9: 599.
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Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systems.
Lopes R. J., Pinho C. J., Santos B., Seguro M., Mata V. A., Egeter B., Vasconcelos R. (2019): Intricate trophic links between threatened vertebrates confined to a small island in the Atlantic Ocean. Ecology and Evolution 9: 4994-5002.
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Trophic networks in small isolated islands are in a fragile balance, and their disturbance can easily contribute toward the extinction vortex of species. Here, we show, in a small Atlantic island (Raso) in the Cabo Verde Archipelago, using DNA metabarcoding, the extent of trophic dependence of the Endangered giant wall gecko Tarentola gigas on endemic populations of vertebrates, including one of the rarest bird species of the world, the Critically Endangered Raso lark Alauda razae. We found that the Raso lark (27%), Iago sparrow Passer iagoensis (12%), Bulwer’s petrel Bulweria bulwerii (15%), and the Cabo Verde shearwater Calonectris edwardsii (10%) are the most frequent vertebrate signatures found in the feces of the giant wall gecko. This work provides the first integrative assessment of their trophic links, an important issue to be considered for the long-term conservation of these small and isolated island ecosystems.
Pereira A., Xavier R., Perera A., Salvi D., Harris D. J. (2019): DNA metabarcoding to assess diet partitioning and feeding strategies in generalist vertebrate predators: a case study on three syntopic lacertid lizards from Morocco. Biological Journal of the Linnean Society 127: 800-809.
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DNA metabarcoding is a fast and simple alternative to traditional microscopy methods, which have been the main tool for identification of prey in dietary studies of lizards. In this study, we applied a metabarcoding approach based on COI and 16S rRNA amplicons to assess diet partitioning and feeding strategies in three syntopic lizards from Taza, Morocco: Scelarcis perspicillata chabanaudi, Scelarcis perspicillata pellegrini and Podarcis vaucheri. In order to avoid competition, these lizards are expected to consume different prey species because they occupy distinct trophic niches, use different foraging strategies and express different dorsal pigmentation patterns. Given the spotted pattern of S. p. chabanaudi, we hypothesize a sit-and-wait foraging strategy with a less diverse diet and a higher consumption of mobile prey relative to the striped S. p. pellegrini and P. vaucheri which, as potential active foragers, are expected to have a higher diet diversity. Previous diet assessments using microscopy on faecal remains seem to contradict these expectations. Our results show that, as expected, the diet of S. p. chabanaudi is less diverse than the diet of S. p. pellegrini. Regarding P. vaucheri, our dietary data are consistent with the hypothesis that this species behaves as an active forager, owing to its high niche overlap with S. p. pellegrini. Advantages and limitations of molecular barcoding compared with the microscopy approach to the analysis of lizard diets are discussed.
Gil V., Pinho C. J., Aguiar C. A., Jardim C., Rebelo R., Vasconcelos R. (2020): Questioning the proverb ‘more haste, less speed’: classic versus metabarcoding approaches for the diet study of a remote island endemic gecko. PeerJ 8: e8084.
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Dietary studies can reveal valuable information on how species exploit their habitats and are of particular importance for insular endemics conservation as these species present higher risk of extinction. Reptiles are often neglected in island systems, principally the ones inhabiting remote areas, therefore little is known on their ecological networks. The Selvagens gecko Tarentola (boettgeri) bischoffi, endemic to the remote and integral reserve of Selvagens Archipelago, is classified as Vulnerable by the Portuguese Red Data Book. Little is known about this gecko’s ecology and dietary habits, but it is assumed to be exclusively insectivorous. The diet of the continental Tarentola species was already studied using classical methods. Only two studies have used next-generation sequencing (NGS) techniques for this genus thus far, and very few NGS studies have been employed for reptiles in general. Considering the lack of information on its diet and the conservation interest of the Selvagens gecko, we used morphological and DNA metabarcoding approaches to characterize its diet. The traditional method of morphological identification of prey remains in faecal pellets collected over a longer period was compared with metabarcoding of samples collected during rapid surveys. Molecular results revealed that this species is a generalist, feeding on invertebrate, plant and vertebrate items, whereas the morphological approaches were unable to detect the latter two. These results opened up new questions on the ecological role of the Selvagens gecko that deserves to be further explored, such as the possible predation on seabirds, plant services or trophic competition with the sympatric Madeira lizard Teira dugesii. Metabarcoding identified a greater diversity of dietary items at higher taxonomic resolution, but morphological identification enabled calculation of relative abundances and biomasses of ingested arthropods, and detected a dietary shift on invertebrate preys between seasons. Results of this study highlight the global applicability of rapid metabarcoding surveys for understudied taxa on remote islands that are difficult to access. We recommend using the metabarcoding approach, even if ‘speedy’ sampling only is possible, but we must highlight that disregarding long-term ecological data may lead to ‘hasty’ conclusion.
