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研究生:許玉靜
研究生(外文):Hsu, Yu-Jing
論文名稱:臺灣低海拔食肉目動物之排遺DNA分析-兼論人為活動對食肉目動物食性之影響
論文名稱(外文):Fecal DNA analysis of carnivores in lowland Taiwan - Are there anthropogenic influences on carnivore diets?
指導教授:李佩珍李佩珍引用關係町田龍二
指導教授(外文):Pei-Jen Lee ShanerRyuji Machida
學位類別:碩士
校院名稱:國立臺灣師範大學
系所名稱:生命科學系
學門:生命科學學門
學類:生物學類
論文出版年:2021
畢業學年度:109
語文別:英文
論文頁數:151
中文關鍵詞:人類-食肉目動物衝突中階掠食者食性排遺DNA源自人類的食物
外文關鍵詞:DietFecal DNAHuman-carnivore conflictsHuman subsidiesMeso-predator
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由於人類活動的擴張,人類與野生動物間的接觸日益頻繁。許多小型食肉目動物可以容忍相當高程度的人類活動,甚至還能因此獲取額外的利益,例如取食源自人類的食物,以及因其掠食者與競爭者避開人造環境而獲得額外的生存空間。本研究分析臺灣低海拔食肉目動物的排遺內含物,藉以檢測這些動物的食性是否隨人類活動壓力而改變。我針對五個常見小型食肉目物種(鼬獾Melogale moschata, 食蟹獴Herpestes urva, 白鼻心Paguma larvata, 麝香貓Viverricula indica, 石虎Prionailurus bengalensis)共161份排遺樣本,進行次世代定序(NGS)分析。我以排遺樣本點位擷取人類足跡指數(Human Footprint)做為人類活動壓力的指標。本研究結果發現,這些食肉目動物取食範圍極廣,包括數百個屬的植物、脊椎動物與無脊椎動物;其中更有46個植物屬有常見的農作物種類。不同物種的排遺內含物豐富度(fecal content richness;Chao1)存在差異,但食性組成相似度高。食肉目動物排遺內含物豐富度,以及排遺中含有人類相關序列(農作物與家畜序列、人類序列)的頻率,並不隨人類活動壓力高低而變化。雖然這些食肉目動物的取食行為並不隨人類活動壓力而改變,但這不代表他們沒有取食源自人類的食物;事實上,本研究結果顯示他們取食許多源自人類的食物種類。此外,在有人類活動的情況下,食肉目動物不只是能取食到新的食物,還可能接觸其他新的生物(例如寄生蟲、病源、微生物)。利用排遺DNA所蘊含的分子生物訊息,我們可以有效地偵測並瞭解人類與野生動物間之接觸程度與方式的改變。
Human-wildlife contacts are on the rise due to expansion of human activities. Many small-sized carnivores can tolerate human activities, and some may even benefit from anthropogenic food and man-made environments where their predators and competitors avoid. In this study, I investigated the fecal contents of carnivores in lowland Taiwan, and examined whether their fecal contents, and more specifically, their diets change with anthropogenic pressures. I performed fecal content analyses on 161 samples of five common small carnivores (Chinese ferret-badger Melogale moschata, crab-eating mongoose Herpestes urva, masked palm civet Paguma larvata, small Indian civet Viverricula indica, leopard cat Prionailurus bengalensis) with next-generation sequencing (NGS). To quantify anthropogenic pressures, I extracted human footprint values based on the locations of carnivore fecal samples. A wide range of dietary items are identified, including hundreds of genera across plants, vertebrates and invertebrates. Among them I also identified 46 plant genera that contain domesticated, crop species. The carnivore species have different levels of fecal content richness (Chao1) but their dietary compositions are similar. Neither fecal content richness or the occurrences of sequences that are related to anthropogenic activities (sequences of domesticated plants or animals, sequences of Home sapiens) changed with human footprint values. Although the carnivores did not appear to adjust their foraging behaviors in response to different anthropogenic pressures, it does not mean they were not feeding on anthropogenic foods. In fact, my findings suggest that the carnivores had access to a wide range of anthropogenic foods. More importantly, increased contacts with human not only allow the carnivores to feed on novel food resources, they may also expose these animals to other novel biological agents such as parasites, pathogens, and microbes. This study demonstrates the efficacies of using molecular information extracted from fecal DNA to inform potential changes in human-wildlife contacts.
Acknowledgements I
中文摘要 II
Abstract III
Table of Contents V
List of Tables VI
List of Figures VII
List of Appendices VIII
Introduction 1
Materials and Methods 6
Results 13
Discussion 18
References 23
Appendices 48
Alexander, J., Chen, P., Damerell, P., Wang, Y., Hughes, J., Shi, K., and Riordan, P. 2015. Human wildlife conflict involving large carnivores in Qilianshan, China and the minimal paw-print of snow leopards. Biological Conservation, 187, 1-9.
