Sains Malaysiana 52(1)(2023): 17-33

http://doi.org/10.17576/jsm-2023-5201-02

 

A Review on Next-Generation Wildlife Monitoring using Environmental DNA (eDNA) Detection and Next-Generation Sequencing in Malaysia

(Kajian Pemantauan Hidupan Liar Generasi Masa Hadapan menggunakan Pengesanan DNA (eDNA) Persekitaran dan Penjujukan Generasi Masa Hadapan di Malaysia)

 

NURSYUHADA OTHMAN1, KAVIARASU MUNIAN1,2, HIDAYAH HARIS1, FARAH FARHANA RAMLI1, NUR HARTINI SARIYATI1, MOHD FAUDZIR NAJMUDDIN1 & MUHAMMAD ABU BAKAR ABDUL-LATIFF1,*

 

1Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600 Muar, Johor Darul Takzim, Malaysia

2Zoology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia

 

Received: 14 February 2022/Accepted: 15 October 2022

 

Abstract

The use of environmental DNA (eDNA) as the genetic tool to monitor biodiversity has been increasing across the world, including Malaysia. Over a decade, the technique has become widely used in wildlife conservation with the technologies called next-generation sequencing (NGS). Unfortunately, as one of the top megadiverse countries, Malaysia is still behind in this field since eDNA methods outperform traditional surveys. Hence, in this study, we analyzed the paper related to eDNA studies in Malaysia, which focused on wildlife monitoring. We conducted a systematic bibliographic search and quantitative review of studies published before June 2021 from Google Scholar and Scopus database. Forty published eDNA studies were found, and each paper was classified based on five themes (species identification, diet assessment, health monitoring, resolve taxonomic, whole-genome sequencing) according to the study analysis. This study aims to identify gaps in eDNA in Malaysia, which can later be useful for future conservation actions and development by applying technology in wildlife monitoring.

 

Keywords: Biodiversity; conservation; environmental DNA; eDNA; next-generation sequencing; NGS

 

Abstrak

Penggunaan DNA persekitaran (eDNA) sebagai alat genetik untuk memantau kepelbagaian biologi telah pun meningkat di seluruh dunia termasuk Malaysia. Setelah sedekad, teknik ini telah digunakan secara meluas dalam pemuliharaan hidupan liar bersama dengan teknologi yang dikenali sebagai penjujukan generasi masa hadapan (NGS). Walau bagaimanapun, Malaysia yang merupakan salah sebuah negara di dunia yang mempunyai kekayaan kepelbagaian biologi yang tinggi masih lagi ketinggalan dalam bidang ini kerana kaedah eDNA sebenarnya mampu mengatasi kaedah tradisi. Dalam ulasan ini, kami telah menganalisis kajian yang berkaitan dengan eDNA di Malaysia yang memberi tumpuan kepada pemantauan hidupan liar. Kami telah menjalankan pencarian secara sistematik biblografi dan juga secara kuantitatif berdasarkan kajian lepas yang telah diterbitkan sehingga Jun 2021 menggunakan Google Scholar dan pangkalan data Scopus. Terdapat 40 kajian eDNA yang telah diterbitkan dan dikelaskan berdasarkan lima tema (pengenalan spesies, penilaian pemakanan, pemantauan kesihatan, penyelesaian taksonomi dan penjujukan keseluruhan genom) mengikut analisis kajian. Tujuan ulasan ini adalah untuk mengenal pasti jurang kajian eDNA di Malaysia yang dapat membantu untuk aktiviti pemuliharaan dan pembangunan masa hadapan dengan menggunakan teknologi yang terkini dalam pemantauan hidupan liar.

 

Kata kunci: DNA persekitaran; eDNA; kepelbagaian biologi; konservasi; NGS; penjujukan generasi masa hadapan

 

REFERENCES

Alberdi, A., Aizpurua, O., Gilbert, M.T.P. & Bohmann, K. 2018. Scrutinizing key steps for reliable metabarcoding of environmental samples. Meth Ecology and Evolution 9: 134-147.

