Molecular Insights into the Genetic Diversity of Marine Zooplankton

  • Angkasa Putra Interdisciplinary Program of Marine and Fisheries Sciences and Convergent Technology, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 48513, Republic of Korea. https://orcid.org/0000-0002-5533-9437
  • Sarifah Aini Interdisciplinary Program of Marine and Fisheries Sciences and Convergent Technology, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 48513, Republic of Korea. https://orcid.org/0009-0001-1065-4724
  • I Nyoman Suyasa Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0003-4508-0051
  • Ilham Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia; Marine and Fisheries Polytechnic of Jembrana (Politeknik Kelautan dan Perikanan Jembrana), Ministry of Marine Affairs and Fisheries, Pengambengan, Negara, Jembrana, Bali 82218, Republic of Indonesia https://orcid.org/0000-0003-1268-7818
  • Fitriska Hapsari Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0009-0000-6480-5877
  • Muhammad Hery Riyadi Alauddin Marine and Fisheries Polytechnic of Bone (Politeknik Kelautan dan Perikanan Bone), Ministry of Marine Affairs and Fisheries, Jl. Sungai Musi KM. 9, Watampone, Bone, South Sulawesi 92718, Republic of Indonesia https://orcid.org/0009-0008-1801-401X
  • Ani Leilani Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0009-0004-2566-6746
  • Heri Triyono Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0001-9700-5702
  • Rina Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0002-7928-7731
  • Mugi Mulyono Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0002-4363-1692
  • Tatty Yuniarti Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0001-7716-8846
  • Mira Maulita Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0009-0004-9883-5440
  • Yenni Nuraini Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0001-8194-6305
  • Ita Junita Puspa Dewi Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0002-8363-3561
  • Sinung Rahardjo Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0002-4698-2623
  • Sinar Pagi Sektiana Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0000-0002-2763-6442
  • Hamdani Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0009-0000-6484-2862
  • Made Ariana Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0009-0009-4504-6073
  • Taufik Hadi Ramli Marine and Fisheries Polytechnic of Karawang (Politeknik Kelautan dan Perikanan Karawang), Ministry of Marine Affairs and Fisheries, Jl. Lingkar Tanjungpura, Karangpawitan, Karawang, West Java 41315, Republic of Indonesia https://orcid.org/0009-0004-3459-369X
  • Lalu Achmad Jani Qhadaffi Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia https://orcid.org/0009-0003-8571-7579
  • Ayu Rizki  Amalia Jakarta Technical University of Fisheries (Politeknik Ahli Usaha Perikanan), Ministry of Marine Affairs and Fisheries, Jl. AUP No. 1, Pasar Minggu, South Jakarta, Special Region of Jakarta 12520, Republic of Indonesia
  • Cici Maulida Samudra University, Jl. Prof. Dr. Syarief Thayeb, Langsa Lama, Langsa, Aceh 24416, Republic of Indonesia https://orcid.org/0009-0009-0931-2389
  • Mhd Aidil Huda J. Matauli College of Fisheries and Marine Sciences (Sekolah Tinggi Perikanan dan Kelautan Matauli), Jl. Ki Hajar Dewantara No. 1, Pandan, Central Tapanuli, North Sumatra 22611, Republic of Indonesia https://orcid.org/0009-0002-9683-6576
  • Muh. Azril Tidar University, Jl. Kapten Suparman No. 39, Potrobangsan, North Magelang, Magelang, Central Java 56116, Republic of Indonesia https://orcid.org/0000-0003-4040-8943
  • Hawati Marine and Fisheries Polytechnic of Bone (Politeknik Kelautan dan Perikanan Bone), Ministry of Marine Affairs and Fisheries, Jl. Sungai Musi KM. 9, Watampone, Bone, South Sulawesi 92718, Republic of Indonesia https://orcid.org/0009-0009-1071-5353
  • Muhammad Misi Muslimin Indonesian Muslim University, Jl. Urip Sumoharjo KM. 5, Makassar, South Sulawesi 90231, Republic of Indonesia https://orcid.org/0009-0004-9901-8872
Keywords: Genomic Tools, Marine Biodiversity, Molecular Ecology, Zooplankton

Abstract

