Cytochrome C Oxidase Subunit 1 (COI) Profile of the Philippine Helicostylinae (Gastropoda: Stylommatophora: Camaenidae)
Gizelle A. Batomalaque1,4,*, Gerard Clinton L. Que1,
Tyrill Adolf B. Itong5, Anna Regina L. Masanga1,
Emmanuel Ryan C. de Chavez3, and Ian Kendrich C. Fontanilla1,2
1Insitute of Biology, College of Science,
University of the Philippines Diliman, Quezon City 1101 Philippines
2Natural Sciences Research Institute,
University of the Philippines Diliman, Quezon City 1101 Philippines
3Institute of Biological Sciences, College of Arts and Sciences,
University of the Philippines Los Baños 4031 Laguna, Philippines
4Department of Biodiversity, Earth and Environmental Sciences,
College of Arts and Sciences, Drexel University, Philadelphia, PA 19104 USA
5College of Science, University of the Philippines Cebu, Cebu City 6000 Philippines
*Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.
ABSTRACT
The Philippines is the center of radiation of the land snail subfamily Helicostylinae, with around 253 recognized species. Despite their morphological diversity, research on their biology and taxonomy is lacking. We present here the first mitochondrial COI profiles of 32 species of Philippine helicostyline land snails. With the addition of sequences downloaded from GenBank, we tested the utility of the COI for species identification. Relative distributions of intraspecific and interspecific distances overlapped; hence, no barcoding gap was observed. However, 90% of uncorrected interspecific comparisons can distinguish species at 14% genetic distance or lower. Furthermore, the COI barcodes could not discriminate several co-distributed species that have similar conchological features, which should be flagged for taxonomic re-evaluation.
INTRODUCTION
The Helicostylinae, a subfamily under family Camaenidae (sensu Bouchet et al. 2017) and order Stylommatophora, are hermaphroditic ground and tree snails whose center of diversity is the Philippine Islands (Parkinson et al. 1987, Abbott 1989, de Chavez et al. 2015) and whose distribution extends to Taiwan, the Moluccas, and the smaller islands off the coast of Borneo (Schileyko 2004, Schilthuizen et al. 2013). Members of this subfamily exhibit a range in shell forms from discoidal, depressed and keeled, globose, to elongated conical forms (Parkinson et al. 1987). Within the Philippines, different helicostyline species vary in distributions, with most occurring in single islands (e.g., Anixa siquijorensis in Siquijor Is. and Helicostyla (Calocochlea) chrysocheila in Luzon Is.) and some occurring in multiple adjacent islands (e.g., Leytia fragilis in Samar and Leyte islands and Trachystyla cryptica in the islands of Samar, Leyte, and Mindanao). There are about 245 species (Batomalaque n/p, Faustino 1930, Richardson 1983, Abbott 1989) belonging to 23 genera (Schileyko 2004, Bouchet et al. 2017). The current taxonomy of the helicostylines is based on shell morphology, although the reproductive anatomy for some species has been described (Schileyko 2004). No molecular work has been done to evaluate their current classification, and phylogenetic relationships among the species are unknown. . . . read more
REFERENCES
ABBOTT RT. 1989. Compendium of landshells: A full-color guide to more than 2,000 of the world’s terrestrial shells. Melbourne, FL: American Malacologist, Inc. 240p.
AKAIKE H. 1973. Information theory and an extension of the maximum likelihood principle. In: Petrov BN, Csaki F eds. 2nd International Symposium on Information Theory. Budapest, Hungary: Akademia Kiado.
AKAIKE H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr 19(6): 716–723.
ALTEKAR G, DWARKADAS S, HUELSENBECK JP, RONQUIST F. 2004. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407–415.
BOUCHET P, ROCROI J, HAUSDORF B, KAIM A, KANO Y, NÜTZEL A, PARKHAEV P, SCHRÖDL M, STRONG EE. 2017. Revised classification, nomenclator and typification of gastropod and monoplacophoran families. Malacologia 61(1–2): 1–526.
CAMERON RAD, COOK LM. 2012. Habitat and the shell polymorphism of Ceparea nemoralis (L.): Interrogating the Evolution Megalab database. J Moll Stud 78: 179–184.
CHIBA S. 1993. Modern and historical evidence of natural hybridization between sympatric species in Mandarina (Pulmonata: Camaenidae). Evolution 47(5): 1539–1556.
