Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentata in the Philippines
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Abstract. Bautista JA, Manubag JJ, Sumaya NH, Martinez JG, Tabugo SR. 2023. Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentatain the Philippines. Biodiversitas 24: 3063-3072. Biodiversity monitoring is the cornerstone for conserving marine fish species. However, classical methods, like the Fish Visual Census (FVC), are often limited due to sampling difficulties, the occurrence of rare and cryptic organisms, and reliance on a taxonomic expert for species identification. Recently, environmental DNA (eDNA) metabarcoding has been suggested as a non-invasive, powerful tool for biomonitoring. This study evaluates the eDNA approach as complementary tool for the FVC data in species detection and identification of important marine fishes from the marine sanctuary of Dalipuga, Iligan City, Philippines. The findings obtained through the eDNA approach provide insights into identifying significant fish species. Notably, the presence of the Hippocampus kuda Bleeker, 1852 (yellow seahorse), categorized as a vulnerable and threatened species, was detected. Additionally, the study identified Herklotsichthys quadrimaculatus Rüppell, 1837 (bluestripe herring), a native species to the Philippines that may pose potential risks to humans and the ecological balance. Furthermore, two demersal fish species, namely Large-scale whiting (Sillaginops macrolepis Bleeker, 1858) and Large-scale mullet (Planiliza macrolepis Smith, 1846), were also detected. The eDNA approach also delineated the morphologically cryptic fishes from Scaridae (parrotfishes) and Mugilidae (mullet fish) taxa to the species level. The highlight of this study was the detectionof the new Indo-pacific atherinomorine fish species Doboatherina magnidentata, which to the best of our knowledge, was the first record in the Philippine marine waters. Despite the efficiency of the eDNA metabarcoding in fish species detection and identification, the viability of eDNA in the marine environment and biases of the primer limit this method. Thus, the classical method must complement the molecular approach for better taxonomic resolution and community analysis. Future studies were also recommended to use a multigene eDNA approach to improve taxonomic sensitivity and reduce primer biases.
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References
Allen, G.R., 2015. Review of Indo-Pacific coral reef fish systematics: 1980 to 2014. Ichthyological Research, 62, pp.2-8.
DOI:10.1007/s10228-014-0411-1.
Asaad, I., Lundquist, C.J., Erdmann, M.V. and Costello, M.J., 2018. Delineating priority areas for marine biodiversity
conservation in the Coral Triangle. Biological Conservation, 222, pp.198-211. DOI: 10.1016/j.biocon.2018.03.037.
Baird, D., and Hajibabaei, M. 2012. Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-
generation DNA sequencing. Molecular Ecology, Vol. 21 (8), 2039-2044. DOI: 10.1111/j.1365-294X.2012.05519.x.
Bohmann, K., Evans, A., Gilbert, M.T.P., Carvalho, G.R., Creer, S., Knapp, M., Douglas, W.Y. and De Bruyn, M., 2014.
Environmental DNA for wildlife biology and biodiversity monitoring. Trends in ecology & evolution, 29(6), pp.358-
DOI: 10.1016/j.tree.2014.04.003.
Brown, J., Pirrung, M. and McCue, L.A., 2017. FQC Dashboard: integrates FastQC results into a web-based, interactive, and
extensible FASTQ quality control tool. Bioinformatics, 33(19), pp.3137-3139. DOI: 10.1093/bioinformatics/btx373.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T.L., 2009. BLAST+: architecture
and applications. BMC bioinformatics, 10, pp.1-9. DOI: 10.1186/1471-2105-10-421.
Cox, M.P., Peterson, D.A., and Biggs, P.J., 2010. SolexaQA: At-a-glance quality assessment of Illumina second-generation
sequencing data. BMC Bioinformatics 11, 485. DOI: 10.1186/1471-2105-11-485.
Dafforn, K.A., Johnston, E.L., Ferguson, A., Humphrey, C.L., Monk, W., Nichols, S.J., Simpson, S.L., Tulbure, M.G. and Baird,
D.J., 2015. Big data opportunities and challenges for assessing multiple stressors across scales in aquatic
ecosystems. Marine and Freshwater Research, 67(4), pp.393-413. DOI: 10.1071/MF15108.
