Abstract
Living fossils are the important components of biodiversity. They represent the connection between the extinct and extant species. A living fossil is a living species that appears to be similar to a species otherwise known only from fossils, typically with no close living relatives and the extant species. The study of primitive species gives an idea about the ancestors from which they diverged and bring out many surprising facts which are unknown to the world. In a case study, species belonging to the phylum Arthropoda, Brachiopoda and Molluscs were collected from Sundarbans where Horshshoe Crab was the living fossils (Carcinoscorpius rotundicauda). Lingula sp and some crab species were included as the outgroup. To position this living fossil, DNA barcoding approach was employed as per standard protocol. COI sequencing and subsequently nucleotide analysis of all the species were done and also the molecular clock was constructed to locate their position along with their divergence time in correspondence with the other sequences of the allied taxa viz, Limulus polyphemus, Tachypleus gigas etc. It is found that the Carcinoscorpius rotundicauda are more closely related to its allied taxon Tachypleus gigas as compared to Limulus poluphemus and their divergence period is calculated which is supposed to be the 550 million years ago. Thus, DNA barcoding approach is a useful technique to properly identify species and to construct phylogenetic relationship among the species and subsequent assessment of the species divergence time.
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References
Avise JC, Bowen BW (1994) Investigating sea turtle migration using DNA markers. Curr Opin Genet Dev 4:882–886
Baek SY, Choi EH, Jang KH, Ryu SH, Park SM et al (2014) Complete mitochondrial genomes of Carcinoscorpius rotundicauda and Tachypleus tridentatus (Xiphosura, Arthropoda) and implications for chelicerate phylogenetic studies. Int J Biol Sci 10:479–489
Bhattacharjee MJ, Laskar BA, Dhar B, Ghosh SK (2012) Identification and re-evaluation of freshwater catfishes through DNA barcoding. PLoS ONE 7:e49950
Borisenko AV, Lim BK, Ivanova NV, Hanner RH, Hebert PD (2008) DNA barcoding in surveys of small mammal communities: a field study in Suriname. Mol Ecol Resour 8:471–479
Briggs DE, Moore RA, Shultz JW, Schweigert G (2005) Mineralization of soft-part anatomy and invading microbes in the horseshoe crab Mesolimulus from the Upper Jurassic Lagerstatte of Nusplingen, Germany. Proc Biol Sci 272:627–632
Briggs DE, Siveter DJ, Sutton MD, Garwood RJ, Legg D (2012) Silurian horseshoe crab illuminates the evolution of arthropod limbs. Proc Natl Acad Sci USA 109:15702–15705
Carroll RL (1997) Patterns and processes of vertebrate evolution. Cambridge University Press, New York. xvi, 448 pp
Chakraborty M, Ghosh SK (2014) An assessment of the DNA barcodes of Indian freshwater fishes. Gene 537:20–28
Cox AJ, Hebert PD (2001) Colonization, extinction, and phylogeographic patterning in a freshwater crustacean. Mol Ecol 10:371–386
Crow JF, Dove WF (2000) Perspectives on genetics: anecdotal, historical, and critical commentaries, 1987–1998. University of Wisconsin Press, Madison. xiii, 723 pp
Dhar B, Ghosh SK (2015) Genetic assessment of ornamental fish species from North East India. Gene 555:382–392
Dick MH, Lidgard S, Gordon DP, Mawatari SF (2009) The origin of ascophoran bryozoans was historically contingent but likely. Proc Biol Sci 276:3141–3148
Dunlop JA, Anderson LI, Kerp H, Hass H (2003) Palaeontology: preserved organs of Devonian harvestmen. Nature 425:916
Faurby S, King TL, Obst M, Hallerman EM, Pertoldi C et al (2010) Population dynamics of American horseshoe crabs—historic climatic events and recent anthropogenic pressures. Mol Ecol 19:3088–3100
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 3:294–299
Freeman G (1999) Regional specification during embryogenesis in the inarticulate brachiopod Discinisca. Dev Biol 209:321–339
Garcia-Horsman JA, Barquera B, Rumbley J, Ma J, Gennis RB (1994) The superfamily of heme-copper respiratory oxidases. J Bacteriol 176:5587–5600
Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci USA 103:968–971
Hebert PD, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270:313–321
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Kin A, Blazejowski B (2014) The horseshoe crab of the genus Limulus: living fossil or stabilomorph? PLoS ONE 9:e108036
Komiya H, Shimizu N, Kawakami M, Takemura S (1980) Nucleotide sequence of 5S ribosomal RNA from Lingula anatina. A study on the molecular evolution of 5S ribosomal RNA from a living fossil. J Biochem 88:1449–1456
Kosakyan A, Heger TJ, Leander BS, Todorov M, Mitchell EA et al (2012) COI barcoding of Nebelid testate amoebae (Amoebozoa: Arcellinida): extensive cryptic diversity and redefinition of the Hyalospheniidae Schultze. Protist 163:415–434
Laskar BA, Bhattacharjee MJ, Dhar B, Mahadani P, Kundu S et al (2013) The species dilemma of northeast Indian mahseer (Actinopterygii: Cyprinidae): DNA barcoding in clarifying the riddle. PLoS ONE 8:e53704