Baker, A. D., and Leberg, P. L. 2018. Impacts of human recreation on carnivores in protected areas. PLOS ONE, 13, e0195436. https://doi.org/10.1371/journal.pone.0195436
Balvočiūtė, M., and Huson, D.H. 2017. SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare? BMC Genomics, 18 (Suppl. 2), 114. doi: 10.1186/s12864-017-3501-4
Becker, D. J., Streicker, D. G., and Altizer, S. 2015. Linking anthropogenic resources to wildlife–pathogen dynamics: a review and meta‐analysis. Ecology Letters, 18, 483-495.
Benítez-López, A., Alkemade, R., and Verweij, P. A. 2010. The impacts of roads and other infrastructure on mammal and bird populations: a meta-analysis. Biological Conservation, 143, 1307-1316.
Best, I., and Pei, K. 2020. Factors influencing local attitudes towards the conservation of leopard cats Prionailurus bengalensis in rural Taiwan. Oryx, 54, 866-872. doi:10.1017/S0030605318000984
Boutin, S. 1990. Food supplementation experiments with terrestrial vertebrates: patterns, problems, and the future. Canadian Journal of Zoology, 68, 203-220.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W. Johnson, A. J. A., and Holmes, S. P. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581-583. doi:10.1038/nmeth.3869
Chang W. T. 2018. A study on diet variation of the carnivore community in northern Taiwan. MS Thesis. Department of Life Science, College of Science, National Taiwan Normal University. Taipei, Taiwan.
Chao, A., Gotelli, N. J., Hsieh, T. C., Sander, E. L., Ma, K. H., Colwell, R. K., and Ellison, A. M. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecological Monographs, 84, 45–67.
Chen H. C. 2012. Food Habits of Three Carnivore Species in Eastern Batongguan Crossing Trail, Yushan National Park. MS Thesis. Department of Natural Resources and Environmental Studies, National Dong Hwa University. Hualien, Taiwan.
Chen, M.T., Liang, Y. J., Kuo, C. C., and Pei, J. C. K. 2016. Home Ranges, Movements and Activity Patterns of Leopard Cats (Prionailurus bengalensis) and Threats to Them in Taiwan. Mammal Study, 41, 77-86.
Chiang P. J. 2007. Ecology and conservation of Formosan clouded leopard, its prey, and other sympatric carnivores in southern Taiwan. PhD dissertation, Virginia Polytechnic Institute and State Univ., Blacksburg, VA.
Chiang, P. J., Pei, K., Vaughan, M. R., and Li, C. F. 2012. Niche Relationships of Carnivores in a Subtropical Primary Forest in Southern Taiwan. Zoological Studies, 51, 500-511.
Chua, M. A. H., Sivasothi, N. and Meier, R. 2016. Population density, spatiotemporal use and diet of the leopard cat (Prionailurus bengalensis) in a human-modified succession forest landscape of Singapore. Mammal Research, 61, 99–108. https://doi.org/10.1007/s13364-015-0259-4
Chuang, S. A., and Lee, L.L. 1997. Food habits of three carnivore species (Viverricula indica, Herpestes urva, and Melogale moschata) in Fushan forest, northern Taiwan. Journal of Zoology, 243, 71-79.
Ciach, M., and Kruszyk, R. 2010. Foraging of white storks Ciconia ciconia on rubbish dumps on non-breeding grounds. Waterbirds, 33,101–104.
Claesson, M. J., O'Sullivan, O., Wang, Q., Nikkilä, J., Marchesi, J.R., Smidt, H., de Vos, W. M., Ross, R. P, and O'Toole, P. W. 2009. Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine. PLOS ONE, 4, e6669. https://doi.org/10.1371/journal.pone.0006669
Corlett, R. T. 2015. The Anthropocene concept in ecology and conservation. Trends in Ecology & Evolution, 30, 36– 41.
Edgar, R. C. 2016. SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences, https://doi.org/10.1101/074161
Edgar, R. C. 2018. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. PeerJ, 6, e4652. doi: 10.7717/peerj.4652. PMID: 29682424; PMCID: PMC5910792.
Fedriani, J. M., Fuller, T. K., and Sauvajot, R. M. 2001. Does availability of anthropogenic food enhance densities of omnivorous mammals? An example with coyotes in southern California. Ecography, 24, 325-331.
