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Hernández M, Hereira-Pacheco S, Alberdi A, Díaz DE LA Vega-Pérez AH, Estrada-Torres A, Ancona S, Navarro-Noya YE. DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species (Phrynosomatidae: Sceloporus). Integr Zool 2024; 19:480-495. [PMID: 37550887 DOI: 10.1111/1749-4877.12755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Diet composition and its ecological drivers are rarely investigated in coexisting closely related species. We used a molecular approach to characterize the seasonal variation in diet composition in four spiny lizard species inhabiting a mountainous ecosystem. DNA metabarcoding revealed that the lizards Sceloporus aeneus, S. bicanthalis, S. grammicus, and S. spinosus mostly consumed arthropods of the orders Hemiptera, Araneae, Hymenoptera, and Coleoptera. The terrestrial lizards S. aeneus and S. bicanthalis mostly predated ants and spiders, whereas the arboreal-saxicolous S. grammicus and saxicolous S. spinosus largely consumed grasshoppers and leafhoppers. The taxonomic and phylogenetic diversity of the prey was higher during the dry season than the rainy season, likely because reduced prey availability in the dry season forced lizards to diversify their diets to meet their nutritional demands. Dietary and phylogenetic composition varied seasonally depending on the species, but only dietary composition varied with altitude. Seasonal dietary turnover was greater in S. spinosus than in S. bicanthalis, suggesting site-specific seasonal variability in prey availability; no other differences among species were observed. S. bicanthalis, which lives at the highest altitude in our study site, displayed interseasonal variation in diet breadth. Dietary differences were correlated with the species' feeding strategies and elevational distribution, which likely contributed to the coexistence of these lizard species in the studied geographic area and beyond.
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Affiliation(s)
- Mauricio Hernández
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Stephanie Hereira-Pacheco
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Aníbal H Díaz DE LA Vega-Pérez
- Consejo Nacional de Ciencia y Tecnología-Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Arturo Estrada-Torres
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Sergio Ancona
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Yendi E Navarro-Noya
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, San Felipe Ixtacuixtla, Tlaxcala, Mexico
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Tobe A, Sato Y, Wachi N, Nakanishi N, Izawa M. Seasonal diet partition among top predators of a small island, Iriomote Island in the Ryukyu Archipelago, Japan. Sci Rep 2024; 14:7727. [PMID: 38565931 PMCID: PMC10987585 DOI: 10.1038/s41598-024-58204-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Small islands tend to lack predators because species at higher trophic levels often cannot survive. However, two exceptional top predators-the Iriomote cat Prionailurus bengalensis iriomotensis, and the Crested Serpent Eagle Spilornis cheela perplexus-live on the small Iriomote Island in the Ryukyu Archipelago. To understand how these predators coexist with limited resources, we focused on their seasonal diets between which conflicts are considered to occur. To compare the diets, we used DNA metabarcoding analysis of faecal samples. In the summer, we identified 16 unique prey items from Iriomote cat faecal samples and 15 unique prey items from Crested Serpent Eagle faecal samples. In the winter, we identified 37 and 14, respectively. Using a non-metric multidimensional scaling and a permutational multivariate analysis of variance, our study reveals significant differences in the diet composition at the order level between the predators during both seasons. Furthermore, although some prey items at the species-to-order level overlapped between them, the frequency of occurrence of most prey items differed in both seasons. These results suggest that this difference in diets is one of the reasons why the Iriomote cat and the Crested Serpent Eagle are able to coexist on such a small island.
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Affiliation(s)
- Alisa Tobe
- Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan.
- Wildlife Research Center, Kyoto University, Sakyo, Kyoto, Japan.
| | - Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- Research Laboratory Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Nakatada Wachi
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Taketomi, Okinawa, Japan
| | - Nozomi Nakanishi
- Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Kitakyushu Museum of Natural History and Human History, Kitakyushu, Fukuoka, Japan
| | - Masako Izawa
- Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan.
- Kitakyushu Museum of Natural History and Human History, Kitakyushu, Fukuoka, Japan.
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Alemany I, Pérez-Cembranos A, Pérez-Mellado V, Castro JA, Picornell A, Ramon C, Jurado-Rivera JA. DNA metabarcoding the diet of Podarcis lizards endemic to the Balearic Islands. Curr Zool 2023; 69:514-526. [PMID: 37637311 PMCID: PMC10449427 DOI: 10.1093/cz/zoac073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/06/2022] [Indexed: 08/29/2023] Open
Abstract
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.