Alfano, N., Dayaram, A., Axtner, J., Tsangaras, K., Kampmann, M-L., Mohamed, A., Wong, S.T., Gilbert, M.T.P., Wilting, A. & Greenwood, A.D. 2021. Non-invasive surveys of mammalian viruses using environmental DNA. Methods in Ecology and Evolution 12: 1941-1952.

Ambardar, S., Gupta, R., Trakroo, D., Lal, R. & Vakhlu, J. 2016. High throughput sequencing: An overview of sequencing chemistry. Indian Journal Microbiology 56(4): 394-404.

Aziz, S.A., Clements, G.R., Peng, L.Y., Campos-Arceiz, A., McConkey, K.R., Forget, P. & Gan, H.M. 2017. Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through illumina next-generation sequencing. PeerJ 5: e3176.

Barnes, M.A., Turner, C.R., Jerde, C.L., Renshaw, M.A., Chadderton, W.L. & Lodge, D.M. 2014. Environmental conditions influence eDNA persistence in aquatic systems. Environmental Science and Technology 48: 1819-1827.

Binladen, J., Gilbert, M.T.P., Bollback, J.P., Panitz, F., Bendixen, C., Nielsen, R. & Willerslev, E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2: 197.

Bohmann, K., Evans, A., Gilbert, M.T., Carvalho, G.R., Creer, S., Knapp, M., Yu, D.W. & de Bruyn, M. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology and Evolution 29(6): 358-367.

Bradley, B.J., Stiller, M., Doran-Sheehy, D.M., Harris, T., Chapman, C.A., Vigilant, L. & Pionar, H. 2007. Plant DNA sequences from feces: Potential means for assessing diets of wild primates. American Journal of Primatology 69: 1-7.

Brandon-Mong, G.J., Gan, H.M., Sing, K.W., Lee, P.S., Lim, P.E. & Wilson, J.J. 2015. DNA metabarcoding of insects and allies: An evaluation of primers and pipelines. Bulletin of Entomological Research 105(6): 717-727.

Burton, A.C., Neilson, E., Moreira, D., Ladle, A., Steenweg, R., Fisher, J.T., Bayne, E. & Boutin, S. 2015. Wildlife camera trapping: a review and recommendations for linking surveys to ecological processes. Journal of Applied Ecology 52: 675-685.

Castañeda-Rico, S., León-Paniagua, L., Edwards, C.W. & Maldonado, J.E. 2020. Ancient DNA from museum specimens and next generation sequencing help resolve the controversial evolutionary history of the critically endangered puebla deer mouse. Frontiers in Ecology and Evolution 8: 94.

Chan, K.S., Tan, J. & Goh, W.L. 2019. Diet profiling of house-farm swiftlets (Aves, Apodidae, Aerodramus sp.) in three landscapes in Perak, Malaysia, using high-throughput sequencing. Tropical Ecology 60(3): 379-388.

Chan, K.S., Tan, J. & Goh, W.L. 2020. Taxonomic assignment of dietary arthropods in Malaysian swiftlets (Aerodramus sp.) based on DNA metabarcoding. Journal of Wildlife and National Parks 35: 73-91.

Chung, H.H., Kamar, C.K.A., Lim, L.W.K., Liao, Y., Lam, T.T. & Chong, Y.L. 2020. Sequencing and characterization of complete mitogenome DNA for Rasbora hobelmani (Cyprinidae) with phylogenetic consideration. Journal of Ichthyology 60(1): 90-98.

Davies, S.E., Goh, W.L., Ball, S.P., Siew, W.S. & Tarburton, M. 2020. Phenotypic variation and polymorphism confirmed among white-bellied swiftlets of the Collocalia esculenta group (Apodidae, Collocaliini) by mitochondrial and nuclear DNA evidence. Bulletin of the British Ornithologists’ Club 140(4): 373-386.

Deagle, B.E., Jarman, S.N., Coissac, E. & Taberlet, P. 2014. DNA metabarcoding and the cytochrome c oxidase subunit I marker: Not a perfect match. Biology Letters 10: 20140562.