Fox-Dobbs, K., Bump, J. K., Peterson, R. O., Fox, D. L., and Koch, P. L. 2007. Carnivore-specific stable isotope variables and variation in the foraging ecology of modern and ancient wolf populations: Case studies from Isle Royale, Minnesota, and La Brea. Canadian Journal of Zoology, 85, 458-471.
Grassman, L., Tewes, M., Silvy, N., and Kreetiyutanont, K. 2005. Spatial organization and diet of the leopard cat (Prionailurus bengalensis) in north-central Thailand. Journal of Zoology, 266, 45-54. doi:10.1017/S095283690500659X
Hannon G (accessed 30 November 2020) FASTX-Toolkit <http://hannonlab.cshl.edu/fastx_toolkit/>.
Hebblewhite, M., White, C. A., Nietvelt, C. G., McKenzie, J. A., Hurd, T. E., Fryxell, J. M., Bayley, S. E., and Paquet, P. C. 2005. Human activity mediates a trophic cascade caused by wolves. Ecology, 86, 2135-2144.
Hsieh, C., Ma, K. H., and Chao, A. 2020. iNEXT: Interpolation and extrapolation for species diversity. R package version 2.0.20.
Irwin, D. M., Kocher, T. D., and Wilson, A. C. 1991. Evolution of the cytochrome b gene of mammals. Journal of Molecular Evolution, 32, 128-144. doi: 10.1007/BF02515385. PMID: 1901092.
Jefferies, R. L., Rockwell, R. F., and Abraham, K. F. 2004. Agricultural Food Subsidies, Migratory Connectivity and Large-Scale Disturbance in Arctic Coastal Systems: A Case Study, Integrative and Comparative Biology, 44, 130–139.
Kumari, P., Dong, K., Eo, K. Y., Lee, W. S., Kimura, J., and Yamamoto, N. 2019. DNA metabarcoding-based diet survey for the Eurasian otter (Lutra lutra): Development of a Eurasian otter-specific blocking oligonucleotide for 12S rRNA gene sequencing for vertebrates. PLOS ONE, 14, e0226253. https://doi.org/10.1371/journal.pone.0226253
Kocher, T. D., Thomas, W. K., Meyer, A., Edwards, S. V., Paabo, S., Villablanca, F. X., and Wilson, A. C. 1989. Dynamics of mitochondrial DNA evolution in aminals: Amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences USA, 86, 6196-6200.
Kounosu, A., Murase, K., Yoshida, A., Maruyama, H., and Kikuchi, T. 2019. Improved 18S and 28S rDNA primer sets for NGS-based parasite detection. Scientific Reports, 9, 15789. https://doi.org/10.1038/s41598-019-52422-z
Lan, Y., Wang, Q., Cole, J. R., and Rosen, G. L. 2012. Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms. PLOS ONE, 7, e32491. https://doi.org/10.1371/journal.pone.0032491
Lin, L. K. 2000. The status and conservation of Taiwan’s mustelids. In HI Griffiths, ed. Mustelids in a modern world. Management and conservation aspects of small carnivore: human interactions. Leiden, the Netherlands: Backhuys Publishers, pp. 331-335.
Lozano, J., Olszańska, A., Morales-Reyes, Z., Castro, A. A., Malo, A. F., Moleón, M., Sánchez-Zapata, J. A., Cortés-Avizanda, A., von Wehrden, H., Dorresteijn, I., Kansky, R., Fischer, J., and Martín-López, B. 2019. Human-carnivore relations: A systematic review. Biological Conservation, 237, 480-492.
Machida, R. J., and Knowlton, N. 2012. PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences. PLOS ONE, 7, e46180. https://doi.org/10.1371/journal.pone.0046180
Machida, R. J., Leray, M., Ho, S., and Knowlton, N. 2017. Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples. Scientific Data, 4, 170027. doi:10.1038/sdata.2017.27
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17, 10-12.
Monterroso, P, Godinho, R, Oliveira, T, Ferreras, P, Kelly, M. J., Morin, D. J., Waits, L. P., Alves, P. C., and Mills, L. S. 2019. Feeding ecological knowledge: the underutilised power of faecal DNA approaches for carnivore diet analysis. Mammal Review, 49, 97-112.
Murphy, W. J., Eizirik, E., O’Brien, S.J., Madsen, O., Scally, M., Douady, C. J., Teeling, E., Ryder, O. A., Stanhope, M. J., de Jong, W. W., and Springer, M. S. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science, 294, 2348–2351.
Murray, M., Cembrowski, A., Latham, A. D. M., Lukasik, V. M., Pruss, S., and St Clair, C. C. 2015. Greater consumption of protein‐poor anthropogenic food by urban relative to rural coyotes increases diet breadth and potential for human–wildlife conflict. Ecography, 38, 1235-1242.
