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DNA barcoding confirms the first record of a Desmodema polystictum (Ogilby, 1898) egg and all-time high adult catches in the Indian Ocean
Marine Biodiversity Records volume 12, Article number: 22 (2019)
The eggs of Polka-dot ribbonfish Desmodema polystictum have been recorded for the first time in the Indian Ocean. Although the only previous information on eggs from this species consists of line drawings from 1973 (Pacific Ocean), the identification was possible by combining morphological and molecular analyses. As far as we are aware, only few confirmed records of adult individuals have been previously reported from the Indian Ocean. We found eggs in the proximity of numerous adults (57 and 42 individuals at two stations) indicating that the Central Indian Ocean is potentially an important spawning ground of D. polystictum.
The ribbonfish family Trachipteridae (Lampriformes) consists of three genera Trachipterus (T. altivelis, T. arcticus, T. fukuzakii, T. ishikawae, T. jacksonensis, T. trachypterus), Desmodema (D. lorum, D. polystictum), and Zu (Z. cristatus, Z. elongatus) (Martin 2015; Froese and Pauly 2019). Like most other species in this family, Polka-dot ribbonfish Desmodema polystictum (Ogilby, 1898) is distributed circumglobally in tropical and temperate regions (Martin 2015; Angulo and López-Sánchez 2017). However, despite its wide distribution and size, with lengths up to 110 cm, D. polystictum is an uncommon, deep dwelling species (Smith-Vaniz 2015). Although the first record of a single specimen of this species (a juvenile) was reported at the end of the twentieth century from the North Indian Ocean (Bauchot and Bianchi 1984), the presence of adults at other locations within the Indian waters were only published very recently (Zacharia and Kannan 2012; Deshmukh et al. 2017). There are few other records only available in reports and online databases. Two records of a single specimen of D. polystictum were from the waters of Pakistan in 2010 and 2015 (Fanning et al. 2011; Froese and Pauly 2019). Furthermore, eight individuals of this species have been found off Tanzanian waters (6° 43′ S, 43° 59′ W) in a survey conducted by the R/V Dr. