New insights into DNA barcoding of seagrasses

References

• Ackerman, J. D. (2006). Sexual reproduction of seagrasses. In A. W. D. Larkum, R. J. Orth, & C. M. Duarte (Eds.), Seagrasses: Biology, ecology and conservation (pp. 89–109). The Netherlands: Springer.
   Google Scholar
• Anonymous. (2015). FigTree (Version 1.4.2). Scotland: The University of Edinburgh. Retrieved from http://tree.bio.ed.ac.uk/software/figtree/ (accessed 27 April, 2015).
   Google Scholar
• Bremer, K. (2000). Phylogenetic nomenclature and the new ordinal system of the angiosperms. In B. Nordenstam, G. Elghazaly, & M. Kassas (Eds.), Plant Systematics for the 21st Century (pp. 125–133). London: Portland Press Ltd.
   Google Scholar
• Bricker, E., Waycott, M., Calladine, A., & Zieman, J. C. (2011). High connectivity across environmental gradients and implications for phenotypic plasticity in a marine plant. Marine Ecology Progress Series, 423, 57–67. doi: 10.3354/meps08962
   Web of Science ®Google Scholar
• Chen, L. Y., Chen, J. M., Gituru, R. W., & Wang, Q. F. (2012). Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae. BioMed Central Evolutionary Biology, 12, 30. doi: 10.1186/1471-2148-12-30
   PubMed Web of Science ®Google Scholar
• Coyer, J. A., Hoarou, G., Kuo, J., Tronholm, A., Veldsink, J., & Olsen, J. L. (2013). Phylogeny and temporal divergence of the seagrass family Zosteraceae using one nuclear and three chloroplast loci. Systematics and Biodiversity, 11, 271–284. doi: 10.1080/14772000.2013.821187
   Web of Science ®Google Scholar
• Cuenca, A., Petersen, G., Seberg, O., Davis, J. I., & Stevenson, D. W. (2010). Are substitution rates and RNA editing correlated? BioMed Central Evolutionary Biology, 10, 349. doi: 10.1186/1471-2148-10-349
   PubMed Web of Science ®Google Scholar
• Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9, 772. doi: 10.1038/nmeth.2109
   PubMed Web of Science ®Google Scholar
• Den Hartog, C. (1970). The sea-grasses of the world. North-Holland: Amsterdam Publishing Company.
   Google Scholar
• Den Hartog, C., & Kuo, J. (2006). Taxonomy and biogeography of seagrasses. In A. W. D. Larkum, R .J. Orth, & C. M. Duarte (Eds.), Seagrasses: Biology, ecology and conservation (pp. 1–23). The Netherlands: Springer.
   Google Scholar
• Felsenstein, J. (1992). Phylogenies from restriction sites: A maximum-likelihood approach. Evolution, 46, 159–175. Retrieved from http://www.stat.wisc.edu/∼larget/phylogeny/felsenstein-evolution-1992.pdf (accessed 27 April 2015).
   Web of Science ®Google Scholar
• Guindon, S., & Gascuel, O. (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology, 52, 696–704. doi: 10.1080/10635150390235520
   PubMed Web of Science ®Google Scholar
• Hollingsworth, P., Forrest, L., Spouge, J., Hajibabaei, M., & Ratnasingham, S. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106, 12794–12797. doi: 10.1073/pnas.0905845106
   PubMed Web of Science ®Google Scholar
• Huson, D. H., & Scornavacca, C. (2012). Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Systematic Biology, 61, 1–7. doi: 10.1093/sysbio/sys062
   PubMed Web of Science ®Google Scholar
• Iles, W. J. D., Smith, S. Y., & Graham, S. W. (2013). A well-supported phylogenetic framework for the monocot order Alismatales reveals multiple losses of the plastid NADH dehydrogenase complex and a strong long-branch effect. In P. Wilkin & S. J. Mayo (Eds.), Early events in monocot evolution (pp. 1–28). Cambridge, UK: Cambridge University Press.