Zooplankton are fundamental components of marine trophic networks and served as bioindicators of environmental changes. Assessing their genetic diversity is essential for biodiversity assessment, ecosystem monitoring, and evidence-based conservation strategies. The conventional morphological identification methods are limited in detecting cryptic species and lack phylogenetic resolution, necessitating the use of molecular approaches. Hence, this review synthesises the recent advancements in genomic tools for investigating marine zooplankton genetic variability, encompassing techniques such as DNA barcoding and metabarcoding, complete mitochondrial genome analysis, as well as environmental DNA profiling. We systematically evaluated the advantages of each method, the application of genetic markers, and their effectiveness in species identification, population genetics, and evolutionary studies. The genetic methods have greatly improved taxonomic resolution, revealed hidden biodiversity, and offered deeper insights into the population structure and community dynamics of marine zooplankton in response to human-induced pressures. Despite these achievements, several challenges persist, including incomplete genetic reference databases, sequencing errors, and the lack of standardised protocols. Accordingly, future research should prioritise the expansion of comprehensive genetic libraries, the refinement of bioinformatics pipelines, and the integration of multi-marker approaches to deepen our understanding of marine zooplankton genetic variation and ecological interactions. Continued improvement in these molecular methodologies will be important for the effective conservation of marine biodiversity, the mitigation of environmental fluctuation impacts, and the promotion of sustainable fisheries management.

References

Agashe, D., 2009. The stabilizing effect of intraspecific genetic variation on population dynamics in novel and ancestral habitats. The American Naturalist, 174(2), pp.255-267. doi: 10.1086/600085.
Amaral-Zettler, L.A. et al., 2009. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE, 4(7), e6372. doi:10.1371/journal.pone.0006372.
Avise, J.S., 1989. Gene trees and organismal histories: A phylogenetic approach to population biology. Evolution, 43 (1989), pp.1192-1208. doi: 10.1111/j.1558-5646.1989.tb02568.x.
Bachimanchi, H. et al., 2024. Deep-learning-powered data analysis in plankton ecology. Limnology and Oceanography, 9(4), pp.324-339. doi: 10.1002/lol2.10392.
Baek, S.Y. et al., 2016. DNA barcoding of metazoan zooplankton copepods from South Korea. PLoS ONE, 11(7), e0157307. doi: 10.1371/journal.pone.0157307.
Bandara, K. et al., 2021. Two hundred years of zooplankton vertical migration research. Biological Reviews, 96(4), pp.1547-1589. doi: 10.1111/brv.12715.
Bashevkin, S.M. et al., 2020. Larval dispersal in a changing ocean with an emphasis on upwelling regions. Ecosphere, 11(1), e03015. doi: 10.1002/ecs2.3015.
Belfiore, N.M. & Anderson, S.L., 2002. Effects of contaminants on genetic patterns in aquatic organisms: A review. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 489(2-3), pp.97-122. doi: 10.1016/S1383-5742(01)00065-5.
Blanco-Bercial, L. & Bucklin, A., 2016. New view of population genetics of zooplankton: RAD-seq analysis reveals population structure of the North Atlantic planktonic copepod Centropages typicus. Molecular Ecology, 25(7), pp.1566-1580. doi: 10.1111/mec.13581.
Blanco-Bercial, L. et al., 2011a. Molecular phylogeny of the Calanoida (Crustacea: Copepoda). Molecular Phylogenetics and Evolution, 59(1), pp.103-113. doi: 10.1016/j.ympev.2011.01.008.
Blanco-Bercial, L. et al., 2011b. Comparative phylogeography and connectivity of sibling species of the marine copepod Clausocalanus (Calanoida). Journal of Experimental Marine Biology and Ecology, 404(1-2), pp.108-115. doi: 10.1016/j.jembe.2011.05.011.
Boore, J.F., 1999. Animal mitochondrial genomes. Nucleic Acids Research, 27(8), pp.1767-1780. doi: 10.1093/nar/27.8.1767.
Botterell, Z.L.R. et al., 2023. An assessment of the ecosystem services of marine zooplankton and the key threats to their provision. Ecosystem Services, 63, 101542. doi: 10.1016/j.ecoser.2023.101542.