Santamaría S., Enoksen C. A., Olesen J. M., Tavecchia G., Rotger A., Igual J. M., Traveset A. (2020): Diet composition of the lizard Podarcis lilfordi (Lacertidae) on 2 small islands: an individual-resource network approach. Current Zoology 66: 39-49.
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Despite it is widely accepted that intrapopulation variation is fundamental to ecological and evolutionary processes, this level of information has only recently been included into network analysis of species/population interactions. When done, it has revealed non-random patterns in the distribution of trophic resources. Nestedness in resource use among individuals is the most recurrent observed pattern, often accompanied by an absence of modularity, but no previous studies examine bipartite modularity. We use network analysis to describe the diet composition of the Balearic endemic lizard Podarcis lilfordi in 2 islets at population and individual levels, based on the occurrence of food items in fecal samples. Our objectives are to 1) compare niche structure at both levels, 2) characterize niche partition using nestedness and modularity, and 3) assess how size, sex, season, and spatial location influence niche structure. At population-level niche width was wide, but narrow at the level of the individual. Both islet networks were nested, indicating similar ranking of the food preferences among individuals, but also modular, which was partially explained by seasonality. Sex and body size did not notably affect diet composition. Large niche overlap and therefore possibly relaxed competition were observed among females in one of the islets and during spring on both islets. Likewise, higher modularity in autumn suggests that higher competition could lead to specialization in both populations, because resources are usually scarce in this season. The absence of spatial location influence on niche might respond to fine-grained spatio-temporally distribution of food resources. Behavioral traits, not included in this study, could also influence resource partitioning.
Anslan S., Dalgo D., Reinhardt T., Peñafiel N., Guayasamin J., Páez-Rosas D., Vences M., Steinfartz S. (2021): DNA metabarcoding reveals fine scale geographical differences of consumed algae in the Galápagos marine iguanas (Amblyrhynchus cristatus). Amphibia-Reptilia 42: 471-480.
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Galápagos marine iguanas are primarily associated with the marine environment and show special nutritional adaptations. They are the only lizards worldwide that forage on marine macroalgae. Until now, consumed algae have been identified by direct observations during their feeding activities and microscopic identification in faeces samples. In this study, we use a novel DNA metabarcoding approach to identify consumed algal species from the faeces of marine iguanas. We developed primers for the ribulose-bisphosphate carboxylase (rbcL) gene and applied a metabarcoding approach to 25 individual faeces samples collected in four representative sites of two subspecies (Amblyrhynchus cristatus mertensi and A. c. godzilla), found in the San Cristóbal Island. We detected 18 consistently occurring macroalgal operational taxonomic units (OTUs). Most of the OTUs were assigned to Rhodophyta (red algae) and only one OTU to Chlorophyta (green algae). Despite the number of consumed algal species did not differ between two subspecies (OTU richness; P = 0.383), diet overlap level between A. c. mertensi and A. c. godzilla was low (Schoener index = 0.345), suggesting that both subspecies consumed different algal species in their natural environment. Further studies are needed to understand whether the difference of consumed algae reflects disparities in the abundance of algal species between sites, or whether iguanas of the two genetically differentiated subspecies prefer distinct algal species.
Kurita T., Toda M. (2022): Comparison of morphological identification and DNA metabarcoding for dietary analysis of faeces from a subtropical lizard. Wildlife Research 50: 224-236.
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The common methods for detecting prey in faeces are traditional morphological examination of digested prey remains and faecal DNA (fDNA) metabarcoding. Although recent studies have shown that fDNA metabarcoding can identify prey that is excreted without morphologically identifiable remains, it is unclear whether fDNA metabarcoding provides a more comprehensive assessment of diet than morphological analyses. We aimed to compare prey detection abilities of morphological and fDNA-metabarcoding assays by evaluating similarities and differences of estimated prey communities. We also aimed to provide the first comprehensive prey composition of an endangered ground-dwelling gecko, Goniurosaurus kuroiwae, which will contribute to the conservation management of this species. We identified the prey consumed by G. kuroiwae by morphological examination and fDNA metabarcoding using the same series of faecal samples. For these two methods, we compared the overall community composition of prey items and the detection rate for each prey type. We also tested for environmental and ontogenetic variation of the composition of prey items consumed. When comparing the two methods there were significant differences in the composition of prey communities that were identified from the same series of faecal samples. The fDNA metabarcoding analyses showed the higher rate of detection of earthworms, amphipods and coleopteran and lepidopteran larvae, which lack hard exoskeleton or have small body sizes. The morphological assay allowed identification of a few prey types, including spiders and earwigs, more frequently than fDNA metabarcoding. Combined use of both methods revealed that G. kuroiwae consumed large-sized invertebrates with a slight ontogenetic shift from small-sized invertebrates to large-sized ones. Although fDNA metabarcoding showed the higher overall prey detection rate, it did not include all the prey items detected by morphological analysis. The complementary use of both methods can yield better understanding of the prey composition of invertebrate-consuming animals represented by reptiles and amphibians. We have shown that the most comprehensive reconstruction of prey composition from faeces will be achieved by combining results from both fDNA metabarcoding and morphological analyses.