   Google Scholar
• Ito, Y., & Takahata, N. (2011). Hybridisation in a tropical seagrass genus, Halodule (Cymodoceaceae), inferred from plastid and nuclear DNA phylogenies. Telopea, 13, 219–231. Retrieved from https://www.rbgsyd.nsw.gov.au/__data/assets/pdf_file/0014/109310/Tel131-2219Ito.pdf (accessed 27 April 2015).
   Web of Science ®Google Scholar
• Janssen, T., & Bremer, K. (2004). The age of major monocot groups inferred from 800+rbcL sequences. Botanical Journal of the Linnean Society, 146, 385–398. doi: 10.1111/j.1095-8339.2004.00345.x
   Web of Science ®Google Scholar
• Kannan, L., & Thangaradjou, T. (2006). Identification and assessment of biomass and productivity of seagrasses. In K. Paterson, A. Murugan, & J. Patterson (Eds.), National training workshop on marine and coastal biodiversity assessment for conservation and sustainable utilization. (pp. 9–15). India: Sungathi Devadason Marine Research Institute.
   Google Scholar
• Kato, Y., Aioi, K., Omori, Y., Takahata, N., & Satta, Y. (2003). Phylogenetic analyses of Zostera species based on rbcL and matK nucleotide sequences: Implications for the origin and diversification of seagrasses in Japanese waters. Genes & Genetic Systems, 78, 329–342. doi: 10.1266/ggs.78.329
   PubMed Web of Science ®Google Scholar
• Keighery, G. J., & Coates, D. J. (1981). Chromosome counts in Posidonia (Posidoniaceae). Systematics Evolution, 137, 221–222. doi: 10.1007/BF00940605
   Web of Science ®Google Scholar
• Kress, W., Wurdack, K., Zimmer, E., Weigt, L., & Janzen, D. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America, 102, 8369–8374. doi: 10.1073/pnas.0503123102
   PubMed Web of Science ®Google Scholar
• Kuo, J., Iizumi, H., Nilsen, B. E., & Aioi, K. (1990). Fruit anatomy, seed germination and seedling development in the Japanese seagrass Phyllospadix (Zosteraceae). Aquatic Botany, 37, 229–245. doi: 10.1016/0304-3770(90)90072-S
   Web of Science ®Google Scholar
• Kuo, J., & Den Hartog, C. (2001). Seagrass taxonomy and identification key. In F. T. Short, C. A. Short, & R. G. Coles (Eds.), Global seagrass research methods (pp. 31–58). Amsterdam: Elsevier Science.
   Google Scholar
• Kuo, J., Kanomoto, Z., Iizumi, H., & Mukai, H. (2006). Seagrasses of the genus Halophila Thours (Hydrocharitaceae) from Japan. Acta Phytotaxonomica et Geobotanica, 57, 129–154. Retrieved from http://ci.nii.ac.jp/naid/110006318345 (accessed 27 April 2015).
   Google Scholar
• Lahaye, R., Van Der Bank, M., Bogarin, D., Warner, J., & Pupulin, F. (2008). DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences of the United States of America, 105, 2923–2928. doi: 10.1073/pnas.0709936105
   PubMed Web of Science ®Google Scholar
• Les, D. H., & Tippery, N. P. (2013). In time and with water … the systematics of alismatid monocotyledons. In P. Wilkin & S. J. Mayo (Eds.), Early events in monocot evolution (pp. 114–164). Cambridge, UK: Cambridge University Press.
   Google Scholar
• Les, D. H., Moody, M. L., & Soros, A. (2006). A reappraisal of phylogenetic relationships in the monocotyledon family Hydrocharitaceae (Alismatidae). Aliso, 22, 211–230. Retrieved from https://repository.uwa.edu.au (accessed 27 April 2015).