Bucklin, A. et al., 2003. Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae. Marine Biology, 142, pp.333-343. doi: 10.1007/s00227-002-0943-1.
Bucklin, A. et al., 2016. Metabarcoding of marine zooplankton: Prospects, progress, and pitfalls. Journal of Plankton Research, 38(3), pp.393-400. doi: 10.1093/plankt/fbw023.
Bucklin, A. et al., 2021a. New insights into biodiversity, biogeography, ecology, and evolution of marine zooplankton based on molecular approaches. ICES Journal of Marine Science, 78(9), pp.3281-3287. doi: 10.1093/icesjms/fsab198.
Bucklin, A. et al., 2021b. Toward a global reference database of COI barcodes for marine zooplankton. Marine Biology, 168, 78. doi: 10.1007/s00227-021-03887-y.
Bucklin, A. et al., 2022. COI metabarcoding of zooplankton species diversity for time-series monitoring of the NW Atlantic Continental Shelf. Frontiers in Marine Science, 9, 867893. doi: 10.3389/fmars.2022.867893.
Bucklin, A. et al., 2018. Population genomics of marine zooplankton. In: Oleksiak, M. & Rajora, O. (eds.) Population Genomics: Marine Organisms. Springer, Cham. doi: 10.1007/13836_2017_9.
Burton, R.S. et al, 2007. Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus. Gene, 403(1-2), pp.53-59. doi: 10. 1016/j.gene.2007.07.026.
Carroll, E.L. et al., 2019. Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator. Scientific Reports, 9, 281. doi: 10.1038/s41598-018-36478-x.
Caudill, C.C. & Bucklin, A., 2004. Molecular phylogeography and evolutionary history of the estuarine copepod, Acartia tonsa, on the Northwest Atlantic Coast. Hydrobiologia, 511, pp.91-102. doi: 10.1023/B:HYDR.0000014032.05680.9d.
Chiba, S. et al., 2018. Zooplankton monitoring to contribute towards addressing global biodiversity conservation challenges. Journal of Plankton Research, 40(5), pp.509-518. doi: 10.1093/plankt/fby030.
Chust, G. et al., 2016. Dispersal similarly shapes both population genetics and community patterns in the marine realm. Scientific Report, 6, 28730. doi: 10.1038/srep28730.
CmarZ., 2025. Census of Marine Zooplankton, viewed 21 February 2025, from https://www.cmarz.org/.
Cole, M. et al., 2013. Microplastic ingestion by zooplankton. Environmental Science & Technology, 47(12), pp.6646-6655. doi: 10.1021/es400663f.
Cornils, A. et al., 2017. Global phylogeography of Oithona similis s.l. (Crustacea, Copepoda, Oithonidae) - A cosmopolitan plankton species or a complex of cryptic lineages? Molecular Phylogenetics and Evolution, 107, pp.473-485. doi: 10.1016/j.ympev.2016.12.019.
Cowen, R.K. & Sponaugle S., 2009. Larval dispersal and marine population connectivity. Annual Review of Marine Science, 1, pp.443-466. doi: 10.1146/annurev.marine.010908.163757.
Cowen, R.K. et al., 2007. Population connectivity in marine systems: An overview. Oceanography, 20(3), pp.14-21. doi: 10.5670/oceanog.2007.26.
Dam, H.G., 2013. Evolutionary adaptation of marine zooplankton to global change. Annual Review of Marine Science, 5, pp.349-370. doi: 10.1146/annurev-marine-121211-172229.
Di Capua, I. et al., 2017. Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA). PLoS ONE, 12(4), e0175662. doi: 10.1371/journal.pone.0175662.
Di Capua, I. et al., 2023. Is integrated taxonomy useful to study diversity and ecology? An example from crustacean zooplankton at the Long-Term ecological research site MareChiara (LTER-MC). Marine Ecology, 44(3), e12752. doi: 10.1111/maec.12752.
Di Capua, I. et al., 2024. Integrative approach to monitoring metazoan diversity and distribution in two Mediterranean coastal sites through morphology and organismal eDNA. Scientific Reports, 14, 19291. doi: 10.1038/s41598-024-69520-2.