Rato C., Dellinger T., Carretero M. A. (2022): Dietary variation is driven by landscape heterogeneity in an insular omnivorous endemic lizard, revealed by DNA metabarcoding. Diversity 14: 1078.
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Living on islands entails numerous challenges for animals, among which population density approaching the carrying capacity of trophic resources stands out. To overcome this limitation, many insular lizards can supplement their insectivorous diet with increasing portions of plant material. The Madeira wall lizard, Teira dugesii, is a medium-sized lacertid, endemic to the Madeira and Selvagens archipelagos. As common in this family, adults are sexually dimorphic with males being bigger than females. Previous dietary studies on morphological scatology identified a higher proportion of plant over animal prey items, changing according to the location and sex. Here, we used DNA metabarcoding to examine the diet of this lizard species quantifying it at a higher taxonomical resolution and enhancing the detection of soft-body prey that often go undetected in morphology-based studies. In a sample of 151 faecal samples from eight populations including different habitats and altitudes in Madeira, we identified 289 prey items belonging to eight animal and three plant Classes, encompassing 58 distinct orders and 140 families. Of these, 63 were identified up to the species level. The results support a strong trend towards herbivory in this species with plants representing almost 74% of the diet occurrences in contrast to the 26% of animal prey. Remarkably, the plant fraction of the diet remained stable across localities but varied with size and mass in males. As males grew bigger and heavier, they significantly increased their plant matter intake. Likely, larger bodies and abdomens allowed allocating longer and more complex digestive tracts harbouring intestinal flora to better decompose plant organic compounds. This allowed heavier animals to have a richer diet regime. However, diet richness and composition were not affected by either sex or size, while the locality had a significant effect on both diet components likely in response to local variation in prey availability. By including an increasing plant fraction into a primarily insectivorous diet, this insular lizard has not only enlarged its trophic niche but is also able to exploit more efficiently the highly variable resources provided by insular environments.
Tercel M. P., Moorhouse‐Gann R. J., Cuff J. P., Drake L. E., Cole N. C., Goder M., Mootoocurpen R., Symondson W. O. (2022): DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair’s skink (Leiolopisma telfairii). Ecology and Evolution 12: e8484.
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Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair’s skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair’s skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair’s skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration.
Alemany I., Pérez-Cembranos A., Pérez-Mellado V., Castro J. A., Picornell A., Ramon C., Jurado-Rivera J. A. (2023): DNA metabarcoding the diet of Podarcis lizards endemic to the Balearic Islands. Current Zoology 69: 514-526.
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Dietary studies are essential to unravel the functioning of ecosystems and ultimately to understand biodiversity. This task, which at first may seem simple, becomes especially complex in those cases of omnivorous species with highly variable diets. In this regard, the emergence of next-generation DNA sequencing methodologies represents a powerful tool to address the problem. Here we implement a high-throughput metabarcoding strategy based on the analysis of four molecular markers aimed at sequencing both mitochondrial (animal prey) and chloroplast (diet plants) genome fragments from fecal samples of two lizard species endemic to the Balearic Archipelago (Podarcis lilfordi and P. pityusensis) obtained through non-invasive methods. The results allowed for the characterization of their diets with a high degree of taxonomic detail and have contributed a large number of new trophic records. The reported diets are based mainly on the consumption of arthropods, mollusks and plants from a diversity of taxonomic orders, as well as carrion and marine subsidies. Our analyses also reveal inter- and intra-specific differences both in terms of seasonality and geographical distribution of the sampled lizard populations. These molecular findings provide new insights into the trophic interactions of these threatened endemic lizards in their unique and isolated ecosystems.
Pekár S., Gajski D., Mifková T., Smolinský R., Gojak T., Martišová M. (2023): Natural diet of European Green Lizards, Lacerta viridis (Squamata: Lacertidae): A comparison of macroscopic and molecular identification methods. Herpetologica 79: 135-143.