Deiner, K., Bik, H.M., Elvira, M., Seymour, M., Creer, S., Bista, I., Lodge, D.M., de-Vere, N., Pfrender, M.E. & Bernatchez, L. 2017. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology 26: 5872-5895.

Drinkwater, R., Schnell, I.B., Bohmann, K., Bernard, H., Veron, G., Clare, E., Gilbert, M.T.P. & Rossiter, S.J. 2019. Using metabarcoding to compare the suitability of two blood‐feeding leech species for sampling mammalian diversity in North Borneo. Molecular Ecology Resources 19(1): 105-117.

Drinkwater, R., Jucker, T., Potter, J.H., Swinfield, T., Coomes, D.A., Slade, E.M., Gilbert, M.T.P., Lewis, O.T., Bernard, H., Struebig, M.J. & Clare, E.L. 2020. Leech blood‐meal invertebrate‐derived DNA reveals differences in Bornean mammal diversity across habitats. Molecular Ecology 30(13): 3299-3312.

Edwards, M.C. & Gibbs, R.A. 1994. Multiplex PCR: Advantages, development and applications. Genome Research 3: 65-75.

Ergüner, B., Üstek, D. & Sağıroğlu, M.S. 2015. Performance comparison of next generation sequencing platforms. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). pp. 6453-6456.

Evans, A.R. 2019. Exploring the biodiversity of the lakes of the Malay Archipelago using environmental DNA metabarcoding. PhD Dissertation (Unpublished).

Farrell, J.A., Whitmore, L. & Duffy, D.J. 2021. The promise and pitfalls of environmental DNA and RNA approaches for the monitoring of human and animal pathogens from aquatic sources. Bioscience 71(6): 609-625.

Ficetola, G.F., Miaud, C., Pompanon, F. & Taberlet, P. 2008. Species detection using environmental DNA from water samples. Biology Letters 4(4): 423-425.

Forestry Department Peninsular Malaysia (FDPM). 2020. https://www.forestry.gov.my/en/2016-06-07-02-53-46/2016-06-07-03-12-29

Hamad, I., Delaporte, E., Raoult, D. & Bittar, F. 2014. Detection of termites and other insects consumed by African Great Apes using molecular fecal analysis. Scientific Reports 4: 4478.

Hebert, P.D., Cywinska, A. & Ball, S.L. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270: 313-321.

Heid, C.A., Stevens, J., Livak, K.J. & Williams, P. 1996. Real time quantitative PCR. Genome Research 6: 986-994.

Helmy, M., Awad, M. & Mosa, K.A. 2016. Limited resources of genome sequencing in developing countries: Challenges and solutions. Applied & Translational Genomics 9: 15-19.

Hibert, F., Taberlet, P., Chave, J., Scotti-Saintagne, C., Sabatier, D. & Richard-Hansen, C. 2013. Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study. PLoS ONE 8(4): e60799.

Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G.A.C. & Baird, D.J. 2011. Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6: e17497.

Ishige, T., Miya, M., Ushio, M., Sado, T., Ushioda, M., Maebashi, K., Yonechi, R., Lagan, P. & Matsubayashi, H. 2017. Tropical-forest mammals as detected by environmental DNA at natural saltlicks in Borneo. Biological Conservation 210: 281-285.

Ishii, K. & Fukui, M. 2001. Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Applied and Environmental Microbiology 67(8): 3753-3755.

Jahari, P.N.S., Mohd Azman, S., Munian, K., Zakaria, N.A., Omar, M.S.S., Richter, S.R. & Mohd Salleh, F. 2021. The first mitochondrial genome data of an old-world fruit bat, Cynopterus sphinx from Malaysia. Mitochondrial DNA Part B 6(1): 53-55.

Kchouk, M., Gibrat, J. & Elloumi, M. 2017. Generations of sequencing technologies: From first to next generation. Biology and Medicine 9(3): 1000395.

