Review of Literature Chapter-2

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1 2.1 REVIEW OF LITERATURE DNA barcoding is a major field of research in fish taxonomy and it is useful for the characterization of fishes existing in the throughout world. India has a wider continental shelf with 8000 km length of coastline with high potential of fishery resources. Eastern part of India, in Bay of Bengal, the Andaman group of Islands has rich marine habitants with good diversity of fishes. Further, it is an isolated, virgin area in terms of exploration as well as exploitation of fishery resources. So, to understand species genetic divergences, evolution of fishes and to develop a faster and reliable tool for commercialisation an attempt was made through barcoding of fishes from Andaman waters. Evaluate the status of barcoding with reference to fish taxonomy a detailed review on existing literature were carried out in worldwide, national and regional level also DNA BARCODING IN FISHES AND OTHER ANIMALS - STATUS Taxonomy is the science assigning names to species and higher taxa. At present the numbers of taxonomists are declined and there are insufficient numbers of specialists (Rubinoff, 2006; Hebert et al., 2003a; Packer et al., 2009) in this field to handle the present taxonomy scenario. Hebert et al., (2003b) estimated that there are 15,000 taxonomists will be required for the identification of million species. It will cumbersome to identify the new species, which is having maximum similarities in morphological and environment identities. In these circumstances, the modern tool of DNA Barcoding evolved and provides a better understanding of morphological classifications, which were appeared due to the slight variation in the environment or other factors (Hebert et al., 2003a,b, 2004a; Ward et al., 2005). Barcoding is a compliment to current research in taxonomic studies by providing detailed information which will be helpful for the identification of taxa in nature (Hajibabaei et al., 2006a; Hebert et al., 2004b; Ball et al., 2005; Saunders, 2005; Ward et al., 2005; Hajibabaei et al., 2007a). Because, the traditional taxonomy able to provide descriptions for less than quarter of the world species using variety of morphological keys as a tool (Packer et al., 2009), so a faster and reliable tool is essential. In fact, DNA-based identification cannot be accomplished without the involvement and expertise of taxonomists who identify specimens from which reference sequences were obtained (Ball et al., 2005; Hebert et al., 2003a; 2005a; 8

2 Coyne and Orr, 2004). Hubert et al. (2008), explained the efficiency of the DNA barcoding hinges on the degree of sequence divergence among species and specieslevel identifications. Further, as reported by Escalante et al., (2011) and Baird and Sweeney (2011) COI gene sequence used for the bio-monitoring in benthology and Sweeney et al., (2011) explain that certain cases where ambiguity existed their morphological data need to be re-examined using the additional molecular data for species clarification. Min and Hickey (2007a) proved that barcoding was sufficient for species identification among the fungi. DNA barcoding has a new milestone achievement of mini-barcoding studies which was carried out by Meusnier et al. (2008). The systems of identification are carried out solely by morphology whereas it fails to identify its characters for some groups of organisms. In which DNA barcoding is an ideal tool for identification (Mitchell, 2008; Pagès et al., 2009; Lewis and Paul, 2005; Zettler et al., 2002; Abriouel et al., 2008; Iliff et al., 2008; Hebert et al., 2003a). A detailed gene and gene classification used for species taxonomy were reviewed and provided in the Table 2.1. Mitochondrial DNA (mtdna) profiling studies are carried out in the cytoplasmic mtdna which is inherited from the female parent so that each copy is identical. It offered the insights for the population structure and greatly contributed to the establishment of phylogeographic information (Avise et al., 1987). The development of Universal primers (Kocher et al., 1989) made possible DNA amplification of COI gene by using PCR and their direct sequencing for many number of phyla. Also, the sequences of mtdna diverged quickly by its information and the gene order with the composition are relatively uniform (Hoy, 1994, Simon et al., 1994 and Simon et al., 2006). When compared to the nuclear genome, the mitochondrial genome lacks introns, which restricted to have an exposure for recombination and has a haploid mode of inheritance (Saccone et al., 1999) were also an added advantage for these DNA barcoding and sequences. Mitochondrial genes are useful to study the species that diverged recently because they have a high rate of substitution. However, if the divergence event was not recent, nuclear genes are ideal for phylogenetic analysis (Lin and Danforth, 2004). 9