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An analysis of the diets of reptiles is essential for understanding the role of reptiles in the ecosystem and the employment of successful conservation management plans. For this purpose, noninvasive and invasive methods to identify consumed prey have been used. Here, we investigated the diet of male and female European Green Lizards (Lacerta viridis) by sampling fecal pellets across 2 yr in the spring and late summer at a single site. We used the following two methods for identifying prey remnants from fecal samples: the classical macroscopic approach that requires competent expert knowledge and the molecular approach based on the dietary metabarcoding of nondegraded prey remnant DNA. According to both methods, lizards consumed mainly insects belonging to 13 orders, with Coleoptera as the dominant prey. The number of prey taxa was similar between the sexes, but the prey composition at the genus level was significantly different, with males capturing some coleopterans more than females. The diets also differed significantly between season. In the spring, lizards consumed many more prey types and many more coleopteran specimens than in late summer. The proportion of identified prey taxa was significantly different between the identification methods. From the total of identified prey, macroscopic identification yielded only about 50% of taxa, whereas molecular identification yielded more than 80% of taxa. Our results show that molecular identification can recover a much higher number of prey than the macroscopic method, yet not all prey. Thus, the integration of both methods best described the natural diet and complex trophic interactions of European Green Lizards.
Pinho C. J., Darwish M., Šmíd J., Carranza S., Vasconcelos R. (2023): Green matters: Dietary assessment of a reptile community using DNA metabarcoding. Global Ecology and Conservation 47: e02667.
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DNA metabarcoding is widely used for diet characterization and is becoming increasingly important for biodiversity conservation, allowing the understanding of trophic networks and community assemblies. However, to our knowledge, few studies have used this approach to investigate trophic interactions for whole communities and none for reptiles. In particular, few studies have examined the diet composition of Saudi Arabian reptiles, and all have used classical methods only. Therefore, in this work, a non-invasive approach using DNA metabarcoding of faecal pellets was implemented to investigate the diet composition of the reptile community of Wadi Ashar, in AlUla County, north-western Saudi Arabia Kingdom. In the overall diet composition of the community, arthropods were present in 90% of the samples, and plants were present in 63%, revealing the unforeseen importance of plants to this community as a secondary, but also a primary dietary item. For some species, this is the first time that plants have been reported in their diet. A significant effect of reptile body size on diet composition was also demonstrated, indicating its strong influence on prey selection and resource partitioning in the community. This study highlights the importance of community assessments and the power of combining these with non-invasive DNA metabarcoding to accurately assess biodiversity and feeding habits, revealing unknown ecological interactions of often neglected groups. This revolutionary tool for conservation and management provided rapid and holistic information at relatively low costs, allowing to inform local authorities about which elements are central to the sustainable management of the Wadi Ashar community.
Hernández M., Ancona S., Hereira‐Pacheco S., Díaz de la Vega‐Pérez A. H., Alberdi A., Navarro‐Noya Y. E. (2024): Seasonal dietary changes relate to gut microbiota composition depending on the host species but do not correlate with gut microbiota diversity in arthropod‐eating lizards. Molecular Ecology 33: e17426.
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The animal gut microbiota is strongly influenced by environmental factors that shape their temporal dynamics. Although diet is recognized as a major driver of gut microbiota variation, dietary patterns have seldom been linked to gut microbiota dynamics in wild animals. Here, we analysed the gut microbiota variation between dry and rainy seasons across four Sceloporus species (S. aeneus, S. bicanthalis, S. grammicus and S. spinosus) from central Mexico in light of temporal changes in diet composition. The lizard microbiota was dominated by Firmicutes (now Bacillota) and Bacteroidota, and the closely related species S. aeneus and S. bicanthalis shared a great number of core bacterial taxa. We report species-specific seasonal changes in gut microbiota diversity and composition: greater alpha diversity during the dry compared to the rainy season in S. bicanthalis, the opposite pattern in S. aeneus, and no seasonal differences in S. grammicus and S. spinosus. Our findings indicated a positive association between gut bacterial composition and dietary composition for S. bicanthalis and S. grammicus, but bacterial diversity did not increase linearly with dietary richness in any lizard species. In addition, seasonality affected bacterial composition, and microbial community similarity increased between S. aeneus and S. bicanthalis, as well as between S. grammicus and S. spinosus. Together, our results illustrate that seasonal variation and dietary composition play a role in shaping gut microbiota in lizard populations, but this is not a rule and other ecological factors influence microbiota variation.
Thuo D., Macgregor N. A., Merson S. D., Scopel D., Keogh J. S., Kenny J., Williams J. L., Guest T., Swan S., McAlpin S., Joseph L. (2024): Metabarcoding clarifies the diet of the elusive and vulnerable Australian tjakura (Great Desert Skink, Liopholis kintorei). Frontiers in Ecology and Evolution 12: 1354138.