Lee MS (1999) Molecular clock calibrations and metazoan divergence dates. J Mol Evol 49:385–391
Legg DA (2014) Sanctacaris uncata: the oldest chelicerate (Arthropoda). Naturwissenschaften 101:1065–1073
Legg DA, Sutton MD, Edgecombe GD, Caron JB (2012) Cambrian bivalved arthropod reveals origin of arthrodization. Proc Biol Sci 279:4699–4704
Lynch M, Jarrell PE (1993) A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics 135:1197–1208
Mahadani P, Ghosh SK (2013) DNA Barcoding: a tool for species identification from herbal juices. DNA Barcodes 1:35–38
Manna S, Chaudhuri K, Bhattacharyya S, Bhattacharyya M (2010) Dynamics of Sundarban estuarine ecosystem: eutrophication induced threat to mangroves. Saline Syst 6:8
Masta SE, Longhorn SJ, Boore JL (2009) Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Mol Phylogenet Evol 50:117–128
Nossa CW, Havlak P, Yue JX, Lv J, Vincent KY et al (2014) Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. Gigascience 3:9
Obst M, Faurby S, Bussarawit S, Funch P (2012) Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species. Mol Phylogenet Evol 62:21–26
Purvis A, Gittleman JL, Brooks T (2005) Phylogeny and conservation. Cambridge University Press, Cambridge. xiii, 431 pp
Rehm P, Pick C, Borner J, Markl J, Burmester T (2012) The diversity and evolution of chelicerate hemocyanins. BMC Evol Biol 12:19
Rubinoff D (2006) Utility of mitochondrial DNA barcodes in species conservation. Conserv Biol 20:1026–1033
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Schoenemann B, Clarkson EN (2013) Discovery of some 400 million year-old sensory structures in the compound eyes of trilobites. Sci Rep 3:1429
Sharma PP, Tarazona OA, Lopez DH, Schwager EE, Cohn MJ et al (2015) A conserved genetic mechanism specifies deutocerebral appendage identity in insects and arachnids. Proc Biol Sci 282:20150698
Shishikura F, Nakamura S, Takahashi K, Sekiguchi K (1982) Horseshoe crab phylogeny based on amino acid sequences of the fibrino‐peptide‐like peptide C. J Exp Zool Part A 223(1):89–91
Shishikura F, Sekiguchi K (1984) Studies on perivitelline fluid of horseshoe crab embryo. II. Purification of agglutinin-binding substance from the perivitelline fluid of Tachypleus gigas embryo. J Biochem 96:629–636
Silvestro D, Antonelli A, Salamin N, Quental TB (2015) The role of clade competition in the diversification of North American canids. Proc Natl Acad Sci USA 112:8684–8689
Simmons RB, Weller SJ (2001) Utility and evolution of cytochrome b in insects. Mol Phylogenet Evol 20:196–210
Srimal S, Miyata T, Kawabata S, Iwanaga S (1985) The complete amino acid sequence of coagulogen isolated from Southeast Asian horseshoe crab, Carcinoscorpius rotundicauda. J Biochem 98:305–318
Staton JL, Daehler LL, Brown WM (1997) Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes. Mol Biol Evol 14:867–874
Stoeckle MY, Hebert PD (2008) Barcode of life. Sci Am 299:82–86, 88
Sykes B (1999) The molecular genetics of European ancestry. Philos Trans R Soc Lond B Biol Sci 354:131–138. Discussion 138–139
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Trivedi S, Affan R, Allesa AHA, Ansari AA, Dhar B, Mahadani P, Ghosh SK (2014) DNA BARcoding of Red Sea fishes from Saudi Arabia—the first approach. DNA Barcodes 2:17–20
Trivedi S, Aloufi AA, Ansari AA, Ghosh SK (2015) Molecular phylogeny of oysters belonging to the genus Crassostrea through DNA barcoding. J Entomol Zool Stud 3(1):21–26
Trivedi S, Aloufi AA, Ansari AA, Ghosh SK (2016a) Role of DNA barcoding in marine biodiversity assessment and conservation: an update. Saudi J Biolog Sci 23(2):161–171
Trivedi S, Aloufi AA, Rehman H, Saggu S, Ghosh SK (2016b) DNA barcoding: tool for assessing species identification in Reptilia. J Entomol Zool Stud 4(1):132–137
Trivedi S, Ansari AA, Rehman H, Saggu S, Abbas ZK, Ghosh SK (2016c) DNA barcoding as a molecular tool for the assessment of plant biodiversity. In: Ansari AA, Gill SS (eds) Plant biodiversity: monitoring assessment and conservation. CABI Publications, UK (in press)
Van Roy P, Orr PJ, Botting JP, Muir LA, Vinther J et al (2010) Ordovician faunas of Burgess Shale type. Nature 465:215–218
Vasquez MC, Murillo A, Brockmann HJ, Julian D (2015) Multiple stressor interactions influence embryo development rate in the American horseshoe crab, Limulus polyphemus. J Exp Biol 218:2355–2364
Wares JP, Cunningham CW (2001) Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 55:2455–2469
Xia X (2000) Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses. Syst Biol 49:87–100
Zhang DX, Hewitt GM (1997) Assessment of the universality and utility of a set of conserved mitochondrial COI primers in insects. Insect Mol Biol 6:143–150
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Dhar, B. et al. (2016). DNA Barcoding: Molecular Positioning of Living Fossils (Horseshoe Crab). In: Trivedi, S., Ansari, A., Ghosh, S., Rehman, H. (eds) DNA Barcoding in Marine Perspectives. Springer, Cham. https://doi.org/10.1007/978-3-319-41840-7_12
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DOI: https://doi.org/10.1007/978-3-319-41840-7_12
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