ARMS Publications

Image: Divers Recovering ARMS in Bali, Indonesia. © David Liittschwager

• Ip, Y.C.A., Chang, J.J.M., Oh, R.M., Quek, Z.B.R., Chan, Y.K.S., Bauman, A.G. and Huang, D., 2022. Seq’and ARMS shall find: DNA (meta) barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs. Molecular Ecology.
• Nichols, P.K., Timmers, M. and Marko, P.B., 2022. Hide ‘n seq: Direct versus indirect metabarcoding of coral reef cryptic communities. Environmental DNA, 4(1), pp. 93-107.
• Patil, H., 2022. Distribution and diversity of reef associated organisms in the Andaman Islands.
• Reid, B.N., Servis, J.A., Timmers, M., Rohwer, F. and Naro-Maciel, E., 2022. 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific. Metabarcoding and Metagenomics, 6, p. e78762.
• Steyaert, M., Mogg, A., Dunn, N., Dowell, R. and Head, C.E., 2022. Observations of coral and cryptobenthic sponge fluorescence and recruitment on autonomous reef monitoring structures (ARMS). Coral Reefs, 41(4), pp. 877-883.
• Sundberg, P., Axberg, A., Daragmeh, N., Panova, M. and Obst, M., 2022. Genetic methods in environmental monitoring: Early detection and monitoring of non-indigenous species based on DNA.
• Timmers, M.A., Vicente, J., Webb, M., Jury, C.P. and Toonen, R.J., 2022. Sponging up diversity: Evaluating metabarcoding performance for a taxonomically challenging phylum within a complex cryptobenthic community. Environmental DNA, 4(1), pp. 239-253.
• Vicente, J., Webb, M.K., Paulay, G., Rakchai, W., Timmers, M.A., Jury, C.P., Bahr, K. and Toonen, R.J., 2022. Unveiling hidden sponge biodiversity within the Hawaiian reef cryptofauna. Coral Reefs, 41(3), pp. 727-742.
• Cahyani, N.K.D., 2021. Delineating macro and micro marine biodiversity in the coral triangle using autonomous reef monitoring structures and DNA metabarcoding.
• Casey, J.M., Ransome, E., Collins, A.G., Mahardini, A., Kurniasih, E.M., Sembiring, A., Schiettekatte, N.M., Cahyani, N.K.D., Wahyu Anggoro, A., Moore, M. and Uehling, A., 2021. DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity. Environmental DNA, 3(6), pp. 1229-1246.
• Longenecker, K., 2021. First record of two sublittoral amphipods from Hawai‘i. Marine Biodiversity Records, 14(1), pp. 1-4.
• Palomino-Alvarez, L.A., Vital, X.G., Castillo-Cupul, R.E., Suárez-Mozo, N.Y., Ugalde, D., Cervantes-Campero, G., Muciño-Reyes, M.R., Homá-Canché, P., Hernández-Díaz, Y.Q., Sotelo-Casas, R. and García-González, M., 2021. Evaluation of the Use of Autonomous Reef Monitoring Structures (ARMS) for Describing the Species Diversity of Two Coral Reefs in the Yucatan Peninsula, Mexico. Diversity, 13(11), p. 579.
• Plaisance, L., Matterson, K., Fabricius, K., Drovetski, S., Meyer, C. and Knowlton, N., 2021. Effects of low pH on the coral reef cryptic invertebrate communities near CO2 vents in Papua New Guinea. Plos one, 16(12), p. e0258725.
• Yang, H.S., Jöst, A.B., Kim, T., Karanovic, I., Yoon, G.T., Heo, S.J., Kim, T.H., Baker, D.M. and Kang, D.H., 2021. Research on the application of the Autonomous Reef Monitoring Structures (ARMS) for the change of marine ecosystem and biodiversity diagnosis in Jeju Island. 2021 년도한국해양학회추계학술대회, pp. 185-185.
• Chang, J.J.M., Ip, Y.C.A., Bauman, A.G. and Huang, D., 2020. MinION-in-ARMS: nanopore sequencing to expedite barcoding of specimen-rich macrofaunal samples from autonomous reef monitoring structures. Frontiers in Marine Science, 7, p. 448.
• Obst, M., Exter, K., Allcock, A.L., Arvanitidis, C., Axberg, A., Bustamante, M., Cancio, I., Carreira-Flores, D., Chatzinikolaou, E., Chatzigeorgiou, G. and Chrismas, N., 2020. A marine biodiversity observation network for genetic monitoring of hard-bottom communities (ARMS-MBON). Frontiers in Marine Science, 7, p. 572680.
• Pearman, J.K., Chust, G., Aylagas, E., Villarino, E., Watson, J.R., Chenuil, A., Borja, A., Cahill, A.E., Carugati, L., Danovaro, R. and David, R., 2020. Pan‐regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures. Molecular Ecology, 29(24), pp. 4882-4897.
• Servis, J.A., Reid, B.N., Timmers, M.A., Stergioula, V. and Naro-Maciel, E., 2020. Characterizing coral reef biodiversity: genetic species delimitation in brachyuran crabs of Palmyra Atoll, Central Pacific. Mitochondrial DNA Part A, 31(5), pp. 178-189.
• Streekstra, M.A., Folkers, M., Schoon, B., Jorissen, H., Nugues, M.M., De Goeij, J.M., Murk, A.J. and Osinga, R., 2020, February. What happens under the reef? A study towards the identity and functioning of the cryptobenthic community in two contrasting coral reef habitats. In WIAS Annual Conference 2020: Frontiers in Animal Sciences (pp. 28-28). WIAS.
• Tran, S.V., 2020. Using Color Thresholding and Contouring to Understand Coral Reef Biodiversity.
