Application of Molecular Phylogeny and Bioinformatics for Identification of Cryptic Species in a Community

Sneha Joseph, Paresh Poriya, Bhavik Vakani, Rahul Kundu

Abstract


Molecular markers like mtDNACOI have proved their identification efficiency in discriminating closely related species which may possibly have a vital effect on biodiversity estimation.Traditional methods based on morphology often fail to identify closely related species causing an over or under estimation of biodiversity. Studies have demonstrated that marine fauna exhibits high degree of cryptism. Thus, a lot of species either remain unidentified or have been identified erroneously. Present study involves the morphological identification of a group of limpet species found in the intertidal zones of Saurashtra coastline Gujarat followed by their COI gene sequence analysis. They were identified as Cellana karachiensis.Interestingly the three sample types: X, Y and Z, sharing the same habitat not only exhibit clear variations in their shell banding pattern but also show minor variations in their COI gene sequence. A total of six COI gene haplotypes were found using DnaSP version 5. A striking association of COI haplotypes to specific morphotypes was seen. Construction of phylogenetic tree using Mr. Bayes 3.2 clarifies the phylogenetic relationships of these samples indicating a split of lineages. This intriguing observation has put forth many possibilities. Is this plasticity due to polymorphism? Could they be a complex of cryptic species undergoing sympatric or peripatric speciation? It is also possible that they had been geographically isolated earlier and after genetic divergence occurred, came back to same location. This study thus points towards the need to reinvent an accurate baseline database of marine speciesand highlights the potential of molecular taxonomy in distinguishing between closely related species.

Keywords


Biodiversity Estimation; Molecular Taxonomy; mtdna Coi; Speciation; Limpet; Kathiawar Peninsula

References


Bickford, D.; Lohman, D.J.; Sohdi, N.S.; Ng, P.K.L.; Meier, R.; Winker, K.; Ingram, K.K. and Das,I. 2007. Cryptic species as a window on diversity and conservation. Trends in Ecology and Evolution 22:148–155.

Bucklin, A.; Steinke,D. andBlanco-Bercial,L. 2011. DNA barcoding of marine metazoan. Annual Review Marine Science 3: 471-508.

Faladu, J.; Vakani, B.; Poriya, P. and Kundu, R. 2014. Habitat preference and population ecology of Limpets Cellana karachiensis (Winckworth) and Siphonaria siphonaria (Sowerby) at Veraval Coast of Kathiawar Peninsula, India. Journal of Ecosystems. Article ID 874013, p 1-6. [Online] doi.org/10.1155/2014/874013.

Folmer, O.; Black, M.; Hoeh, W.; Lutz, R. and Vrijenhoek, R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294–299.

Herbert, P. D. N.;Cywinska, A.; Ball,S. L. anddeWaard,J. R. 2003. Biological identification through DNA Barcodes. Proceedings of the Royal SocietyB. 270(1512): 313-21.

Neusser, T.P.; Jörger, K.M. and Schrödl, M. 2011. Cryptic species in tropic sands – interactive 3d anatomy, molecular phylogeny and evolution of meiofaunal Pseudunelidae (Gastropoda, Acochlidia). PLoS ONE 6(8): e23313. [online] doi:10.1371/journal.pone.0023313.

Payne, J.L.; Mazzucco, R. and Dieckmann, U. 2011. The evolution of conditional dispersal and reproductive isolation along environmental gradients. Journal of Theoretical Biology 273: 147–155.

Prasad, M. N.;Malli, P.C. and Mansur, A.P. 1984. The color banding pattern and frequencies in a tropical limpet Cellana radiata (Born) on the Veraval coast of western India. Journal of the Marine Biological Association of India 24: 67-68.

Ronquist, F.; Teslenko, M.; Van Der Mark, P.; Ayres, D.L.; Darling, A.; Höhna, S.; Larget, B.; Liu, L.; Suchard, M.A. and Huelsen-beck, J.P. 2012. Mr Bayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539-42.

Rozas, J. 2009. DNA sequence polymorphism analysis using DnaSp. Pages 337-350, In: Posada, D. (Editor) Bioinformatics for DNA Sequence Analysis: Methods in Molecular Biology Series 537. Humana Press, New Jersey.

Silvestro, D. and Michalak, I. 2012. raxmlGUI: a graphical front-end for RAxML. Organisms Diversity & Evolution 12: 335–337.

Schön, I.; Pinto, R. L.; Halse, S.; Smith, A.J.; Martens,K. and Birky, C.W. 2012. Cryptic species in putative ancient asexual Darwinulids (Crustacea, Ostracoda). PLoS ONE 7: e39844. [online] doi:10.1371/journal.pone.0039844.

Sneha Joseph; Poriya, P. and Kundu, R. 2014. Probing the phylogenetic relationships of a few newly recorded intertidal zoanthid of Gujarat coast (India) with mtDNA COI sequences. Mitochondrial DNA [online] doi/abs/10.3109/19401736.2014.971239.

Sneha Joseph; Poriya, P.; Vakani, B.; Singh, S. P. and Kundu, R. 2016a. Identification of a group of cryptic marine limpet species, Cellana karachiensis (Mollusca: Patellogastropoda) off Veraval coast, India, using mtDNA COI sequencing. Mitochondrial DNA Part A 27(2): 1328–1331.

Sneha Joseph; Vakani, B. and Kundu, R. 2016b. Molecular phylogenetic study on few morphotypes of a Patellogastropod Cellana karachiensis from northern Arabian Sea reveals unexpected genetic diversity. Mitochondrial DNA Part A. (In press).

Vakani, B.; Poriya, P. and Kundu, R. 2013. Spatio-temporal variations in the population ecology of two limpets in a rocky intertidal shore of south Saurashtra coast (Gujarat: India). The Ecoscan 8 (1 & 2): 71-75.

Vrijenhoek, R. C. 2009. Cryptic species, phenotypic plasticity, and complex life histories: Assessing deep-sea faunal diversity with molecular markers. Deep-Sea Research II 56:1713–1723.

Zafar, F.S.H. and Ayub, Z. 2013. Allometric variations and condition factor in Cellana karachiensis (Winckworth, 1930) found at two adjacent rocky of Karachi, Pakistan. Indian Journal of Geo-marine Sciences 42: 794-799.


Full Text: PDF

Refbacks

  • There are currently no refbacks.


Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.

COPYRIGHT of this Journal vests fully with the National Instional Institute of Ecology. Any commercial use of the content on this site in any form is legally prohibited.