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Accurately quantifying the diet of species has implications for our understanding of their ecology and conservation. Yet, determining the dietary composition of threatened and elusive species in the wild is often difficult. This study presents the first dietary assessment of tjakura (Liopholis kintorei) using non-invasive sampling of scats and high-throughput sequencing techniques. The tjakura in Uluru consumed 48 invertebrates, 27 plants, and two vertebrate taxa. Fruit flies (Leucophenga spp.), beetles (Harpalus spp. and Omorgus spp.), mosquitos (Culicidae spp.), termites (Termitidae spp.), spiked mallow (Malvastrum americanum), bush tomatoes (Solanum centrale), and wild turnip (Brassica tournefortii) comprised the majority of the diet. Analysis of similarity revealed that food items did not differ significantly between tjakura age groups, seasons, or time since the last fire, however, adults, hot season, and fire scar of 2018 showed a relatively higher prey diversity. These high similarities in diet composition between age classes and fire scars indicate potential intraspecific competition when food resources are scarce. The diet diversity and potential plasticity observed in this study reflect a dietary ecology influenced by food availability rather than preference. Our study demonstrates that scat DNA metabarcoding is an important complementary tool to conventional scat analysis or indigenous knowledge as most food items we identified were previously not recorded through those methods.
SNAKES
Reading C., Jofré G. (2013): Diet composition changes correlated with body size in the Smooth snake, Coronella austriaca, inhabiting lowland heath in southern England. Amphibia-Reptilia 34: 463-470.
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The diet of Smooth snakes (Coronella austriaca) inhabiting lowland heath in southern England was studied over a nine-year period (2004-2012) by analysing 226 faecal samples obtained from 19 females and 41 males of varying age/size from juveniles to sexually mature adults. The main prey species belonged to the families Lacertidae (48%), Soricidae (32%) and Muridae (13%) with the remaining 7% comprising Anguidae (6%), Colubridae (0.5%) and Bufonidae (0.5%). Small mammals were absent from the diet of the smallest snakes but were a major component in the diet of large snakes. Lacertids were a major component of the diet of juvenile snakes whilst they formed a progressively smaller part of the diet of adult snakes. The data demonstrates a shift in diet, with increasing snake size, from Lacertids to small mammals. The highest number of small mammals was found in the diet during the early part of the activity period (April-June) with females apparently preying mainly upon Lacertids in late summer (August-October). A detailed understanding of the diet of C. austriaca, and how it changes with increasing snake body size, may have implications for the conservation of the species in the UK. Management of heathland that damages the preferred habitat of small Lacertids, the main prey of the smallest juvenile snakes, is likely to have a negative impact on recruitment and, as a consequence, a negative impact on the survival of C. austriaca populations.
Brown D. S., Ebenezer K. L., Symondson W. O. (2014): Molecular analysis of the diets of snakes: changes in prey exploitation during development of the rare smooth snake Coronella austriaca. Molecular Ecology 23: 3734-3743.
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Reptiles are declining in many parts of the world, mainly due to habitat loss and environmental change. A major factor in this is availability of suitable food. For many animals, dietary requirements shift during developmental stages and a habitat will only be suitable for conserving a species if it supports all stages. Conventional methods for establishing diet often rely on visual recognition of morphologically identifiable features of prey in faeces, regurgitation or stomach contents, which suffer from biases and poor resolution of taxa. DNA‐based techniques facilitate noninvasive analysis of diet from faeces without these constraints. We tested the hypothesis that diet changes during growth stages of smooth snakes (Coronella austriaca), which have a highly restricted distribution in the UK but are widespread in continental Europe. Small numbers of the sympatric grass snake (Natrix natrix) were analysed for comparison. Faecal samples were collected from snakes and prey DNA analysed using PCR, targeting amphibians, reptiles, mammals and invertebrates. Over 85% of smooth snakes were found to have eaten reptiles and 28% had eaten mammals. Predation on mammals increased with age and was entirely absent among juveniles and subadults. Predation on reptiles did not change ontogenetically. Smooth snakes may, therefore, be restricted to areas of sufficiently high reptile densities to support young snakes.
Ortiz-Catedral L., Christian E., Skirrow M. J., Rueda D., Sevilla C., Kirtana K., Reyes E. M., Daltry J. C. (2019): Diet of six species of Galapagos terrestrial snakes (Pseudalsophis spp.) inferred from fecal samples. Herpetology Notes 12: 701-704.
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The Galapagos terrestrial snakes, or ‘Galapagos racers’ (Pseudalsophis spp.) are a monophyletic group of nine species within Dipsadidae, exclusively found in the Galapagos Islands. To contribute to the knowledge of the feeding ecology of Galapagos racers, and to shed light on the biology of these poorly studied reptiles, we conducted a field study on the prey diversity of six species at nine localities in the Galapagos Islands from 2015 to 2018. We examined 79 faecal samples opportunistically collected in the field during our ongoing studies on the morphological variability of Galapagos racers and, in particular, the demographics of Floreana racers (P. biserialis biserialis). We obtained faecal samples using a palpation technique.