Deiner, K., Bik, H.M., Mächler, E., Seymour, M., Lacoursière?Roussel, A., Altermatt, F., Creer, S., Bista, I., Lodge, D.M., De
Vere, N. and Pfrender, M.E., 2017. Environmental DNA metabarcoding: Transforming how we survey animal and
plant communities. Molecular ecology, 26(21), pp.5872-5895. DOI: 10.1111/mec.14350.
Deiner, K., Walser, J. C., Machler, E., and Altermatt, F. 2015.
Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA.
Biological Conservation, 183, 53-63. DOI: 10.1016/j.biocon.2014.11.018.
Ebisawa, A., Ohta, I., Uehara, M., Nakamura, H., Kanashiro, K., and Yasui, R. 2016. Life history variables, annual change in sex
ratios with age, and total mortality observed on commercial catch on Pacific steephead parrotfish, Chlorurus
microrhinos in waters off the Okinawa Island, southwestern Japan. Regional Studies in Marine Science, 8, 65-76. DOI:
1016/j.rsma.2016.09.008.
Edwards, C.B., Friedlander, A.M., Green, A.G., Hardt, M.J., Sala, E., Sweatman, H.P., Williams, I.D., Zgliczynski, B., Sandin,
S.A. and Smith, J.E., 2014. Global assessment of the status of coral reef herbivorous fishes: evidence for fishing
effects. Proceedings of the Royal Society B: Biological Sciences, 281(1774), p.20131835. DOI:
1098/rspb.2013.1835.
Evans, N. T., Li, Y., Renshaw, M. A., Olds, B. P., Deiner, K., Turner, C. R., Jerde, C. L., Lodge, D. M., Lamberti, G. A., and
Pfrender, M. E., 2017. Fish community assessment with eDNA metabarcoding: effects of sampling design and
bioinformatic filtering. Canadian Journal of Fisheries and Aquatic Sciences. 74(9): 1362-1374. DOI: 10.1139/cjfas-
-0306.
Go, K.T.B., Anticamara, J.A., de Ramos, J.A.J., Gabona, S.F., Agao, D.F., Hererra, E.C. and Bitara, A.U., 2015. Species richness
and abundance of non-cryptic fish species in the Philippines: a global center of reef fish diversity. Biodiversity and
Conservation, 24, pp.2475-2495. DOI: 10.1007/s10531-015-0938-0.
Gonzales, B.J., Secretariat, I.R. and No, J.M.M.T., 2013. Field guide to coastal fishes of Palawan. Coral Triangle Institute.
González-Castro, M. and Ghasemzadeh, J., 2016. Morphology and morphometry based taxonomy of Mugilidae. Biology, ecology
and culture of grey mullets (Mugilidae), 18(5), pp.1-21.
Hallam, J., Clare, E.L., Jones, J.I. and Day, J.J., 2021. Biodiversity assessment across a dynamic riverine system: A comparison
of eDNA metabarcoding versus traditional fish surveying methods. Environmental DNA, 3(6), pp.1247-1266. DOI:
1002/edn3.241.
Hopkins, G. W., and Freckleton, R. P. 2002. Declines in the numbers of amateur and professional taxonomists: implications for
conservation. Animal conservation forum, Vol 5, No. 3, pp. 245-249. DOI:10.1017/S1367943002002299.
Katoh, K., Rozewicki, J., and Yamada, K. D. 2019. MAFFT online service: multiple sequence alignment, interactive sequence
choice and visualization. Briefings in bioinformatics, 20(4), 1160-1166. DOI: 10.1093/bib/bbx108.
Kelly, R.P., Port, J.A., Yamahara, K.M., Martone, R.G., Lowell, N., Thomsen, P.F., Mach, M.E., Bennett, M., Prahler, E.,
Caldwell, M.R. and Crowder, L.B., 2014. Harnessing DNA to improve environmental
management. Science, 344(6191), pp.1455-1456. DOI: 10.1126/science.1251156.
Kimura, S., Iwatsuki, Y., and Yoshino, T. 2002. A new silverside, Atherinomorus aetholepis sp. nov., from the West Pacific
(Atheriniformes: Atherinidae). Ichthyol Res. 49:240–244. DOI:10.1007/s102280200034.
Labrosse, P., Kulbicki, M. and Ferraris, J., 2002. Underwater visual fish census surveys: proper use and implementation.