CHIBA S. 1996. Ecological and morphological diversification within single species and character displacement in Mandarina, endemic land snails of the Bonin Islands. J Evol Bio 9: 277–291.
CHIBA S. 1999. Character displacement, frequency-dependent selection, and divergence of shell colour in land snails Mandarina (Pulmonata). Biol J Linn Soc 66: 465–479.
CHIBA S, 2009. Morphological divergence as a result of common adaptation to a shared environment in land snails of the genus Hirasea. J Molluscan Stud 75: 253–259.
DARRIBA D, POSADA D, STAMATAKIS A. 2015. ModelTest-NG. Retrieved from https://github.com/ddarriba/modeltest
DAVISON A, CHIBA S. 2006. Labile ecotypes accompany rapid cladogenesis in an adaptive radiation of Mandarina (Bradybaenidae) land snails. Biol J Linn Soc 88: 269–282.
DAVISON A, BLACKIE RLE, SCOTHERN GP. 2009. DNA barcoding of stylommatophoran land snails: A test of existing sequences. Mol Ecol Resour 9(4): 1092–1101.
DE CHAVEZ ERC, FONTANILLA IKC, BATOMALAQUE GA, CHIBA S. 2015. A new Helicostyla species (Bradybaenidae: Helicostylinae) from Patnanungan Island, Philippines. Asia Life Sci 24(1): 37–49.
FAUSTINO LA. 1930. Summary of Philippine land shells. Philipp J Sci 42(1): 85–198.
FELSENSTEIN J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17(6): 368–376.
FELSENSTEIN J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evol. 39(4): 783–791.
FOLMER O, BLACK M, HOEH W, LUTZ R, VRIJENHOEK R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3(5): 294–299.
FONTANILLA IKC, NAGGS F, WADE CM. 2017. Molecular phylogeny of the Achatinoidea (Mollusca: Gastropoda). Mol Phylogenet Evol 114: 382–385.
GOODFRIEND GA. 1986. Variation in land-snail shell form and size and its causes: A review. Syst Zool 35(2): 204–223.
HALL TA. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95–98.
HALL R. 2002. Conozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: Computer-based reconstructions, model and animations. J. Asian Earth Sci. 20: 353–431.
HEBERT PDN, CYWINSKA A, BALL SL, DEWAARD JR. 2003. Biological identifications through DNA barcodes. Proc R Soc Britain 270: 313–321.
HEBERT PDN, STOECKLE MY, ZEMLAK TS, FRANCIS CM. 2004. Identification of birds through DNA barcodes. PLoS Biol 2: e312.
HIRANO T, KAMEDA Y, KIMURA K, CHIBA S. 2014. Substantial incongruence among the morphology, taxonomy, and molecular phylogeny of the land snails Aegista, Landouria, Trishoplita, and Pseudobulimus (Pulmonata: Bradybaenidae) occurring in East Asia. Mol Phylogenet Evol 70: 171–181.
HURVICH C, TSAI C. 1993. A corrected Akaike information criterion for vector autoregressive model selection. J Time Ser Anal 14(3): 271–279.
HUSON DH, SCORNAVACCA C. 2012. Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Syst Biol 61(6): 1061–1067.
MEYER CP, PAULAY G. 2005. DNA barcoding: Error rates based on comprehensive sampling. PLoS Biol 3(12): e422. Available from: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0030422
PARK DS, FOOTTIT R, MAW E, HEBERT PDN. 2011. Barcoding bugs: DNA-based identification of the true bugs (Insecta: Hemiptera: Heteroptera). PLoS ONE 6: e18749.
PARKINSON B, HEMMEN J, GROH K. 1987. Tropical land shells of the world. Berlin, Germany: Verlag. 279p.
PEREZ KE, DEFREITAS N, SLAPCINSKY J, MINTON RL, ANDERSON FE, PEARCE TA. 2014. Molecular phylogeny, evolution of shell shape, and DNA barcoding in Polygyridae (Gastropoda: Pulmonata), an endemic North American clade of land snails. Am Malacol Bull 32(1): 1–31.
PFENNIGER M, POSADA D. 2002. Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution 56: 1776–1788.
RAMBAUT A. 2016. FigTree: Tree figure drawing tool, version 1.4.3. Retrieved from http://tree.bio.ed.ac.uk/software/figtree/
RICHARDSON L. 1983. Bradybaenidae: Catalogue of Species: Tryonia. Philadelphia, PA: Academy of Natural Sciences – Department of Malacology. 253p.