Jones M. D., Crane M. S., Silva I. M., Artchawakom T., Waengsothorn S., Suwanwaree P., Strine C. T., Goode M. (2020): Supposed snake specialist consumes monitor lizards: diet and trophic implications of king cobra feeding ecology. Ecology 101: e03085.
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The king cobra (Ophiophagus hannah) is an iconic elapid snake species distributed throughout tropical forests from southwestern India to the Philippines, and southern China to the Indonesian archipelago (Stuart et al., 2012). As the generic epithet suggests, king cobras are thought to specialize on snake prey. Documenting feeding habits of snakes in nature can be difficult due to their low detectability and long intervals between feeding bouts (Maritz et al., 2018). Radiotelemetry allows researchers to reliably locate individuals, making it possible to document predation by direct observation in the field.
Durso A. M., Kieran T. J., Glenn T. C., Mullin S. J. (2022): Comparison of three methods for measuring dietary composition of Plains Hog-nosed Snakes. Herpetologica 78: 119-132.
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Wild animal diets are challenging to quantify, and the various methods for doing so have strengths and weaknesses. Combining multiple methods can allow ecologists to assess their level of confidence in particular results, increase sample size, and investigate diet over varying time scales. The biases of traditional gut content–based methods are mostly well understood. Newer methods may have important biases that can only be worked out through comparison to established ones. We collected data on the diet of wild Plains Hog-nosed Snakes (Heterodon nasicus) using multiple, fundamentally dissimilar methods, combined analytically using a Bayesian framework to describe an ontogenetic dietary shift. Gut contents were the most straightforward, but yielded a small sample size that fell below any reasonable threshold for making generalizations. Stable isotopes indicated an obvious ontogenetic dietary shift, but were labor-intensive, and conclusions are limited by multiple methodological caveats including similarity among prey groups, maternal carryover effects, and uncertainty in trophic enrichment factors. Fecal environmental DNA (eDNA) was intermediate in terms of effort, yielding results congruent with the other two methods, but the interpretation of which would likely have been confounded by contaminants had we not used all three methods in tandem. Several apparent artifacts are discussed. There are some reassuring similarities among methods. There are also several differences. The most complete picture uses data from all methods taken together. Future studies should attempt to compare the biases, expense, and potential drawbacks of these and other methods in greater detail.
Swinehart A., Partridge C., Russell A., Thacker A., Kovach J., Moore J. (2023): Diet of a threatened rattlesnake (eastern massasauga) revealed by DNA metabarcoding. Ecology and Evolution 13: e10029.
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Characterizing the diet of imperiled species using minimally invasive methods is crucial to understanding their ecology and conservation requirements. Here, we apply a DNA metabarcoding approach to study the diet of the eastern massasauga rattlesnake (Sistrurus catenatus), a Federally Threatened snake found throughout the Great Lakes region. Eighty-three fecal samples collected across 10 different massasauga populations located in Michigan, USA, were sequenced, with 70 samples containing prey DNA. We used universal metazoan primers and developed a host-specific oligonucleotide blocker to characterize their diet. We identified at least 12 different prey species, with eastern massasaugas exhibiting opportunistic feeding and a strong preference towards small mammals. Meadow voles (Microtus pennsylvanicus) were the most common prey item (70% of diet) followed by the northern short-tailed shrew (Blarina brevicauda) and masked shrew (Sorex cinereus; 15.7% of diet each), along with occasional bird and snake prey. Adult individuals exhibited a more generalized diet, consuming a larger number of prey taxa on average. Younger snakes consumed a smaller variety of prey items and tended to consume smaller-sized mammals such as masked shrews (Sorex cinereus) and northern short-tailed shrews (Blarina brevicauda). We conclude that small mammals are a crucial part of eastern massasauga rattlesnake diet and recommend this be taken into consideration when conservation strategies are developed. The methods developed in this study can be applied to other reptile species, providing an accurate, minimally invasive, and thorough diet assessment for at-risk reptile species.
TURTLES
Koizumi N., Mori A., Mineta T., Sawada E., Watabe K., Takemura T. (2017): Plant species identification using fecal DNAs from red-eared slider and Reeves’ pond turtle in agricultural canals for rural ecosystem conservation. Paddy and Water Environment 15: 723-730.