• Bhodia, N., 2019. Using Computer Vision to Quantify Coral Reef Biodiversity.
• Carvalho, S., Aylagas, E., Villalobos, R., Kattan, Y., Berumen, M. and Pearman, J.K., 2019. Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome. Proceedings of the Royal Society B, 286(1896), p. 20182697.
• David, R., Uyarra, M.C., Carvalho, S., Anlauf, H., Borja, A., Cahill, A.E., Carugati, L., Danovaro, R., De Jode, A., Feral, J.P. and Guillemain, D., 2019. Lessons from photo analyses of Autonomous Reef Monitoring Structures as tools to detect (bio-) geographical, spatial, and environmental effects. Marine Pollution Bulletin, 141, pp. 420-429.
• HAZERI, G., RAHAYU, D.L., SUBHAN, B., SEMBIRING, A., ANGGORO, A.W., GHOZALI, A.T. and MADDUPPA, H.H., 2019. Latitudinal species diversity and density of cryptic crustacean (Brachyura and Anomura) in micro-habitat Autonomous Reef Monitoring Structures across Kepulauan Seribu, Indonesia. Biodiversitas Journal of Biological Diversity, 20(5).
• Pearman, J.K., Aylagas, E., Voolstra, C.R., Anlauf, H., Villalobos, R. and Carvalho, S., 2019. Disentangling the complex microbial community of coral reefs using standardized Autonomous Reef Monitoring Structures (ARMS). Molecular ecology, 28(15), pp. 3496-3507.
• 양현성 and 강도형, 2018, May. International cooperation for participating the Marine Global Earth Observatory (Marine-GEO) project and its fundamental application in Jeju. In International Marine GEO Symposium in Jeju (pp. 10-10). Korea Institute of Ocean Science & Technology.
• Moews-Asher, M., Castor, C.B., Reardon, K. and Timmers, M.A., 2018. Field Guide to Cryptic Marine Invertebrates of the Philippines: A Sample of Biodiversity from Autonomous Reef Monitoring Structures.
• Pearman, J.K., Leray, M., Villalobos, R., Machida, R.J., Berumen, M.L., Knowlton, N. and Carvalho, S., 2018. Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority. Scientific reports, 8(1), pp. 1-17.
• Pennesi, C. and Danovaro, R., 2017. Assessing marine environmental status through microphytobenthos assemblages colonizing the Autonomous Reef Monitoring Structures (ARMS) and their potential in coastal marine restoration. Marine Pollution Bulletin, 125(1-2), pp. 56-65.
• Ransome, E., Geller, J.B., Timmers, M., Leray, M., Mahardini, A., Sembiring, A., Collins, A.G. and Meyer, C.P., 2017. The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia. PloS one, 12(4), p. e0175066.
• Al-Rshaidat, M.M., Snider, A., Rosebraugh, S., Devine, A.M., Devine, T.D., Plaisance, L., Knowlton, N. and Leray, M., 2016. Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea. Genome, 59(9), pp. 724-737.
• Hurley, K.K., Timmers, M.A., Godwin, L.S., Copus, J.M., Skillings, D.J. and Toonen, R.J., 2016. An assessment of shallow and mesophotic reef brachyuran crab assemblages on the south shore of O‘ahu, Hawai‘i. Coral Reefs, 35(1), pp. 103-112.
• Pearman, J.K., Anlauf, H., Irigoien, X. and Carvalho, S., 2016. Please mind the gap–Visual census and cryptic biodiversity assessment at central Red Sea coral reefs. Marine Environmental Research, 118, pp. 20-30.
• Perez, Karen Camille, and Ma Carmen Ablan-Lagman. 2016. Comparison of abundance and diversity of invertebrates in sediments from CO2 and non-exposed reefs. De La Salle Research Congress.
• Ransome, E.J., Timmers, M., Hartmann, A., Collins, A. and Meyer, C., 2016. Cryptic Coral Reef Diversity Across the Pacific Assessed using Autonomous Reef Monitoring Structures and Multi-omic Methods. American Geophysical Union, 2016, pp. OD34B-2512.
• Leray, M. and Knowlton, N., 2015. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proceedings of the National Academy of Sciences, 112(7), pp. 2076-2081.
• RECORDS, S.B., 2015. Records of Lamellaria snails in Singapore.
• Villalobos Vazquez de la Parra, R., 2015. Biodiversity Patterns on an Inshore to Offshore Gradient Using Metabarcoding and Barcoding Molecular Tools.
• Morgan, J.A., 2014. NOAA Coral Reef Conservation Program: national coral reef monitoring plan.
• Kuwahara, A., Meyer, C. and Collins, A., 2013. Assessing Autonomous Reef Monitoring Structures (ARMS) as Biodiversity Monitors. INTEGRATIVE AND COMPARATIVE BIOLOGY, 53, pp. E119-E119.
• Plaisance, L., Brainard, R., Caley, M.J. and Knowlton, N., 2011. Using DNA Barcoding and Standardized Sampling to Compare Geographic and Habitat Differentiation of Crustaceans: A Hawaiian Islands Example. Diversity, 4(4), pp. 581-591.
• Plaisance, L., Caley, M.J., Brainard, R.E. and Knowlton, N., 2011. The diversity of coral reefs: what are we missing? PloS one, 6(10), p. e25026.
• Brainard, R., Moffitt, R., Timmers, M., Paulay, G., Plaisance, L., Knowlton, N., Caley, J., Fohrer, F., Charette, A., Meyer, C. and Toonen, R., 2009, March. Autonomous Reef Monitoring Structures (ARMS): A tool for monitoring indices of biodiversity in the Pacific Islands. In 11th Pacific Science Inter-Congress, Papeete, Tahiti.