Liu, B., Yan, Y., Zhang, N., Guo, H., Liu, B., Yang, J., Zhu, K. and Zhang, D., 2022.
DNA Barcoding Is a Useful Tool for the Identification of the Family Scaridae in Hainan. Journal of Marine Science
and Engineering, 10(12), p.1915. DOI: 10.3390/jmse10121915.
Maestro, M., Pérez-Cayeiro, M.L., Chica-Ruiz, J.A. and Reyes, H., 2019. Marine protected areas in the 21st century: Current
situation and trends. Ocean & Coastal Management, 171, pp.28-36. DOI: 10.1016/j.ocecoaman.2019.01.008.
Mago?, T. and Salzberg, S.L., 2011. FLASH: fast length adjustment of short reads to improve genome
assemblies. Bioinformatics, 27(21), pp.2957-2963. DOI: 10.1093/bioinformatics/btr507.
Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J.Y., Sato, K., Minamoto, T., Yamamoto, S., Yamanaka, H., Araki, H. and
Kondoh, M., 2015. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes:
detection of more than 230 subtropical marine species. Royal Society open science, 2(7), p.150088. DOI:
1098/rsos.150088.
Mumby PJ, Dahlgren CP, Harborne AR, Kappel CV, Micheli F, Brumbaugh DR, Holmes KE, Mendes JM, Broad K, Sanchirico
JN, Buch K. 2006. Fishing, trophic cascades, and the process of grazing on coral reefs. science. 311(5757):98-101.
DOI: 10.1126/science.1121129.
Nakagawa, H., Yamamoto, S., Sato, Y., Sado, T., Minamoto, T., and Miya, M. 2018.
Comparing local?and regional?scale estimations of the diversity of stream fish using eDNA metabarcoding and
conventional observation methods. Freshwater Biology, 63(6), 569-580. DOI: 10.1111/fwb.13094.
Nester, G. M., De Brauwer, M., Koziol, A., West, K. M., DiBattista, J. D., White, N. E., Power,
M., Heydenrych, M. J., Harvey, E., and Bunce, M. 2020. Development and evaluation of fish eDNA metabarcoding
assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae). Environmental DNA, edn3.93–.
DOI:10.1002/edn3.93.
Niemiller, M.L., Porter, M.L., Keany, J., Gilbert, H., Fong, D.W., Culver, D.C., Hobson, C.S., Kendall, K.D., Davis, M.A. and
Taylor, S.J., 2018. Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with
endangered Stygobromus (Amphipoda: Crangonyctidae). Conservation Genetics Resources, 10, pp.247-257. DOI:
1007/s12686-017-0785-2.
Oka, S. and Miyamoto, K., 2015. Reproductive biology and growth of bluestripe herring H erklotsichthys quadrimaculatus
(Rüppell, 1837) in the northernmost waters. Journal of Applied Ichthyology, 31(4), pp.709-713. DOI: 10.1111/jai.12811.
Pereira, P.H.C., Macedo, C.H., Nunes, J.D.A.C., Marangoni, L.F.D.B. and Bianchini, A., 2018. Effects of depth on reef fish
communities: Insights of a “deep refuge hypothesis” from Southwestern Atlantic reefs. PLoS One, 13(9), p.e0203072.
DOI: 10.1371/journal.pone.0203072.
Pikitch, E. K. 2018. A tool for finding rare marine species. Science, 360(6394), 1180-1182. DOI: 10.1126/science.aao3787.
Rambaut A. 2009. FigTree v1. 3.1. http://tree.bio.ed.ac.uk/software/figtree/.Accessed date:May 2022.
Riera, R. and Delgado, J.D., 2019. Canary Islands. In World Seas: an Environmental Evaluation (pp. 483-500). Academic Press.
DOI: 10.1016/B978-0-12-805068-2.00024-3.
Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-
DOI: 10.1093/bioinformatics/btg180.
Ruppert, K. M., Kline, R. J., and 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. DOI: 10.1016/j.gecco.2019.e00547.
Russ, G.R., Questel, S.L.A., Rizzari, J.R. and Alcala, A.C., 2015. The parrotfish–coral relationship: refuting the ubiquity of a
prevailing paradigm. Marine Biology, 162, pp.2029-2045. DOI: 10.1007/s00227-015-2728-3.