3 mtdna sequences divergences had been successfully used to discriminate between species of North American birds (Hebert et al., 2004b), spiders (Hebert and Barrett, 2005b), cryptic species of butterflies (Hebert et al., 2004a), mosquitoes (Besansky et al., 2003), leeches (Siddall and Budinoff, 2005), springtails (Stevens and Hogg, 2003; Hogg and Hebert, 2004), beetles (Monaghan et al., 2005), oligochaetes (Nylander et al., 1999), naidid worms (Bely and Wray, 2004), extinct moas (Lambert et al., 2005), and various other species of vertebrates and invertebrates (Saccone et al., 1999; Hebert et al., 2003b). The barcode system was based on sequence diversity in a single gene (Schander and Willassen, 2005) region i.e. a section of the mitochondrial DNA cytochrome C oxidase I gene, (COI). These sequences demonstrated higher order relationship than the shallower divergence (Seifert et al., 2007; Clare, 2008). This technique provides higher flexibility for the identification of species in large taxonomic assemblages (Caterino et al., 2006; Pegg et al., 2006; Hajibabaei et al., (2006c and 2007b). The ability to use COI gene to identify species would enable the identification of cryptic and polymorphic taxa and also identify and associate individuals of life stages other than adult to their correct species (Schander and Willassen, 2005; Kartavtsev et al., 2009; Kochzius et al., 2010; Duo et al., 2010). Further, COI locus sequence analysis was an economically feasible option for taxonomic study (Ball et al., 2005). The use of COI barcodes is a powerful tool for species identification of individually isolated fish eggs, larvae and fillets and fins (Ward et al., 2005; Hubert et al., 2008; Steinke et al., 2009b). Nguyen and Seifert (2008) were discovered three new species of Leohumicola using morphological characters and phylogenetic analyses of DNA barcodes using COI sequences. According to Min and Hickey (2007b), the reducing sequence length had a profound effect on the accuracy of resulting phylogenetic trees but surprisingly short sequences still yield accurate species identifications. It would be beneficial to have a standard segment (such as the barcoding region) to use for routine identifications. DNA barcodes have potential to be useful for species identification without the aid of a taxonomist in certain situations. Barcoding had been proposed as a quality control measure to confirm the identity of specimens (Mitchell, 2008). The commercial uses of barcoding, excited in pest identification, 10

4 invasive species detection and fishery management were also worth pursuing (Mitchell, 2008; Rock et al., 2008). The fish taxonomy mainly consists of environmental factors and its dynamics of larval dispersal. Many unanswered issues in the ecology and evolution of marine population centre on how far planktonic larvae disperse away from their parents (Levin, 2006). Regardless of the importance of the ecological processes affected by larval fish dynamics, the inability of unambiguous taxonomic identification of early life stages of many taxa is still a major burden that impairs the proficient management of these populations. Early larval studies attend several scientific groups facing difficult to distinguish to genus and species level (Chow and Walsh, 1992; Victor, 2009). Despite the great promise of DNA barcoding, it had been controversial in some scientific circles (Will and Rubinoff, 2004). Yet, recent results illustrated some straightforward benefits from the use of a standardised molecular approach for identification (Hebert et al., 2003a and 2005a). Similarly, intraspecific phenotypic variation often overlapped that of sister taxa in nature, which lead to incorrect identifications, if based on phenotype only (Pfenninger et al., 2006). The recently introduced next-generation sequencing (NGS) approaches in biodiversity science have the potential to further extend the application of DNA information (Hajibabaei et al., 2011). Further, Ratnasingham and Hebert (2007) reported that DNA technology promised that the development of portable devices which will both gather barcode sequences in minutes and use an on-board barcode reference library to generate identifications. The taxonomic ambiguity existed for several fish genera / species and a proper identification was imperative for management and trade (Eschmeyer et al., 1998; Wiens and Servedio, 2000; Hebert et al., 2003b and 2005a,b; Nelson, 2006; Ward et al., 2009) which the DNA barcode resolve this problem and also help to discovery of new/cryptic species. Further, the morphological based studies need lot of taxonomist who are dwindling due to nature of hard work (Steinke et al., 2009a). So, the barcode methods may provide new taxonomist. The barcode studies also provide the understanding of the eco-diversity, especially for the marine fishes which cannot be 11