Djurhuus, A. et al., 2018. Evaluation of marine zooplankton community structure through environmental DNA metabarcoding. Limnology and Oceanography, 16(4), pp.209-221. doi: 10.1002/lom3.10237.
El-khodary, G.M. et al., 2020. Phylogenetic identification and assessment of the nutritional value of different diets for a copepod species isolated from Eastern Harbor coastal region. Egyptian Journal of Aquatic Research, 46(2), pp.173-180. doi: 10.1016/j.ejar.2020.03.003.
Ezard, T.H.G. & Travis, J.M.J., 2006. The impact of habitat loss and fragmentation on genetic drift and fixation time. OIKOS, 114(2), pp.367-375. doi: 10.1111/j.2006.0030-1299.14778.x.
Feng, Y. et al., 2023. COI metabarcoding better reveals the seasonal variations in the zooplankton community in the western Pacific Warm Pool. Ecological Indicators, 156, 111183. doi: 10.1016/j.ecolind.2023.111183.
Fields, P.D. et al., 2018. Mitogenome phylogeographic analysis of a planktonic crustacean. Molecular Phylogenetics and Evolution, 129, pp.138-148. doi: 10.1016/j.ympev.2018.06.028.
Filatov, D.A. et al., 2021. The mode of speciation during a recent radiation in open-ocean phytoplankton. Current Biology, 31(24), pp.5439-5449. doi: 10.1016/j.cub.2021.09.073.
Filatov, D.A., 2023. How does speciation in marine plankton work? Trends in Microbiology, 31(10), pp.989-991. doi: 10.1016/j.tim.2023.07.005.
Gao, X. et al., 2019. Responses of zooplankton body size and community trophic structure to temperature change in a subtropical reservoir. Ecology and Evolution, 9(22), pp.12544-12555. doi: 10.1002/ece3.5718.
Gary, S.F. et al., 2020. Larval behaviour, dispersal, and population connectivity in the deep sea. Scientific Report, 10, 10675. doi: 10.1038/s41598-020-67503-7.
Genome 10K Community of Scientists., 2009. Genome 10K: A proposal to obtain whole-genome sequence for 10 000 vertebrate species. Journal of Heredity, 100(6), pp.659-674. doi: 10.1093/jhered/esp086.
GIGA Community of Scientists., 2014. The Global Invertebrate Genomics Alliance (GIGA): Developing community resources to study diverse invertebrate genomes. Journal of Heredity, 105(1), pp.1-18. doi: 10.1093/jhered/est084.
Gluchowska, M. et al., 2017. Variations in the structural and functional diversity of zooplankton over vertical and horizontal environmental gradients en route to the Arctic Ocean through the Fram Strait. PLoS ONE, 12(2), e0171715. doi: 10.1371/journal.pone.0171715.
Goetze, E. et al., 2015. Temporal stability of genetic structure in a mesopelagic copepod. PLoS ONE, 10(8), e0136087. doi: 10.1371/journal.pone.0136087.
González, C.E. et al., 2020. Genetic diversity and novel lineages in the cosmopolitan copepod Pleuromamma abdominalis in the Southeast Pacific. Scientific Reports, 10, 1115. doi: 10.1038/s41598-019-56935-5.
Goswami, P. et al., 2014. Monitoring of genotoxicity in marine zooplankton induced by toxic metals in Ennore estuary, Southeast coast of India. Marine Pollution Bulletin, 88(1-2), pp.70-80. doi: 10.1016/j.marpolbul.2014.09.025.
Grossart, H.P. et al., 2020. Linking metagenomics to aquatic microbial ecology and biogeochemical cycles. Limnology and Oceanography, 65(S1), pp.S2-S20. doi: 10.1002/lno.11382.
Gupta, S. et al., 2024. Genomic intelligence: Metagenomics and artificial intelligence. Taylor & Francis Ltd.
Havird, J.C. et al., 2016. Sex, mitochondria, and genetic rescue. Trends in Ecology & Evolution, 31(2), pp.96-99. doi: 10.1016/j.tree.2015.11.012.
Hebert, P.D.N. et al., 2003. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1), pp.S96-999. doi: 10.1098/rsbl.2003.0025.