   Google Scholar
• Les, D. H., Moody, M. L., Jacobs, S. W. L., & Bayer, R. J. (2002). Systematics of seagrasses (Zosteraceae) in Australia and New Zealand. Systematic Botany, 27, 468–484. doi: 10.1043/0363-6445-27.3.468
   Web of Science ®Google Scholar
• Les, D. H., Cleland, M. A., & Waycott, M. (1997). Phylogenetic studies in Alismatidae, II: Evolution of marine Angiosperms (seagrasses) and hydrophily. Systematic Botany, 22, 443–463. doi: 10.2307/2419820
   Web of Science ®Google Scholar
• Li, X., & Zhou, Z. (2009). Phylogenetic studies of the core Alismatales inferred from morphology and rbcL sequences. Progress in Natural Science, 19, 931–945. doi: 10.1016/j.pnsc.2008.09.008
   Web of Science ®Google Scholar
• Liu, K., Liu, F. L., Wang, F. J., Sun, X. T., Wang, W. J., Ding, C. L., … Li, T. (2012). Survey and identification of Zosteraceae along Shandong Peninsula coast. Progress in Fishery Sciences, 6, 99–105. Retrieved from http://en.cnki.com.cn/Article_en/CJFDTOTAL-HYSC201206019.htm (accessed 27 April, 2015).
   Web of Science ®Google Scholar
• Lucas, C., Thangaradjou, T., & Papenbrock, J. (2012). Development of a DNA barcoding system for seagrasses: Successful but not simple. Public Libray of Science ONE, 7, e29987. doi: 10.1371/journal.pone.0029987
   Google Scholar
• Maddison, W. P., & Maddison, D. R. (2015). Mesquite: A modular system for evolutionary analysis (3.01). Retrieved from http://mesquiteproject.org (accessed 27 April, 2015).
   Google Scholar
• Nguyen, X. V., Detcharoen, M., Tuntiprapas, P., Soe-Htun, U., Japar, S. B., Muta, A., … Papenbrock, J. (2014). Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean. BioMed Central Evolutionary Biology, 14, 92. doi: 10.1186/1471-2148-14-92
   PubMed Web of Science ®Google Scholar
• Nguyen, X. V., Holzmeyer, L., & Papenbrock, J. (2013a). New record of the seagrass species Halophila major (Zoll.) Miquel in Vietnam: Evidence from leaf morphology and ITS analysis. Botanica Marina, 4, 313–321. doi: 10.1515/bot-2012-0188
   Web of Science ®Google Scholar
• Nguyen, X. V., Bujang, J. S., & Papenbrock, J. (2013b). Variability of leaf morphology and marker genes of members of the Halophila complex collected in Vietnam. Aquatic Botany, 110, 6–15. doi: 10.1016/j.aquabot.2013.04.003
   Web of Science ®Google Scholar
• Papenbrock, J. (2012). Highlights in seagrasses' phylogeny, physiology and metabolism: What makes them special? International Scholarly Research Notices Botany, 2012, 1–15. doi: 10.5402/2012/103892
   Google Scholar
• Petersen, G., Seberg, O., Short, F. T., & Fortes, M. D. (2014). Complete genomic congruence but non-monophyly of Cymodocea (Cymodoceaceae), a small group of seagrasses. Taxon, 63, 3–8. doi: 10.12705/631.2
   Web of Science ®Google Scholar
• Petersen, G., Seberg, O., Davis, J. I., & Stevenson, D. W. (2006). RNA editing and phylogenetic reconstruction in two monocot mitochondrial genes. Taxon, 55, 871–886. doi: 10.1534/genetics.110.118000
   Web of Science ®Google Scholar
• Pillon, Y., Munzinger, J., Amir, H., Hopkins, H. C. F., & Chase, M. W. (2009). Reticulate evolution on a mosaic of soils: Diversification of the New Caledonian endemic genus Codia (Cunoniaceae). Molecular Ecology, 18, 2263–2275. doi: 10.1111/j.1365-294X.2009.04178.x
   PubMed Web of Science ®Google Scholar
• Ravikumar, K., & Ganesan, R. (1990). A new subspecies of Halophila ovalis (R.Br.) J. D. Hook (Hydrocharitaceae) from the eastern coast of Peninsular India. Aquatic Botany, 36, 351–358).