Newsome, T.M., Ballard, G.A., Fleming, P.J.S., van de Ven, R., Story, G. L., and Dickman, C.R. 2014. Human-resource subsidies alter the dietary preferences of a mammalian top predator. Oecologia, 175, 139-150. https://doi.org/10.1007/s00442-014-2889-7
Newsome, T. M., Dellinger, J. A., Pavey, C. R., Ripple, W. J., Shores, C. R., Wirsing, A. J., and Dickman, C. R. 2015. The ecological effects of providing resource subsidies to predators. Global Ecology and Biogeography, 24, 1-11.
Newsome, D., and Rodger, K. 2008. To feed or not to feed: a contentious issues in wildlife tourism. Lunney, D., Munn, A., and Meikle W. (Eds.), Too Close for Comfort: Contentious Issues in Human-Wildlife Encounters, Royal Zoological Society of New South Wales, Mosman , pp. 255-270.
Oro, D., Genovart, M., Tavecchia, G., Fowler, M. S., and Martínez‐Abraín, A. 2013. Ecological and evolutionary implications of food subsidies from humans. Ecology Letters, 16, 1501-1514.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., and Glöckner, F. O. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41, D590-D596.
Riaz, T., Shehzad, W., Viari, A., Pompanon, F., Taberlet, P., and Coissac, E. 2011. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research, 39, e145.
Rognes. T., Flouri, T., Nichols, B., Quince, C., and Mahé, F. 2016. VSEARCH: a Versatile open source tool for metagenomics. PeerJ, 4, e2584. doi:10.7717/peerj.2584
Shehzad, W., Riaz, T., Nawaz, M.A., Miquel, C., Poillot, C., Shah, S.A., Pompanon, F., Coissac, E., and Taberlet, P. 2012. Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Molecular Ecology, 21, 1951-1965.
Trombulak, S. C., and Frissell, C. A. 2000. Review of ecological effects of roads on terrestrial and aquatic communities. Conservation Biology, 14, 18-30.
Venter, O., Sanderson, E. W., Magrach, A., Allan, J.R., Beher, J., Jones, K.R., Possingham, H.P., Laurance, W.F., Wood, P., Fekete, B.M., Levy, M. A., and Watson, J. E. 2018. Last of the Wild Project, Version 3 (LWP-3): 2009 Human Footprint, 2018 Release. Palisades, NY: NASA Socioeconomic Data and Applications Center (SEDAC). https://doi.org/10.7927/H46T0JQ4. Accessed 1st December 2020
Vestheim, H., and Jarman, S. N. 2008. Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology, 5, 12. https://doi.org/10.1186/1742-9994-5-12
Vilo, C., and Dong, Q. 2012. Evaluation of the RDP classifier accuracy using 16S rRNA gene variable regions. Metagenomics. 1. 10.4303/mg/235551.
Wang, H., and Fuller, T. K. 2003. Food habits of four sympatric carnivores in southeastern China. Mammalia, 67. 10.1515/mamm-2003-0405.
Wang, Q., Garrity, G. M., Tiedje, J., and Cole, J. R. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261-5267. doi:10.1128/AEM.00062-07
Wong, R. H. 2011. Establishment and Application of a Method for Species Identification from Fecal DNA of Sympatric Carnivores. MS Thesis. Department of Natural Resources and Environmental Studies, National Dong Hwa University. Hualien, Taiwan.
Xiong, M., Wang, D., Bu, H., Shao, X., Zhang, D., Li, S., Wang, R., and Yao, M. 2017. Molecular dietary analysis of two sympatric felids in the Mountains of Southwest China biodiversity hotspot and conservation implications. Scientific Reports, 7, 41909.
Yen, S. C., Ju, Y. T., Shaner, P. J. L., and Chen, H. L. 2019. Spatial and temporal relationship between native mammals and free-roaming dogs in a protected area surrounded by a metropolis. Scientific Reports, 9, 8161.
Young, J. K., K. A. Olson, R. P. Reading, S. Amgalanbaatar, and J. Berger. 2011. Is wildlife going to the dogs? Impacts of feral and free‐roaming dogs on wildlife populations. BioScience, 61, 125– 132.
Zhou, Y., Zhang, J., Slade, E., Zhang, L., Palomares, F., Chen, J., Wang, X., and Zhang, S. 2008. Dietary Shifts in Relation to Fruit Availability among Masked Palm Civets (Paguma larvata) in Central China, Journal of Mammalogy, 89, 435–447. https://doi.org/10.1644/07-MAMM-A-048R1.1
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