Hebert, P.D.N. et al., 2018. A sequel to Sanger; Amplicon sequencing that scales. BMC Genomics, 19, 219. doi: 10.1186/s12864-018-4611-3.
Helfenbein, K.G. et al., 2004. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proceedings of the National Academy of Sciences of the United States of America, 101(29), pp.10639-10643. doi: 10.1073/pnas.0400941101.
Hwang, D.S. et al., 2014. Complete mitochondrial genome of the jellyfish, Chrysaora quinquecirrha (Cnidaria, Scyphozoa). Mitochondrial DNA, 25(1), pp.25-26. doi: 10. 3109/19401736.2013.775272.
Jeunen, G.J. et al., 2019. Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecology and Evolution, 9(3), pp.1323-1335. doi: 10.1002/ece3.4843.
Johnson, S.B. et al., 2022. Speciation of pelagic zooplankton: Invisible boundaries can drive isolation of oceanic ctenophores. Frontiers in Genetics, 13, 970314. doi: 10.3389/fgene.2022.970314.
Jung, S.O. et al., 2006. The complete mitochondrial genome of the intertidal copepod Tigriopus sp. (Copepoda, Harpactidae) from Korea and phylogenetic considerations. Journal of Experimental Marine Biology and Ecology, 333(2), pp.251-262. doi: 10.1016/j.jembe.2005.12.047.
Kayal, E. et al. 2011. Evolution of linear mitochondrial genomes in medusozoan cnidarians. Genome Biology and Evolution, 4(1), pp.1-12. doi: 10.1093/gbe/evr123.
Ki, J.S. et al., 2009. Phylogeography of the copepod Tigriopus japonicus along the Northwest Pacific rim. Journal of Plankton Research, 31(2), pp.209-221. doi: 10.1093/plankt/fbn100.
Ki, J.S. et al., 2010. Complete mitochondrial genome sequence of the Arctic gammarid, Onisimus nanseni (Crustacea; Amphipoda): Novel gene structures and unusual control region features. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 5(2), pp.105-115. doi: 10.1016/j.cbd.2010.02.002.
Kim, S. et al, 2013. The complete mitochondrial genome of Arctic Calanus hyperboreus (Copepoda, Calanoida) reveals characteristic patterns in calanoid mitochondrial genome. Gene, 520(1), pp.64-72. doi: 10.1016/j.gene.2012.09.059.
Kim, S. et al., 2012. Complete mitochondrial genome of the northern mauxia shrimp Acetes chinensis (Decapoda, Dendrobranchiata, Sergestoidae). Mitochondrial DNA, 23(1), pp.28-30. doi: 10.3109/19401736.2011.643878.
Kobari, T. & Ikeda, T., 2001. Ontogenetic vertical migration and life cycle of Neocalanus plumchrus (Crustacea: Copepoda) in the Oyashio region, with notes on regional variations in body sizes. Journal of Plankton Research, 23(3), pp.287-302. doi: 10.1093/plankt/23.3.287.
Kohn, A.B. et al., 2012. Rapid evolution of the compact and unusual mitochondrial genome in the ctenophore, Pleurobrachia bachei. Molecular Phylogenetics and Evolution, 63(1), pp.203-207. doi: 10.1016/j.ympev.2011.12.009.
Lenz, P.H. et al., 2021. Transcriptomics and metatranscriptomics in zooplankton: Wave of the future? Journal of Plankton Research, 43(1) pp.3-9. doi: 10.1093/plankt/fbaa058.
Lewin, H.A. et al., 2018. Earth BioGenome project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences of the United States of America, 115(17), pp.4325-4333. doi: 10.1073/pnas.1720115115.
Li, H. & Roossinck, M.J., 2004. Genetic bottlenecks reduce population variation in an experimental RNA virus population. Journal of Virology, 78(19), pp.10582-10587. doi: 10.1128/JVI.78.19.10582-10587.2004.
Li, P. et al., 2016. Complete mitochondrial genome sequence of the pelagic chaetognath, Sagitta ferox. Mitochondrial DNA, 27(6), pp.1-2. doi: 10.3109/19401736.2015.1106508.