5 monitored continuously (Dasmahapatra and Mallet, 2006). Moreover, the fisheries managers and scientists are struggling with a lack of basic information for many shark and ray species which can be carried out through barcode of confiscated materials like shark meat, fin, bones, etc., which provide much missed details which can be used for scientific and also for conservation and management (Holmes et al., 2009). Larval fishes were frequently not identified to species level due to their small size and limited morphological development (Webb et al., 2006; Richardson et al., 2006). This problem leads to difficulties for understanding the life histories of fishes, that also marine fishes, it further cumbersome the task. Very few species or genus only explored for the taxonomic identification, early life history and phylogenetic relationships (perches fishes - Lutjanus) which was far from complete and continually reviewed (Rivas, 1949; Chow and Walsh, 1992; Leis, 1986, 2005; Miller and Cribb, 2007). Shirak et al. (2009) studied the barcoding and taxonomic analysis of the five Tilapiine species. The larvae and newly-settled juveniles of the Cubera Snapper were identified by DNA barcoding (Victor et al., 2009). The stomotopod larvae were studied under barcode technique (Barber and Boyce, 2006) to understand the biodiversity of gonodactylid (manis shrimp). Zemlak et al., (2009) had been reported that Indo-pacific fishes, for a substantial number, were overlooked under the category of commercially important fishes. Moreover, the COI gene sequence for marine fishes were successfully carried out in Australia (Ward et al., 2005), Pacific Canada (Steinke et al., 2009a), North Atlantic (Ward et al., 2008), South Africa (Zemlak et al., 2009), Finland (Salokannel et al., 2010) and Great Barrier Reef (Pegg et al., 2006). The faunal studies used the COI sequence for their taxonomy was listed out in the Table 2.2. At present fishes were the most studied marine groups and were currently barcoded within two global campaigns, FISH-BOL ( and SHARK-BOL ( (Ward et al., 2009). Existing fish barcoding results were reviewed and lacunas were presented in detail (Ward et al., 2009; Radulovici et al., 2010). According to Johnson (1984) the earlier works based on the groupers fishes had been intended to increase the understanding of relationship of phylogenetic studies with related families. Maggio et al. (2005) carried out mitochondrial 12

6 cytochrome b and 16S rdna sequences analysis. Craig and Hastings (2007) carried out barcoding to understand the phylogenetic relationships among the fishes in the perciform tribe Epinephelinae (Serranidae) which had been poorly understood. Smith and Craig (2007) studied the limits and relationships of Serranid and percid fishes using the nucleotide characters. Koedprang et al. (2007) studied the genetic diversity among the grouper species (eight species) using microsatellite marker. 2.2 NATIONAL REVIEWS The National level status was reviewed to understand the molecular fish taxonomy of Andaman Islands marine environment. Indian Marine fishes were attempted for DNA barcoding in east coast as well as west coastal region. These barcodes results reported that the average (K2P) distances within species, genera, families, orders were 0.30 %, 6.60 %, 9.91 % and %, respectively (Lakra et al., 2010). Persis et al., (2009) studied the Carangid fishes from Kakinada coastal region based on mtdna COI gene sequence based approach. Jhon et al. (2010) studied Stolephorus spp. using mtdna COI method for Parangipettai coastal water. Govindaraju and Jayasankar, (2004) reported that phenotypic identification of groupers genus Epinephelus samples drawn from southeast and southwest coasts of India using the RAPD analysis. Jayasankar et al., (2004) carried out a complete approach to Indian mackerel in the east and west coasts of India using the RAPD study revealed that significant genetic different observed. Lakra et al., (2007a) studied five Indian Sciaenids using the DNA (RAPD) markers. DNA barcoding of Lates calcarifer was studied in Porto Nova coastal region using COI gene for the phylogenetic analysis and GC content and genetic distances compared with world-wide Species (Jhon et al., 2010). Kumar et al., (2011) worked in cryptic species of Mugilidae fishes using DNA barcoding tools for phylogenetic and haplotype diversity as revealed by intra-species genetic distances. Sachithanandam et al., (2011, 2012) brought out barcode details for the grouper subfamily Epinephelinae species of Andaman waters. Based on the above review of literature suggested the study on monophyly of fishes was not carried out in systematic in India as well as in International fishery sciences. So, an attempt was made to understand the genetic relationship among the 13