Kurata, S., Kanagawa, T., Magariyama, Y., Takatsu, K., Yamada, K., Yokomaku, T. & Kamagata, Y. 2004. Re-evaluation and reduction of a PCR bias caused by reannealing of templates. Applied and Environmental Microbiology 70: 7545-7549.

Lacoursière-Roussel, A., Dubois, Y., Normandeau, E. & Bernatchez, L. 2016. Improving herpetological surveys in eastern North America using the           environmental DNA method. Genome 59: 991-1007.

Lalam, M. 2006. Estimation of the reaction efficiency in polymerase chain reaction. Journal of Theoretical Biology 242: 947-953.

Lavoué, S., Bertrand, J.A., Shen, K.N., Ratmuangkhwang, S., Sado, T., Miya, M. & Siti Azizah, M.N. 2019. Deep genetic differentiation between two morphologically similar species of wolf herrings (Teleostei, Clupeoidei, Chirocentridae). Journal of Applied Ichthyology 35(3): 693-700.

Lee, P.S., Gan, H.M., Clements, G.R. & Wilson, J.J. 2016. Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests. Genome 59(11): 1008-1022.

Liedigk, R., Kolleck, J., Böker, K.O., Meijaard, E., Md-Zain, B.M., Abdul-Latiff, M.A.B., Ampeng, A., Lakim, M., Abdul-Patah, P., Tosi, A.J. & Brameier, M. 2015. Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis). BMC Genomics 16(1): 1-11.

Lim, L.W.K., Chung, H.H., Lau, M.M.L., Aziz, F. & Gan, H.M. 2021. Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers. Gene 791: 145708.

Liu, G., Zhang, S., Zhao, X., Li, C. & Gong, M. 2021. Advances and limitations of next generation sequencing in animal diet analysis. Genes 12(12): 1854.

Lueders, T., Wagner, B., Claus, P. & Friedrich, M.W. 2004. Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic    interactions with fungi and protozoa in oxic rice field soil. Environmental Microbiology 6: 60-72.

Lunt, D.H., Zhang, D.X., Szymura, J.M. & Hewitt, G.M. 1996. The insect cytochrome oxidase I gene: Evolutionary patterns and conserved primers for phylogenetic studies. Insect Molecular Biology 5(3): 153-165.

Luo, C., Tsementzi, D., Kyrpides, N., Read, T. & Konstantinidis, K.T. 2012. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7(2): e30087.

Mace, G.M. 2004. The role of taxonomy in species conservation. Philosophical Transactions of the Royal Society B: Biological Sciences 359(1444): 711-719.

Mallot, E.K., Garver, P.A. & Malhi, R.S. 2018. trnL outperforms rbcL as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faces capuchins (Cebus capucinus, Primates). PLoS ONE 13(6): e0199556.

Manning, S.R. & La Claire II., J.W. 2010. Multiplex PCR methods for the species -specific detection and quantification of Prymnesium parvum (Haptophyta).    Journal of Applied Phycology 22: 587-597.

Mansor, M.S., Halim, M.R.A., Abdullah, N.A., Ramli, R. & Cranbrook, E. 2020. Barn Swallows Hirundo rustica in Peninsular Malaysia: Urban winter roost counts after 50 years, and dietary segregation from house-farmed swiftlets Aerodramus sp. Raffles Bulletin of Zoology 68: 238-248.

Mansor, M.S., Nor, S.M. & Ramli, R. 2018. Assessing diet of the Rufous-winged Philentoma (Philentoma pyrhoptera) in lowland tropical forest using next-generation sequencing. Sains Malaysiana 47(5): 1045-1050.

Matheson, C.D., Gurney, C., Esau, N. & Letho, R. 2010. Assessing PCR inhibition from humic substances. The Open Enzyme Inhibition Journal 3: 38-45.

Mckee, A.M., Spear, S.F. & Pierson, T.W. 2015. The effect of dilution and the use of a post-extraction nucleic acid purification column on the accuracy, precision, and inhibition of environmental DNA samples. Biological Conservation 183: 70-76.