Lindeque, P.K. et al., 2013. Next Generation Sequencing reveals the hidden diversity of zooplankton assemblages. PLoS ONE, 8(11), e81327. doi: 10.1371/journal.pone.0081327.
Litchman, E. et al., 2013. Trait-based approaches to zooplankton communities, Journal of Plankton Research, 35(3), pp.473-484. doi: 10.1093/plankt/fbt019.
Machida, R.J. et al, 2002. Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Marine Biotechnology, 4, pp.406-417. doi: 10.1007/s10126-002-0033-x.
Machida, R.J. et al., 2021. Comparative analysis of zooplankton diversities and compositions estimated from complement DNA and genomic DNA amplicons, metatranscriptomics, and morphological identifications. ICES Journal of Marine Science, 78(9), pp.3428-3443. doi: 10.1093/icesjms/fsab084.
Makino, W. & Tanabe, A.S., 2009. Extreme population genetic differentiation and secondary contact in the freshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago. Molecular Ecology, 18(17), pp.3699-3713. doi: 10.1111/j.1365-294X.2009.04307.x.
McGinty, N. et al., 2021. Anthropogenic climate change impacts on copepod trait biogeography. Global Change Biology, 27(7), pp.1431-1442. doi: 10.1111/gcb.15499.
Millette, K.L. et al., 2011. Pleistocene-driven diversification in freshwater zooplankton: Genetic patterns of refugial isolation and postglacial recolonization in Leptodora kindtii (Crustacea, Cladocera). Limnology and Oceanography, 56(5), pp.1725-1736. doi: 10.4319/lo.2011.56.5.1725.
Minxiao, W. et al, 2011. Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies. BMC Genomics, 12, 73. doi: 10.1186/1471-2164-12-73.
Miyamoto, H. et al., 2010. Genetic diversity and cryptic speciation of the deep sea chaetognath Caecosagitta macrocephala (Fowler, 1904). Deep Sea Research Part II: Topical Studies in Oceanography, 57(24-26), pp.2211-2219. doi: 10.1016/j.dsr2.2010.09.023.
Modica, M. V. et al., 2017. Do larval types affect genetic connectivity at sea? Testing hypothesis in two sibling marine gastropods with contrasting larval development. Marine Environmental Research, 127, pp.92-101. doi: 10.1016/j.marenvres.2017.04.001.
Möllmann, C. et al., 2008. Effects of climate and overfishing on zooplankton dynamics and ecosystem structure: Regime shifts, trophic cascade, and feedback loops in a simple ecosystem. ICES Journal of Marine Science, 65(3), pp.302-310. doi: 10.1093/icesjms/fsm197.
Monchamp, M.È. et al., 2022. Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis? Environmental DNA, 4(6), pp.1250-1264. doi: 10.1002/edn3.335.
Moutinho, J. et al., 2024. Advancements in DNA metabarcoding protocols for monitoring zooplankton in marine and brackish environments. Journal of Marine Science and Engineering, 12, 2093. doi: 10.3390/jmse12112093.
Norris, R.D. & Hull, P.M., 2012. The temporal dimension of marine speciation. Evolutionary Ecology, 26, pp.393-415. doi: 10.1007/s10682-011-9488-4.
Ogoh, K. & Ohmiya, Y., 2004. Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions. Gene, 327(1), pp.131-139. doi: 10.1016/j.gene.2003.11.011.
Papillon, D. et al., 2004. Identification of chaetognaths as protostomes is supported by the analysis of their mitochondrial genome. Molecular Biology and Evolution, 21(11), pp.2122-2129. doi: 10.1093/molbev/msh229.
Parent, G.J. et al., 2012. Natural hybridization between Calanus finmarchicus and C. glacialis (Copepoda) in the Arctic and Northwest Atlantic. Limnology and Oceanography, 57(4), pp.897-1255. doi:10.4319/lo.2012.57.4.1057.
Peijnenburg, K.T.C.A. & Goetze, E., 2013. High evolutionary potential of marine zooplankton. Ecology and Evolution, 3(8), pp.2765-2781. doi: 10.1002/ece3.644.
Peluso, L. et al., 2024. Oceanographical-driven dispersal and environmental variation explain genetic structure in an upwelling coastal ecosystem. Scientific Reports, 14, 21942. doi: 10.1038/s41598-024-72841-x.
Pett, W. et al., 2011. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome. Mitochondrial DNA, 22(4), pp.130-142. doi: 10.3109/19401736.2011.624611.
Porter, T.M. & Hajibabaei, M., 2018. Over 2.5 million COI sequences in GenBank and growing. PLoS One, 13(9), e0200177. doi: 10.1371/journal.pone.0200177.
Putra, A. et al., 2025. Impact of global climate shifts on the biodiversity and functionality of marine zooplankton communities. Journal of Tropical Biodiversity and Biotechnology, 10(1), jtbb14575. doi: 10.22146/jtbb.14575.
Putra, A., 2025. Zooplankton Community around Seogwipo in Jeju Island, Republic of Korea. Pukyong National University.
Ratnarajah, L. et al., 2023. Monitoring and modelling marine zooplankton in a changing climate. Nature Communications, 14, 564. doi: 10.1038/s41467-023-36241-5.
Rawoot, A. et al., 2024. Strengthening the DNA barcode reference library for marine copepods in South Africa. African Journal of Marine Science, 46(4), pp.281-289. doi: 10.2989/1814232X.2022.2108144.
Riginos, C. et al., 2014. Dispersal capacity predicts both population genetic structure and species richness in reef fishes. The American Naturalist, 184(1), pp.52-64. doi: 10.1086/676505.
Shao, Z. et al., 2006. Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase. Gene, 381, pp.92-101. doi: 10.1016/j.gene.2006.06.021.
Shen, X. et al., 2010. The mitochondrial genome of Euphausia superba (Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers. Molecular Biology Reports, 37(2), pp.771-784. doi: 10.1007/s11033-009- 9602-7.
Shen, X. et al., 2011. The complete mitochondrial genome sequence of Euphausia pacifica (Malacostraca: Euphausiacea) reveals a novel gene order and unusual tandem repeats. Genome, 54(11), pp.911-922. doi: 10.1139/g11-053.
Singer, G.A.C. et al., 2020. The utility of a metagenomics approach for marine biomonitoring. bioRxiv, pp.1-13. doi: 10.1101/2020.03.16.993667.
Song, C.U. et al., 2021. Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis. Scientific Reports, 11, 24339. doi: 10.1038/s41598-021-03656-3.
Spitze, K., 1995. Quantitative genetics of zooplankton life histories. Experientia, 51, pp.454-464. doi: 10.1007/BF02143198.
Steinberg, D.K. et al., 2008. Bacterial vs. zooplankton control of sinking particle flux in the ocean’s twilight zone. Limnology and Oceanography, 53(4), pp.1327-1338. doi: 10.4319/lo.2008.53.4.1327.
Stepien, C.A. et al., 2024. Evaluating metabarcoding markers for identifying zooplankton and ichthyoplankton communities to species in the Salish sea: Morphological comparisons and rare, threatened or invasive species. DNA, 4(1), pp.1-33. doi: 10.3390/dna4010001.
Sun, C. et al., 2015. Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities. Aquatic Biology, 24, pp.9-15. doi: 10.3354/ab00629.
Takahashi, M. et al., 2023. Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. Science of The Total Environment, 873, 162322. doi: 10.1016/j.scitotenv.2023.162322.
Thomas, B.K. et al., 2023. Metabarcoding the zooplankton species of the Saudi Arabian Gulf: A study employing mock communities and two gene markers. Egyptian Journal of Aquatic Research, 49(3), pp.319-325. doi: 10.1016/j.ejar.2023.03.003.
Treml, E.A. et al., 2008. Modeling population connectivity by ocean currents, a graph-theoretic approach for marine conservation. Landscape Ecology, 23(1), pp.19-36. doi: 10.1007/s10980-007-9138-y.
Tringe, S.G. & Rubin, E.M., 2005. Metagenomics: DNA sequencing of environmental samples. Nature Reviews Genetics, 6, pp.805-814. doi: 10.1038/nrg1709.