7 sub family Epinephelinae with five genus and thirty three species under the monophyly nature DNA barcoding emphases Applications of DNA barcoding tools are emerging in the fields of fish conservation, management aspects such as quota, by-catch monitoring and sustainable fisheries monitoring science (Holmes et al., 2009; Steinke et al., 2009a, b; Rasmussen et al., 2009). In the fields of food safety aspects, DNA barcoding has demonstrated that 25% of fish samples from markets and restaurants in USA and Canada were mislabeled or substituted observed (Wong and Hanner, 2008). DNA barcoding can also be applied successfully to cooked or processed fish meat (Smith et al., 2008), grilled or deep-fried fillets (Wong and Hanner, 2008), and boiled samples (Shirak et al., 2009) and canning sample use of shorter fragments called minibarcodes (Hajibabaei et al., 2006a; Meusnier et al., 2008; Rasmussen et al., 2009; Ward et al., 2009) DNA barcoding progress FISH-BOL has the primary goal of gathering DNA barcode records for all the world s fishes, about 32,500 species (Ward et al., 2009; Eschmeyer, 2010). The aim of the FISH-BOL organisation to the develop COI gene sequences all over the worldwide. But these efforts are reflected in a high coverage from Arctic (74%) and Antarctic (50%). Other regions such as Australia, America, and Oceania showed good progress with coverage near about 20%. However, extremely species-rich regions such as Asia and Africa showed lower progress. This might be explained with an observed bias toward the processing of marine species. Because of the 7800 species recorded as barcoded in FISH-BOL about are 5700 (73.1%) marine (Eschmeyer, 2010). In Indian fish fauna of 11,023 species morphologically reported but till date species barcoded only 1918 species around 17.4% progressed reported by Mecklenburg et al. (2011). Therefore, sampling in the coming years should focus on the collection of marine and freshwater species in Indian and Southeast Asian. Similarly, Becker et al. (2011) mentioned in future Indian need more study in barcoding sampling campaigns toward neglected orders and families. 14

8 2.2.3 DNA barcoding success rate The fish DNA barcoding observation seems to be reflected in species identification results 98% of investigated in marine species (Ward et al., 2009). The current DNA barcoding methodology it is possible to separate the species. Further, DNA barcoding COI gene sequences produced regional genetic differentiation and shared haplotypes genetic differences due to the different habitants (Hubert et al., 2008; Ward et al., 2009) Some Limitation and Cautions Ward et al. (2009) analysed DNA barcoding sequences in fishes and birds and opined that the success for barcoding depend upon recent speciation, incorrect taxonomy, or hybridization, where barcoding could not differentiate between species. There are many drawbacks to the use of barcoding for species identification so the scientific community must be cautious in accepting it. Some biological phenomena that potentially interfere with barcoding are heteroplasmy, hybridization, paternal leakage, introgression, polyploidization, recent speciation, incomplete lineage sorting, error in specimen identification, incorrect taxonomy above phenomena are known to occur to different degrees depending on the dataset (Hebert et al., 2003b, 2004a; Mitchell, 2008; Ward et al., 2009; Rubinoff, 2006; Rock et al., 2008; Langhoff et al., 2009). So, it is essential to have more number of data on individual species and correct identification of species through traditional morphology as well as uploading of correct sequence for right species are highly essential to have a best barcoding technology for species identification. 15