Miyamoto, D.T., Zheng, Y., Wittner, B.S., Lee, R.J., Zhu, H., Broderick, K.T., Desai, R., Fox, D.B., Brannigan, B.W., Trautwein, J., Arora, K.S., Desai, N., Dahl, D.M., Sequist, L.V., Smith, M.R., Kapur, R., Wu, C.L., Shioda, T., Ramaswamy, S., Ting, D.T., Toner, M., Maheswaran, S. & Haber, D.A. 2015. RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance. Science 349(6254): 1351-1356.

Mohd-Azlan, J., Yi, M.C.K., Lip, B. & Hon, J. 2019. Camera trapping of wildlife in the newly established Baleh National Park, Sarawak. Journal of Sustainability Science Management 14(4): 38-51.

Mohd-Yusof, N.S., Abdul-Latiff, M.A.B., Mohd-Ridwan, A.R., Badrulisham, A.S., Othman, N., Yaakop, S., Md-Nor, S. & Md-Zain, B.M. 2022. First report on metagenomic analysis of gut microbiome in Island Flying Fox (Pteropus hypomelanus) revealing latitudinal correlation as opposed to host phylogeny in island populations of Malaysia. Biodiversity Data Journal 10: e69631.

Nasron, A.G., Amir, A.M.A.H., Adam, L., Hasnan, M.S.H., Yazi, M.F., Patah, P.A., Rozi, M.S.F.M., Rasid, A.F.FA. & Cheng, T.C. 2019. Wildlife monitoring at Labis Timur Ecological Corridor (CFS2:PL1) in Johor, Malaysia. Journal of Wildlife and Parks 34: 9-22.

Nurul, A.A.N., Danish-Daniel, A.M., Okomoda, V.T. & Asma, N.A. 2020. Microbiota composition of captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839). Applied Microbiology and Biotechnology 104(17): 7391-7407.

Okomoda, V.T., Nurul, A.N.A., Danish-Daniel, A.M., Oladimeji, A.S., Abol-Munafi, A.B., Alabi, K.I. & Nur, A.A. 2020. Microbiota composition data for wild and captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839). Data in Brief 32: 106120.

Osman, N.A., Abdul-Latiff, M.A.B., Mohd-Ridwan, A.R., Yaakop, S., Nor, S.M. & Md-Zain, B.M. 2020. Diet composition of the wild stump-tailed macaque (Macaca arctoides) in Perlis State Park, Peninsular Malaysia, using a chloroplast tRNL DNA metabarcoding approach: A preliminary study. Animals 10: 2215.

Othman, N., Haris, H., Fatin, Z., Najmuddin, M.F., Sariyati, N.H., Md-Zain, B.M. & Abdul-Latiff, M.A.B. 2021. A review on environmental DNA (eDNA) metabarcoding markers for wildlife monitoring research. IOP Conf. Series: Earth and Environmental Science 736: 012054.

Pompanon, F., Deagle, B.E., Symondson, W.O.C., Brown, D.S., Jarman, S.N. & Taberlet, P. 2012. Who is eating what: Diet assessment using next generation sequencing? Molecular Ecology 21: 1931-1950.

Prévost-Bouré, N.C., Christen, R., Dequiedt, S., Mougel, C., Lelièvre, M., Jolivet, Shahbazkia, H.R., Guillou, L., Arrouays, D. & Ranjard, L. 2011. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR. PLoS ONE 6(9): e24166.

Quandt, D. & Stech, M. 2005 Molecular evolution of the trnLUAA intron in bryophytes. Molecular Phylogenetics and Evolutions 36(3): 429-443.

Quéméré, E., Hibert, F., Miquel, C., Lhuillier, E., Rasolondraibe, E., Champeau, J., Rabarivola, C., Nusbaumer, L., Chatelain, C., Gautier, L., Ranirison, P., Crouau-Roy, B., Taberlet, P. & Chikhi, L. 2013. A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range. PLoS ONE 8(3): e58971.

Rosli, N., Sitam, F.T., Rovie-Ryan, J.J., Gan, H.M., Lee, Y.P., Ithnin, H., Gani, M., Razak, M.F.A.A., Md-Zain, B.M. & Abdullah, M.T. 2019. The complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) from Peninsular Malaysia. Mitochondrial DNA Part B 4(2): 2535-2536.