Sasaki, D. and Kimura, S., 2020. A new atherinomorine genus Doboatherina (Atheriniformes: Atherinidae) with a review of
included species. Ichthyological Research, 67, pp.225-261. DOI: 10.1007/s10228-019-00718-5.
Sato, Y., Miya, M., Fukunaga, T., Sado, T., and Iwasaki, W. 2018. MitoFish and MiFish pipeline: a mitochondrial genome
database of fish with an analysis pipeline for environmental DNA metabarcoding. Molecular Biology Evolution, 10:
-423. DOI: 10.1093/molbe-v/msy07-4.
Schmieder, R., Lim, Y.W., Rohwer, F. and Edwards, R., 2010. TagCleaner: Identification and removal of tag sequences from
genomic and metagenomic datasets. BMC bioinformatics, 11, pp.1-14. DOI: 10.1186/1471-2105-11-341.
Seale, A. 1910. New species of Philippine fishes. Philipp J Sci, Section A. 4:491–543.
Semmens, B.X., Buhle, E.R., Salomon, A.K. and Pattengill-Semmens, C.V., 2004. A hotspot of non-native marine fishes:
evidence for the aquarium trade as an invasion pathway. Marine Ecology Progress Series, 266, pp.239-244.
DOI:10.3354/meps266239.
Strickler, K. M., Fremier, A. K., and Goldberg, C. S., 2015. Quantifying effects of UV-B, temperature, and pH on eDNA
degradation in aquatic microcosms. Biological Conservation, 183, 85-92. DOI: 10.1016/j.biocon.2014.11.038
Thomsen, P. F., and Willerslev, E. 2015. Environmental DNA – An emerging tool in conservation for monitoring past and
present biodiversity. Biological Conservation, 183, 4-8. DOI: 10.1016/j.biocon.2014.11.019.
Thomsen, P. F., Kielgast, J., Iversen, L. L., Moller, P. R., Rasmusen, M., and Willerslev, E. 2012. Detection of a Diverse Marine
Fish Fauna Using Environmental DNA from Seawater Samples. PLoS ONE, 7(8): e41732.
DOI:10.1371/journal.pone.0041732.
Vincent, A. C., Foster, S. J., and Koldewey, H. J., 2011. Conservation and management of
seahorses and other Syngnathidae. Journal of fish biology, 78(6), 1681-1724. DOI: 10.1111/j.1095-8649.2011.03003.x.
Wairara, S.M. and Elviana, S., 2021, May. Distribution patterns and abundance
of mullet fish populations (Mugil sp.) estuary areas. In Journal of Physics: Conference Series (Vol. 1899, No. 1, p.
. IOP Publishing. DOI: 10.1088/1742-6596/1899/1/012019.
West, K., Travers, M.J., Stat, M., Harvey, E.S., Richards, Z.T., DiBattista, J.D., Newman, S.J., Harry, A., Skepper, C.L.,
Heydenrych, M. and Bunce, M., 2021. Large?scale eDNA metabarcoding survey reveals marine biogeographic break
and transitions over tropical north?western Australia. Diversity and Distributions, 27(10), pp.1942-1957. DOI:
1111/ddi.13228.
Wu, M.L., Yang, C.C., Deng, J.F. and Wang, K.Y., 2014. Hyperkalemia, hyperphosphatemia, acute kidney injury, and fatal
dysrhythmias after consumption of palytoxin-contaminated goldspot herring. Annals of emergency medicine, 64(6),
pp.633-636. DOI: 10.1016/j.annemergmed.2014.06.001.
Xiong, F., Shu, L., Zeng, H., Gan, X., He, S. and Peng, Z., 2022. Methodology for fish biodiversity monitoring with
environmental DNA metabarcoding: the primers, databases and bioinformatic pipelines. Water Biology and
Security, 1(1), p.100007. DOI: 10.1016/j.watbs.2022.100007.
Yamamoto, S., Masuda, R., Sato, Y., Sado, T., Araki, H., Kondoh, M., Minamoto, T., and Miya, M. 2017. Environmental DNA
metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific Reports, 7,
–. DOI:10.1038/srep40368
Zou, K., Chen, J., Ruan, H., Li, Z., Guo, W., Li, M., and Liu, L. 2020. eDNA metabarcoding
as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared
to bottom trawling. Science of the Total Environment, 702, 134704. DOI: 10.1016/j.scitotenv.2019.134704.