9 Sl. No Table 2.1 Synoptic view of DNA barcoding which employed COI gene to identify animals taxa and its K2P values Reference Taxa Name& No. % identified 1 Hebert et al., 2003a 2238 Annelida, Arthopoda, Chordata, Cnidaria, Echinodermata, Mollusca, Nematoda, Platyheliminthes 2 Remigio et al., 2003 K2P % intra vs. inter specific >98 overall <2 vs Remark The efficacy of COI in identifying species from eight major and several minor phyla plus a variety of arthropod classes assessed. Cnidarians showed less COI variation between species then all other taxonomic groups, 94.1% vs. 1.9% showing <2% k2p between spp. (p<0.0001). 70 Gastropod spp. DNA barcoded to identify species and insertion or deletions more common in COI in this taxonomic group. 3 Hebert et al., 2004b 260 Avian spp vs Four possible cryptic species identified. 4 Penton et al., Daphnia spp. 100 Identification of morphologically cryptic species with overlapping distribution. (Crustacean) 5 Barrett et al., arachnid spp vs Mean intra-and interspecific nucleotide divergences did not overlap expect. 6 Ward et al., marine fishes from Australia vs Efficacy of COI at identifying species and taxonomic relationships assessed. 7 Dooh et al., crustacean spp. 1.5 vs. 27 Using barcodes to examine the Phycology of two glacial relict crustacean taxa in North America. 8 Hajibabaei et al., 2006a Lepidopteran and 100% vs Using mini-barcodes to identify species. 16

10 Sl. Reference Taxa Name& No. % K2P % intra vs. Remark No identified inter specific 9 Hajibabaei et al., 2006b 521 lepidopteron spp % vs. 4-6 Morphologically distinct sympatric species from three families identified. 10 Costa et al., 2007 DNA barcoding of Crustacean species 11 Elias-Gutierrez et al., Cladoceran spp. 14.3% A New cryptic species (Crustacea, Chydoridae) from the desert region of Mexican. 12 Moura et al., Holmes et al., Radulovici et al., Steinke et al., 2009a 16 Vargas et al., genera of elasmobranchs DNA barcoding used to resolve within genera identification problems in deep water sharks 20 shark spp. 7 ray spp Identifying shark species from dried fins for conservation purposes Marine crustaceans from the COI gene used to identify 80 Mollusca Gulf of St Lawrence species 391 fish spp vs Producing a DNA database of ornamental fish from Pacific Canada 5 sea turtle spp. 100 DNA barcoding of Brazilian sea turtles 17

11 Table2.2. Identified K2P values for the COI gene and other genes, for species identifications. Sl. No. Authors & Year 1 Hebert et al., 2004b 2 Clare et al., Ward et al., Steinke et al., 2009b 5 Khedkar et al., Odeny et al., Oliveira et al., Rasmussen et al., 2009 Intraspecific K2P values (%) Intra or inter generic level (%) mean K2P 0.27% [within species 0.43% ] Intraspecific variation (mean = 0.60%), 0.028% (n=22) of Z. faber; Aveg K2P 0.20 and 0.23% Intra-specific variation (mean = 0.21%) Molecular variance analysis revealed that 96% / 6 haplotypes per species Within species was 0.11%. Average = 0.6%) within species Intra-species divergences (mean 0.26%) range 0.04 to 1.09%. Within genus 7.93% Congeners (mean =7.80%), Congeneric K2P 10.81% Average =8.7%) within genera Congeneric K2P values of 32-fold greater, at 8.22% (range %). Within family & order K2P (%) Within family 12.71% Within family Average K2P = 17.6% within families. Animal included in DNA barcoding paper tile Identification of Birds through DNA Barcode DNA barcoding of Neo tropical bats DNA barcoding of shared fish species from the North Atlantic and Australasia DNA identifications for the Ornamental fish trade. DNA Barcoding of Fish in the Godavari river, India. Para taxonomy for Fishery surveys using DNA Barcoding DNA Barcode of Freshwater Fishes of Brazil. Commercially important Salmon through DNA Barcoding of in North America 18