Roy, M., Belliveau, V., Mandrak, N.E. & Gagné, N. 2018. Development of environmental DNA (eDNA) methods for detecting high-risk freshwater fishes in live trade in Canada. Biology Invasions 20: 299-314.

Ruppert, K.M., Kline, R.J. & Rahman, M.S. 2019. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation 17: e00547.

Sanger, F., Nicklen, S. & Coulson, A.R. 1977. DNA sequencing with chain terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America 74: 5463-5467.

Schloss, P.D., Gevers, D. & Westcott, S.L. 2011. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6(12): e27310.

Shokralla, S., Spall, J.L., Gibson, J.F. & Hajibabaei, M. 2012. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21: 1794-1805.

Smith, C.J. & Osborn, A.M. 2009. Advantages and limitations of quantitative PCR (q-PCR) based approaches in microbial ecology. FEMS Microbiology Ecology 67: 6-20.

Srivathsan, A., Ang, A., Vogler, A.P. & Meier, R. 2016. Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate. Frontiers in Zoology 13: 17.

Sutra, J., Saadu, H., Hashim, A.M., Saad, M.Z., Yasin, I.S.M. & Amal, M.N.A. 2021. Diversity, relative abundance, and functional genes of intestinal microbiota of tiger grouper (Epinephelus fuscoguttatus) and Asian seabass (Lates calcarifer) reared in a semi-closed hatchery in dry and wet seasons. Pertanika Journal of Tropical Agricultural Science 44(2): JTAS-2178-2020.

Suzuki, M.T. & Giovannoni, S.J. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology 62: 625-630.

Taberlet, P., Waits, L.P. & Luikart, G. 1999. Noninvasive genetic sampling: Look before you leap. Trends Ecology Evolution 14: 323-327.

Tan, C.H. & Tan, K.Y. 2021. De novo venom-gland transcriptomics of spine-bellied sea snake (Hydrophis curtus) from Penang, Malaysia - Next-generation sequencing, functional annotation and toxinological correlation. Toxins 13(2): 127.

Tawfik, G.M., Dila, K.A.S., Mohamed, M.Y.F., Tam, D.N.H., Kien, N.D., Ahmed, A.M. & Huy, N.T. 2019. A step by step guide for conducting a systematic review and meta-analysis with simulation data. Tropical Medicine and Health 47: 46.

Thomsen, P.F. & Willerslev, E. 2015. Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation 183: 4-18.

Tillmar, A.O., Dell'Amico, B., Welander, J. & Holmlund, G. 2013. A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures. PLoS ONE 8(12): e83761.

Valentini, A., Miquel, C., Nawaz, M.A., Bellemain, E., Coissac, E., Pompanon, F., Gielly, L., Cruaud, C., Nascetti, G., Wincker, P., Swenson, J.E. & Taberlet, P. 2009. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: The trnL approach. Molecular Ecology Resources 9: 51-60. 

Willerslev, E. & Cooper, A. 2005. Review paper. Ancient DNA. Proceedings of the Royal Society B 272: 3-16.

Wilson, J., Sing, K., Chen, P. & Zieritz, A. 2017. Tracking the southern river terrapin (Batagur affinis) through environmental DNA: Prospects and challenges. Mitochondrial DNA Part A 29(6): 862-866.

Zhong, Q., Bhattacharya, S., Kotsopoulos, S., Olson, J., Taly, V., Griffiths, A.D., Link, D.R. & Larson, J.W. 2011. Multiplex digital PCR: Breaking the one target per color barrier of quantitative PCR. Lab Chip 11: 2167.

Zoqratt, M.Z.H.M., Eng, W.W.H., Thai, B.T., Austin, C.M. & Gan, H.M. 2018. Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: Implications for aquaculture research and management. PeerJ 6: e5826.

 

*Corresponding author; email: latiff@uthm.edu.my

 

 

 

previous