357
Views
5
CrossRef citations to date
0
Altmetric
Research Article

rDNA analysis of the Red Sea seagrass, Halophila, reveals vicariant evolutionary diversification

, , , & ORCID Icon
Pages 668-679 | Received 10 Feb 2018, Accepted 29 May 2018, Published online: 17 Oct 2018

References

  • Bandelt, H. J., Forster, P., & Rohl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37–48.
  • Benzecry, A. & Brack-Hanes, S. (2016). Evolutionary trends in Hydrocharitaceae seagrasses. Annual Research & Review in Biology, 9, 1–8. doi:10.9734/ARRB/2016/24354
  • Birnboim, H. C., Doly J. (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Research, 7, 1513–1523.
  • Bonatti, E., Cipriani, A., & Lupi, L. (2015). The red sea: Birth of an ocean. In N.M.A. Rasul & I.C.F. Stewart (Eds.), The Red Sea: The Formation, Morphology, Oceanography and Environment of a young ocean basin (pp. 29–44). Berlin Heidelberg: Springer-Verlag Springer Earth System Sciences.
  • Cancemi, G., Terlizzi, A., Scipione, M. B., & Mazzella, L. (1994). II pratoad Halophila stipulacea (Forssk.) Aschers. di G. Naxos (Sicilia): Caratteristiche della planta e del popolamento a fauna vagile. Biologia Marina Mediterranea, 1, 401–402.
  • 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
  • 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
  • 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.
  • El Shaffai, A. (2016). Field guide to seagrasses of the Red Sea. In A. Rouphael & A. Abdulla (Eds.), Second Edition, Vol. 8 (pp. 56). Gland, Switzerland: IUCN and Courbevoie, France: Total Foundation.
  • Excoffier, L., & Lischer, H. E. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resource, 10, 564–567. doi:10.1111/j.1755-0998.2010.02847.x
  • Gkafas, G. A., Orfanidis, S., Vafidis, D., Panagiotaki, P., Kupper, F. C., & Exadactylos, A. (2016). Genetic diversity and structure of Cymodocea nodosa meadows in the Aegean sea, Eastern Mediterranean. Applied Ecology and Environmental Research, 15, 145–160. doi:10.15666/aeer/1401_145160
  • Guindon, S., & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696–704. doi:10.1080/10635150390235520
  • Hall, K. B. (2011). Evolution: Principles and processes. Massachusetts, USA: Jones and Bartlett Publishers.
  • Harrison, R. G. (2012). Language of speciation. Evolution, 66, 3643–3657. doi:10.1111/j.1558-5646.2012.01785.x
  • Karako, S., Achituv, Y., Perl-Treves, R., & Katcoff, D. (2002). Asterina burtoni (Asteroidea; Echinodermata) in the Mediterranean and the Red Sea: Does asexual reproduction facilitate colonization? Marine Ecology Progress Series, 234, 139–145. doi:10.3354/meps234139
  • 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. doi:10.1111/j.1439-0485.2006
  • Li, X., Duke, N. C., Yang, Y., Huang, L., Zhu, Y., Zhang, Z.,…Shi, S. (2016). Re-evaluation of phylogenetic relationships among species of the mangrove genus Avicennia from Indo-West Pacific based on multilocus analyses. Public Library of Science One, 11, e0164453. doi:10.1371/journal.pone.0164453
  • Lucas, C., Thangaradjou, T., & Papenbrock, J. (2012). Development of a DNA barcoding system for seagrasses: Successful but not simple. Public Library of Science One, 7, e29987. doi:10.1371/journal.pone.0029987
  • Müller, K. (2006). Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution, 38, 667–676. doi:10.1016/j.ympev.2005.07.011
  • Nguyen, X. V., Bujang, J. S., & Papenbrock, J. (2013). Variability of leaf morphology and marker genes of members of the Halophila complex collected in Viet Nam. Aquatic Botany, 110, 6–15. doi:10.1016/j.aquabot.2013.04.003
  • Nguyen, V. X., Detcharoen, M., Tuntiprapas, P., Soe-Htun, U., Sidik, J. B., Harah, M. Z.,…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
  • Nguyen, X. V., Höfler, S., Glasenapp, Y., Thangaradjou, T., Lucas, C., & Papenbrock, J. (2015). New insights into DNA barcoding of seagrasses. Systematics and Biodiversity, 13, 496–508. doi:10.1080/14772000.2015.1046408
  • Nguyen, X. V., Holzmeyer, L., & Papenbrock, J. (2013). New record of the seagrass species Halophila major (Zoll.) Miquel in Vietnam: Evidence from leaf morphology and ITS analysis. Botanica Marina, 56, 313–321. doi:10.1515/bot-2012-0188
  • Nguyen, X. V., Thangaradjou, T., & Papenbrock, J. (2013). Genetic variation among Halophila ovalis (Hydrocharitaceae) and closely related seagrass species from the coast of Tamil Nadu, India – an AFLP fingerprint approach. Systematics and Biodiversity, 11, 467–476. doi:10.1080/14772000.2013.838317
  • Papenbrock, J. (2012). Highlights in seagrasses’ phylogeny, physiology and metabolism: What makes them special? International Scholarly Research Notices: Botany, doi:10.5402/2012/103892.