RONQUIST F, TESLENKO M, VAN DER MARK P, AYRES D, DARLING A, HÖHNA S, LARGET B, LIU L, SUCHARD M, HUELSENBECK J. 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3): 539–542.
ROZAS J, FERRER-MATA A, SÁNCHEZ-DELBARRIO JC, GUIRAO-RICO S, LIBRADO P, RAMOS-ONSINS SE, SÁNCHEZ-GRACIA A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol Evol 34: 3299–3302.
SAITOU N, NEI M. 1987. The neighbor-joining method: A new method for reconstructing evolutionary trees. Mol Biol Evol 4: 406–425.
SCHEFFER SJ, LEWIS ML, JOSHI RC. 2006. DNA barcoding applied to invasive leafminers (Diptera: Agromyzidae) in the Philippines. Ann Entomol Soc Am 99(2): 204–210.
SCHILEYKO AA. 2004. Treatise on recent terrestrial pulmonated molluscs, Part 12: Bradybaenidae, Ruthenica 2(Supp.): 138.
SCHILTHUIZEN M, LIEW TS, LIEW TH, BERLIN P, KING JP, LAKIM M. 2013. Species diversity patterns in insular land snail communities of Borneo. J Geol Soc London 170: 539–545.
SEI M, ROBINSON DG, GENEVA AJ, ROSENBERG G. 2017. Double helix: Sagdoidea is the overlooked sister group of Helicoidea (Mollusca: Gastropoda: Pulmonata). Biol J Linn Soc 20: 1–32.
SIDDALL ME, KVIST S, PHILLIPS A, OCEGUERA-FIGUERO A. 2012. DNA barcoding parasitic nematodes: Is it kosher? J Parasitol 98: 692–684.
SPRINGSTEEN FJ, LEOBRERA FM. 1986. Shells of the Philippines. Manila, Philippines: Carfel Seashell Museum. 377p.
STADEN R, BEAL KF, BONFIELD JK. 2000. The Staden package, 1998. Methods Mol Biol 132: 115–130.
STAMATAKIS A, HOOVER P, ROUGEMONT J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57(5): 758–771.
STAMATAKIS A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9): 1312–1313.
SWOFFORD DL. 2003. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sunderland, MA: Sinauer Associates.
TAMURA K. 1999. TreeExplorer. Retrieved from: http://evol.gen.biol.metro-u.ac.jp/TE/TE_man.html
TAVARE S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Some mathematical questions in biology – DNA sequence analysis. Providence, RI: American Mathematical Society. p. 57–86.
THOMPSON J, HIGGINS D, GIBSON T. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22): 4673–4680.
VIRGILIO M, BACKELJAU T, NEVADO B, MEYER MD. 2010. Comparative performances of DNA barcoding across insect orders. BMC Bioinformatics 11: 206.
WARD RD, COSTA FO, HOLMES BH, STEINKE D. 2008. DNA barcoding of shared fish species from North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species. Aquat. Biol. 3: 71–78.
WATANABE Y, CHIBA S. 2001. High within-population mitochondrial DNA variation due to microvariance and population mixing in the land snail Euhadra quaesita (Pulmonata: Bradybaenidae). Mol Ecol 10: 2635–2645.
WOODRUFF DS, GOULD SJ. 1987. Fifty years of interspecific hybridization: Genetics and morphometrics of a controlled experiment on the land snail Cerion in the Florida Keys. Evolution 41(5): 1022–1045.
XIA X. 2013. DAMBE5: A comprehensive software package for Data Analysis in Molecular Biology and Evolution. Mol Biol Evol 30(7): 1720–1728.
XIA X. 2017. DAMBE6: New tools for microbial genomics, phylogenetics, and molecular evolution. J Hered 108(4): 431–437.
XIA X, LEMEY P. 2009. Assessing substitution saturation with DAMBE. In: The phylogenetic handbook: a practical approach to DNA and protein phylogeny, 2nd ed. Lemey P, Salemi M, Vandamme A eds. Cambridge: Cambridge University Press. p. 615–630.
XIA X, XIE Z, SALEMI M, CHEN L, WANG Y. 2003. An index of substitution saturation and its application. Mol Phylogenet Evol 26(1): 1–7.