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Fecal DNA samples from the red-eared slider and Reeves’ pond turtle, suspected pests of lotus root paddies, were used to identify the plant species eaten by these turtles in order to develop a strategy for rural ecosystem conservation. The fecal samples were obtained from young and adult individuals (mostly female) of both species living in agricultural canals surrounding lotus root paddies in Tokushima Prefecture, Japan. The samples were screened for the presence or absence of DNA from nine plant species using PCR and plant species-specific primers for the rbcL gene of chloroplast DNA. In the red-eared slider, our analysis identified seven plant species in the fecal DNA samples of adults and three plant species in those of young individuals. In Reeves’ pond turtle, our analysis identified two plant species from adult fecal samples and one species from those of young individuals. Thus, adult red-eared sliders consume a greater range of plants than young red-eared sliders or Reeves’ pond turtles. Both turtle species, independently of age, consumed lotus plants and were likely to cause feeding damage to lotus roots. Considering the plant species detected in adult red-eared sliders and these plant habitats, we suggest that this adult turtle is likely to travel between the agricultural canals and the lotus root paddies. These findings will help the development of strategies for preventing damage to lotus roots by these turtles; furthermore, they indicate that fecal DNA analysis will be applicable to investigation of the feeding habits of other animal species.
Ottonello D., D’Angelo S., Oneto F., Malavasi S., Zuffi M. A. L. (2017): Feeding ecology of the Sicilian pond turtle Emys trinacris (Testudines, Emydidae) influenced by seasons and invasive aliens species. Ecological Research 32: 71-80.
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Feeding ecology of a species is the result of its evolutionary history, biology, physiology and local constraints, such as prey availability, intra‐ and inter‐specific interactions and environmental characteristics. In this study we investigated the still unknown diet of the Sicilian pond turtle, with special emphasis to the relationships with recently introduced alien species in the “Lake Preola and Gorghi Tondi” Nature Reserve (Sicily, Italy). A total of 83 faecal samples were collected in three different periods. Emys trinacris seems an opportunistic and generalist species. The main prey taxa were aquatic invertebrates, including the invasive Procambarus clarkii, while non‐aquatic preys are found sporadically. Plant matter, mainly leaves and roots of aquatic forms, was also found in high frequency with a high occurrence of fruits and seeds in spring. We did not find a significant difference in diet composition within sex and age, while an evident divergence was found between periods and sites. In particular, we noticed a decrease in prey abundance and in food‐niche breadth from pre‐reproductive period to post‐reproductive period. Moreover a very clear difference was found between a site with allochthonous fishes and a site fish‐free, with a more abundant and wide diet spectrum in the last one, as a result of the increased availability of prey. We highlighted the importance to take any possible actions to avoid the spread of fishes in other basins and to study the indirect impact of Procambarus clarkii, as possible vector of harmful trace element.
Cunha F. L., Bernhard R., Vogt R. C. (2020): Diet of an assemblage of four species of turtles (Podocnemis) in the Rio Uatumã, Amazonas, Brazil. Copeia 108: 103-115.
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The structure and functioning of freshwater turtle communities remain understudied topics, especially in tropical regions where biodiversity is higher. The objective of our study was to compare the diets of Podocnemis erythrocephala, P. expansa, P. sextuberculata, and P. unifilis living in syntopy in Amazonas, Brazil. We tested for qualitative and quantitative variations in the way different species used the same available food resources. We collected fresh stomach flushings from all turtles captured in trammel nets in three lakes in 2012. Sampling was conducted in the four distinct tropical seasons: beginning of rainy season (rising water), peak of rainy season (rapidly rising water), end of rainy season (highest flooded forest water level), and dry season (when water levels were receding). We tested the hypothesis that different food items are available in different quantities at different times of the year due to the seasonality of fruiting trees and other plants in response to the wet and dry conditions. We examined whether food items consumed were related to turtle body size and if there was feeding niche overlap among species. Podocnemis sextuberculata consumed the least amount of food by volume, while P. expansa consumed the highest diversity of food items. All four species are primarily herbivorous, and their diets were composed mainly of fruits and seeds (85.4% mean proportion by volume). Genipa americana (Rubiaceae) was most important in the diet of all species, except in P. sextuberculata. We found some evidence of seasonal differences in the consumption of some plant species. Body size did not influence qualitative (diversity of food items eaten) or quantitative variation of food items (volume), except in P. erythrocephala for which we detected a significant linear relationship between carapace length and the volume of stomach contents. The highest food niche overlap was between P. expansa and P. unifilis, and the lowest niche overlap was between P. erythrocephala and P. sextuberculata. Turtles tended to partition food resources more in areas that had more species feeding in syntopy than in areas with fewer syntopic species.
Ducotterd C., Crovadore J., Lefort F., Guisan A., Ursenbacher S., Rubin J. F. (2020): The feeding behaviour of the European pond turtle (Emys orbicularis, L. 1758) is not a threat for other endangered species. Global Ecology and Conservation 23: e01133.