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Affiliation(s)
- Iris Alemany
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
| | - Ana Pérez-Cembranos
- Department of Animal Biology, Universidad de Salamanca, Campus Miguel de Unamuno s/n, 37007, Salamanca, Spain
| | - Valentín Pérez-Mellado
- Department of Animal Biology, Universidad de Salamanca, Campus Miguel de Unamuno s/n, 37007, Salamanca, Spain
| | - José Aurelio Castro
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
| | - Antònia Picornell
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
| | - Cori Ramon
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
| | - José A Jurado-Rivera
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
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Swinehart A, Partridge C, Russell A, Thacker A, Kovach J, Moore J. Diet of a threatened rattlesnake (eastern massasauga) revealed by DNA metabarcoding. Ecol Evol 2023; 13:e10029. [PMID: 37122773 PMCID: PMC10131807 DOI: 10.1002/ece3.10029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
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.
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Affiliation(s)
- Alyssa Swinehart
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
| | - Charlyn Partridge
- Annis Water Resources InstituteGrand Valley State UniversityMuskegonMichiganUSA
| | - Amy Russell
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
| | - Arin Thacker
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
| | - Jennifer Kovach
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
| | - Jennifer Moore
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
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Nordstrom B, Mitchell N, Byrne M, Jarman S. A review of applications of environmental DNA for reptile conservation and management. Ecol Evol 2022; 12:e8995. [PMID: 35784065 PMCID: PMC9168342 DOI: 10.1002/ece3.8995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 11/28/2022] Open
Abstract
Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio-temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.
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Affiliation(s)
- Bethany Nordstrom
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Nicola Mitchell
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Margaret Byrne
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation SciencePerthWestern AustraliaAustralia
| | - Simon Jarman
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- UWA Oceans InstituteThe University of Western AustraliaCrawleyWestern AustraliaAustralia
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Rajabizadeh M, Morinière J, Rajaei H. Adaptation to the hottest spot on earth: Dietary ecology of an enigmatic desert gecko based on DNA metabarcoding. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mahdi Rajabizadeh
- Department of Biodiversity Institute of Science and High Technology and Environmental Sciences Graduate University of Advanced Technology Kerman Iran
- Inria Startup StudioAI.Nature Team Paris France
| | - Jérôme Morinière
- Advanced Identification Methods – AIM GmbH Niemeyerstr 1 Leipzig Germany
| | - Hossein Rajaei
- Entomology Department State Museum of Natural History Stuttgart Germany
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Petrosky AL, Rowsey DM, Heaney LR. Molecular assessment of dietary niche partitioning in an endemic island radiation of tropical mammals. Mol Ecol 2021; 30:5858-5873. [PMID: 34460971 DOI: 10.1111/mec.16158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 07/27/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023]
Abstract
Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here, we use DNA metabarcoding to investigate dietary niche partitioning in an endemic radiation of mammals in the Philippines. Our data reveal niche partitioning as well as phylogenetically-uncorrelated adaptive evolution in this small mammal community. Because 70% of the focal species belong to the tribe Chrotomyini, an endemic Philippine radiation of murid rodents that feed extensively on earthworms, this study sheds light on dietary adaptation and its role in the co-occurrence of closely related species. Our results reveal fine-scale resource partitioning within this community; our data provide compelling evidence for niche partitioning of diet that was masked by previous diet categories and will help in further dissecting the model adaptive radiation of endemic small mammals on Luzon. This study reinforces the notion that DNA metabarcoding can be a valuable tool for investigating both ecological relationships and evolutionary ecology at the community and phylogenetic level, respectively.
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Affiliation(s)
- Anna L Petrosky
- Field Museum of Natural History, Chicago, Illinois, USA.,Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
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Pereira A, Samlali MA, S’Khifa A, Slimani T, Harris DJ. A pilot study on the use of DNA metabarcoding for diet analysis in a montane amphibian population from North Africa. AFR J HERPETOL 2021. [DOI: 10.1080/21564574.2021.1921058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ana Pereira
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Vairão, Portugal
| | - Mohamed Amine Samlali
- Faculty of Sciences Semlalia, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Abderrahim S’Khifa
- Faculty of Sciences Semlalia, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Tahar Slimani
- Faculty of Sciences Semlalia, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - D James Harris
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Vairão, Portugal
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