Trubovitz, S. et al., 2020. Marine plankton show threshold extinction response to Neogene climate change. Nature Communications, 11, 5069, doi: 10.1038/s41467-020-18879-7.
Unal, E. & Bucklin, A., 2010. Basin-scale population genetic structure of the planktonic copepod Calanus finmarchicus in the North Atlantic Ocean. Progress in Oceanography, 87(1–4), pp.175-185. doi: 10.1016/j.pocean.2010.09.017.
van Straalen, N.M. & Timmermans, M.J.T.N., 2002. Genetic variation in toxicant-stressed populations: An evaluation of the “genetic erosion” hypothesis. Human and Ecological Risk Assessment: An International Journal, 8(5), pp.983-1002. doi: 10.1080/1080-700291905783.
Vereshchaka, A., 2024. Navigating the zooplankton realm: Oceans of diversity beneath the sea surface. Diversity, 16, 717. doi: 10.3390/d16120717.
Viitasalo, M. & Bonsdorff, E. 2022. Global climate change and the Baltic Sea ecosystem: direct and indirect effects on species, communities, and ecosystem functioning. Earth System Dynamics, 13(2), pp.711-747. doi: 10.5194/esd-13-711-2022, 2022.
Wang, L. et al., 2023. Research and prospects of environmental DNA (eDNA) for detection of invasive aquatic species in East Asia. Frontiers in Marine Science, 10, 1284953. doi: 10.3389/fmars.2023.1284953.
Ward, B.A. et al., 2012. A size-structured food-web model of the global ocean. Limnology and Oceanography, 57(6), pp.1877-1891. doi: 10.4319/lo.2012.57.6.1877.
Wei, S. et al., 2016. The mitochondrial genome of the pelagic chaetognath, Pterosagitta draco. Mitochondrial DNA Part B, 1(1), pp.515-516. doi: 10.1080/23802359.2016. 1197055.
Weydmann, A. et al., 2014. Microsatellite markers for the Arctic copepod Calanus glacialis and cross-amplification with C. finmarchicus. Conservation Genetics Resources, 6, pp.1003-1005. doi: 10.1007/s12686-014-0269-6.
Weydmann, A. et al., 2017. Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non-coding regions. Scientific Report, 7, 13702. doi: 10.1038/s41598-017- 13807.
Wood, S.A. et al., 2019. A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR, and metabarcoding for species-specific detection in environmental DNA. Molecular Ecology Resources, 19(6), pp.1407-1419. doi: 10.1111/1755-0998.13055.
Yan, Z.G. et al., 2023. Environmental DNA sequencing reveals the regional difference in diversity and community assembly mechanisms of eukaryotic plankton in coastal waters. Frontiers in Microbiology, 14, 1132925. doi: 10.3389/fmicb.2023.1132925.
Yang, Q. et al., 2014. Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications. BioMed Research International, 3, 493825. doi: 10.1155/2014/493825.
Zaiko, A. et al., 2018. Advantages and limitations of environmental DNA/RNA tools for marine biosecurity: Management and surveillance of non-indigenous species. Frontiers in Marine Science, 5, 322. doi: 10.3389/fmars.2018.00322.
Zhao, S.Y. et al., 2023. Rapidly evolving zooplankton in a salinizing world: To what extent does microevolutionary adaptation to one salt increase tolerance to another one? Limnology and Oceanography, 68(11), pp.2576-2586. doi: 10.1002/lno.12443.
Published
2025-11-21
How to Cite
Putra, A., Aini, S., Suyasa, I. N., Ilham, Hapsari, F., Alauddin, M. H. R., Leilani, A., Triyono, H., Rina, Mulyono, M., Yuniarti, T., Maulita, M., Nuraini, Y., Dewi, I. J. P., Rahardjo, S., Sektiana, S. P., Hamdani, Ariana, M., Ramli, T. H., Qhadaffi, L. A. J., Amalia, A., Maulida, C., J., M. A. H., Azril, M., Hawati and Muslimin, M. M. (2025) “Molecular Insights into the Genetic Diversity of Marine Zooplankton”, Journal of Tropical Biodiversity and Biotechnology, 10(4), p. jtbb21198. doi: 10.22146/jtbb.21198.
Section
Review Article