  • Procaccini, G., Acunto, S., Famà, P., & Maltagliati, F. (1999). Structural, morphological and genetic variability in Halophila stipulacea (Hydrocharitaceae) populations in the western Mediterranean. Marine Biology, 135, 181–189. doi:10.1007/s002270050615
  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Hohna, 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
  • Ruggiero, V. M., & Procaccini, G. (2004). The rDNA ITS region in the Lessepsian marine angiosperm Halophila stipulacea (Forssk.) Aschers. (Hydrocharitaceae): Intragenomic variability and putative pseudogenic sequences. Molecular Evolution, 58, 115–121. 10.1007/s00239-003-2536-0
  • Serra, I. A., Innocenti, A. M., Di Maida, G., Calvo, S., Migliaccio, M., Zambianchi, E.,…Procaccini, G. (2010). Genetic structure in the Mediterranean seagrass Posidonia oceanica: disentangling past vicariance events from contemporary patterns of gene flow. Molecular Ecology, 19, 557–568. doi:10.1111/j.1365-294X.2009.04462.x
  • Short, F., Carruthers, T., Dennison, W., & Waycott, M. (2007). Global seagrass distribution and diversity: A bioregional model. Experimental Marine Biology and Ecology, 350, 3–20. doi:10.1016/j.jembe.2007.06.012
  • 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
  • Short, F. T., Polidoro, B., Livingstone, S. R., Carpenter, K.E., Bandeira, S., Bujang, J. S.,…Zieman, J. C. (2011). Extinction risk assessment of the world’s seagrass species. Biological Conservation, 144, 1961–1971. doi:10.1016/j.biocon.2011.04.010
  • 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
  • Stanford, A. M., Harden, R., & Parks, C. R. (2000). Phylogeny and biogeography of Juglans (Juglandaceae) based on matK and ITS sequence data. American Journal of Botany, 87, 872–882. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/10860918 (accessed 24 July 2018).
  • 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. doi:10.1093/oxfordjournals.molbev.a040023
  • Tenggardjaja, K., Jackson, A., Leon, F., Azzurro, E., Golani, D., & Bernardi, G. (2013). Genetics of a Lessepsian sprinter: The bluespotted cornetfish, Fistularia commersonii. Israel Journal of Ecology & Evolution, 59, 181–185. doi:10.1080/15659801.2013.898402
  • Thompson, J. D., Gibson, T.J., Plewniak, F., Jeanmougin, F., & Higgins, D.G. (1997). The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876–4882. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC147148/ (accessed 22 March 2018).
  • Tikochinski, Y., Russell, B., Hyams, Y., Motro, U., & Golani, D. (2016). Molecular analysis of the recently described lizardfish Saurida lessepsianus (Synodontidae) from the Red Sea and the Mediterranean, with remarks on its phylogeny and genetic bottleneck effect. Marine Biology Research, 12, 419–425. doi:10.1080/17451000.2016.1148821
  • Triest, L., & Sierens, T. (2014). Seagrass radiation after Messinian Salinity Crisis reflected by strong genetic structuring and out-of-Africa scenario (Ruppiaceae). Public Library of Science One, 9, e104264. doi:10.1371/journal.pone.0104264
  • Uchimura, M., Jean Faye, E., Shimada, 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
  • Vermaatl, J. E., Agawin, N. S. R., Duarte, C. M., Fortes, M. D., Marbà, N., Uri, J. S. (1995). Meadow maintenance, growth and productivity of a mixed Philippine seagrass bed. Marine Ecological Progress Series, 124, 215–225. Retrieved from http://www.int-res.com/articles/meps/124/m124p215.pdf (accessed 22 March 2018).
  • Waycott, M., Freshwater, D. W., York, R. A., Calladine, A., & Kenworthy, W. J. (2002). Evolutionary trends in the seagrass genus Halophila (Thouars): Insights from molecular phylogeny. Bulletin of Marine Science, 71, 1299–1308. Retrieved from https://libres.uncg.edu/ir/uncw/f/freshwaterw2002-1.pdf (accessed 22 March 2018).
  • White, T. J., Bruns, T., Lee, S., & Taylor, J. W. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelf, J. J. Sninsky, & T. J. White (Eds.), PCR Protocols: A guide to methods and applications (pp. 315–322). New York: Academic Press.
  • Wu, K., Chen, C. N. N., & Soong, K. (2016). Long distance dispersal potential of two seagrasses Thalassia hemprichii and Halophila ovalis. Public Library of Science One, 11, e0156585. doi:10.1371/journal.pone.0156585
  • Yağlıoğlu, D., & Turan, C. (2012 ). Colonization and genetic changes of Indo-Pacific immigrant Saurida undosquamis (Richardson, 1848) (Lizardfish) in the Mediterranean Sea. Journal of Black Sea/Mediterranean Environment, 18, 329–340. Retrieved from http://dergipark.ulakbim.gov.tr/jbme/article/view/5000144373 (accessed 22 March 2018).
  • Yang, Y., Duke, N. C., Peng, F., Li, J., Yang, S., Zhong,…Shi, S. (2016). Ancient geographical barriers drive differentiation among Sonneratia caseolaris populations and recent divergence from S. lanceolata. Frontiers in Plant Science, 7, 1618. doi:10.3389/fpls.2016.01618

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.