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Molecular technologies, such as metabarcoding, have become powerful tools for conservation purposes. Here, we present a non-invasive study analyzing the diet of one population of European pond turtle (Emys orbicularis) during its whole activity period and of four other populations during the same period, based on faecal sample, and using for the first time on this species, a long metabarcoding approach. Emys orbicularis is an emblematic freshwater species of wetlands in Europe. In several countries, this species is endangered and, in Switzerland, Emys orbicularis is ranked as critically endangered on the Swiss Red List. A national conservation program was created to reintroduce this species and raised the question if this reintroduced species could be a threat for other endangered species. We developed a new method of long metabarcoding analysis, using universal PCR primers to determine prey species occurrence in the faeces. The analysis conducted on 174 faeces collected on 142 individuals revealed 1153 preys from 270 species. Emys orbicularis consumed plants throughout the year with a more diverse diet during the reproduction period (April–June). This study therefore not only determines precisely the omnivorous and opportunistic diet of the Emys orbicularis, but also shows that this species is not a threat to its environment, as 85.5% of the consumed species were not list on the Swiss Red List. Moreover, it also demonstrated that the genetic analyses of faeces could be an efficient tool to determine trophic interaction with a high level of precision, yielding promising perspectives for food web ecology.
Ducotterd C., Crovadore J., Lefort F., Rubin J. F., Ursenbacher S. (2021): A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758). Molecular Ecology Resources 21: 433-447.
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High-throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose-1,5-bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL-trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.
Vučenović J., Lindeman P. V. (2021): The diets of the Pearl and Pascagoula map turtles (Graptemys pearlensis and Graptemys gibbonsi). Herpetologica 77: 121-127.
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Patterns of interspecific differences in the diets of nonavian reptiles may be complicated by intraspecific dietary diversity that is related to variation in body size and trophic morphology. Graptemys pearlensis and Graptemys gibbonsi are sister map turtle species endemic to adjacent Gulf Coastal river drainages and both are candidates for federal listing. Little has been reported about the diet of either species. We examined fecal samples collected from turtles captured throughout their respective ranges in the Pearl and Pascagoula river drainages. Females of both species primarily consumed invasive Asian clams (Corbicula spp.), with adult females being nearly exclusively molluscivorous while juvenile females also consumed softer-bodied prey items. Adult males and unsexed juveniles primarily consumed insects; males in particular specialized on trichopteran larvae and also ate more mollusks than did unsexed juveniles. In comparisons to each species’ sympatric congeneric sawback species, the two focal species’ avoidance of sponges caused large interspecific differences. Due to their greater consumption of insect prey than mollusks, unsexed juvenile G. pearlensis and unsexed juvenile and adult male G. gibbonsi were slightly more similar in diet to their respective sympatric congeneric sawbacks than to conspecific large juvenile females and adult females. Scoring of similarity in diet was greatly influenced by strongly predominant prey items found within each class of each species. Future studies of interspecific dietary differences in sympatric species should include consideration of intraspecific variation in diet as it relates to body size and sexual dimorphism.
Díaz-Abad L., Bacco-Mannina N., Madeira F. M., Neiva J., Aires T., Serrao E. A., Regalla A., Patrício A. R., Frade P. R. (2022): eDNA metabarcoding for diet analyses of green sea turtles (Chelonia mydas). Marine Biology 169: 18.
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Understanding sea turtle diets can help conservation planning, but their trophic ecology is complex due to life history characteristics such as ontogenetic shifts and large foraging ranges. Studying sea turtle diet is challenging, particularly where ecological foraging observations are not possible. Here, we test a new minimally invasive method for the identification of diet items in sea turtles. We fingerprinted diet content using DNA from esophageal and cloacal swab samples by metabarcoding the 18S rRNA gene. This approach was tested on samples collected from green turtles (Chelonia mydas) from a juvenile foraging aggregation in the Bijagós archipelago in Guinea-Bissau. Esophagus samples (n = 6) exhibited a higher dietary richness (11 ± 5 amplicon sequence variants (ASVs) per sample; average ± SD) than cloacal ones (n = 5; 8 ± 2 ASVs). Overall, the diet was dominated by red macroalgae (Rhodophyta; 48.2 ± 16.3% of all ASVs), with the main food item in the esophagus and cloaca being a red alga belonging to the Rhodymeniophycidae subclass (35.1 ± 27.2%), followed by diatoms (Bacillariophyceae; 7.5 ± 7.3%), which were presumably consumed incidentally. Seagrass and some invertebrates were also present. Feeding on red algae was corroborated by field observations and barcoding of food items available in the benthic habitat, validating the approach for identifying diet content. We conclude that identification of food items using metabarcoding of esophageal swabs is useful for a better understanding of the relationships between the feeding behavior of sea turtles and their environment.