   Web of Science ®Google Scholar
• Ramamurthy, K., Balakrishnan, N. P., Ravikumar, K., & Ganesan, R. (1992). Seagrasses of Coromandel Coast, India. Coimbatore, India: B.S.I. Publication.
   Google Scholar
• Reusch, T. B. H., Hukreide, W., Stam, W. T., & Olsen, J. L. (1999). Differentiating between clonal growth and limited gene flow using spatial autocorrelation of microsatellites. Heredity, 83, 120–126. doi: 10.1046/j.1365-2540.1999.00546.x
   PubMed Web of Science ®Google Scholar
• Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., … Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539–542. doi: 10.1093/sysbio/sys029
   PubMed Web of Science ®Google Scholar
• Scornavacca, C., Zickmann, F., & Huson, D. H. (2011). Tanglegrams for rooted phylogenetic trees and networks. Bioinformatics, 27, 248–256. doi: 10.1093/bioinformatics/btr210
   PubMed Web of Science ®Google Scholar
• Short, F. T., Moore, G. E., & Peyton, K. A. (2010). Halophila ovalis in the tropical Atlantic Ocean. Aquatic Botany, 93, 141–146. doi: 10.1016/j.aquabot.2010.05.001
   Web of Science ®Google Scholar
• Stamatakis, A. (2014). RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313. doi: 10.1093/bioinformatics/btu033
   PubMed Web of Science ®Google Scholar
• Tamura, K., & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512–526. Retrieved from http://mbe.oxfordjournals.org/content/10/3/512.full.pdf+html (accessed 27 April 2015).
   PubMed Web of Science ®Google Scholar
• Tanaka, N., Setoguchi, H., & Murata, J. (1997). Phylogeny of the family Hydrocharitaceae inferred from rbcL and matK gene sequence data. Journal of Plant Research, 110, 329–337. doi: 10.1007/BF02524931
   Web of Science ®Google Scholar
• Tanaka N., Uehara K., & Murata J. (2004). Correlation between pollen morphology and pollination mechanisms in the Hydrocharitaceae. Journal of Plant Research, 117, 265–276. doi: 10.1007/s10265-004-0155-5
   PubMed Web of Science ®Google Scholar
• Uchimura, M., Faye, E. J., Shimada, S., Arai, S., Inoue, T., & Nakamura, Y. (2006). A re-evaluation of the taxonomic status of Halophila euphlebia Makino (Hydrocharitaceae) based on morphological features and ITS sequence data. Botanica Marina, 49, 111–121. doi: 10.1515/BOT.2006.015
   Web of Science ®Google Scholar
• Uchimura, M., Faye, E. J., Shimada, S., Arai, S., Inoue, T., & Nakamura, Y. (2008). A reassessment of Halophila species (Hydrocharitaceae) diversity with special reference to Japanese representatives. Botanica Marina, 51, 258–268. doi: 10.1515/BOT.2008.036
   Web of Science ®Google Scholar
• Waycott, M., Procaccini, G., Les, D., & Reusch, T. (2006). Seagrass evolution, ecology and conservation: A genetic perspective. In A. W. D. Larkum, R. J. Orth, & C. M. Duarte (Eds.), Seagrasses: Biology, ecology and conservation (pp. 25–50). The Netherlands: Springer.
   Google Scholar
• Waycott, M., Freshwater, D., York, R., Calladine, A., & Kenworthy, W. (2002). Evolutionary trends in the seagrass genus Halophila (Thouars): Insights from molecular phylogeny. Bulletin of Marine Science, 71, 1299–1308. Retrieved from http://www.dcbd.nl (accessed 27 April 2015).
   Web of Science ®Google Scholar