12 9 Zemlak et al., Aliabadian et al., Steinke et al., 2009a K2P distances between African & Australian (mean = 5.10%) COI: Intraspecific K2P distances averaged 0.24% (SD = 0.59%. Cyto - b gene: Intraspecific K2P averaged 0.74% (SD = 1.21%). 16S gene: Intraspecific K2P averaged 0.48% (SD = 1.06%) Intraspecific pacific Canada fishes 0.25%, COI: Intrageneric K2P 24- fold higher than the mean intraspecific K2P distances. Cyto - b gene: Intrageneric K2P 11- fold higher than the mean intraspecific K2P distances 16S gene: Intrageneric K2P distances seven fold higher than the mean intraspecific K2P distance Genera 3.75%. COI: Mean K2P within families = 11.46% & orders = 15.80%. Cyto - b gene: Mean divergences within families = 13.97% and orders level = 19.50%. 16S gene: Mean K2P within families = 6.51% & orders = 10.69%. DNA barcoding reveals overlooked marine fishes. Molecular identification of birds: performance of Distance-based DNA barcoding in three genes Pacific Canada s fishes discrimination using COI gene sequences. 19

13 12 Kartavtsev et al., Persis et al., Lakra et al., 2010 Average intraspecies, 0.11 ± 0.04%, Mean Intraspecific K2P values in family = 0.24% Mean K2P 0.30% 15 Zhang, 2011 K2P average 0.319% for intraspecific individuals 16 Zhang and among conspecifics K2P Hanner, average of 0.3% 2011 intra-genus 1.87 ± 0.68%, Aveg congeneric K2P = 17.2% Within genus mean K2P 6.66%. K2P average % among congeners genetic distances averaged 17.6% among congeners Intra-family ± 0.28%, Intra-order ±0.10%. mean K2P family = 0.875% Families mean K2P 9.91, order mean K2P 16.00%. Molecular phylogenetics of prickle backs and other percoid fishes from the Sea of Japan. DNA barcoding of Carangid fishes from Andhra coast, India Indian marine fishes barcoding 115 species, 79 genera, 37 families. DNA Barcoding of marine fishes in China DNA barcoding of marine fishes from Japan 17 Hubert et al., 2011 Unpublished data Within species %; Sargocentron caudimaculatum and S. spiniferum that diverged only by 0.007% on average, this result reinforces the view that no canonical threshold applies to the frontier separating populations and species in fishes (Hubert et al., 2008). Among genera from an average of in Myripristis % on average for Acanthurus; Hubert et al., 20

14 18 Pramual et al., Carolan et al., Lorz et al., Turanov et al., 2012 intraspecific K2P range from 0% to 9.28%, with a mean of 2.75%, Within species B. cryptarum, B. lucorum and B. magnus for 0.004, and within the species of R. chathamensis and R.abyssalis (K2P = 0.000) 24 specimen R. aculeata (0.0089), 9 specimen R. helleri (K2P = %); 13individual R. inflata (K2P=0.037) 0.06% among the species K2P value Interspecific K2P ranges from 0.34% to 16.05% Interspecific genetic distances to Inter-clade 0.143% 0.370% with an overall average divergence 0.284% Mean K2P within genus 0.37% Within family K2P 11.83%; within order 15.22% Cryptic biodiversity & phylogenetic relationships revealed by DNA barcoding of Oriental black DNA Barcoded of Bumblebee species complex and colour Patterns do not diagnose species Description of a New Species Crustacea, Amphipoda Rhachotropis using COI gene sequences. Molecular phylogenetic study of eelpout fishes from Eastern Seas. 21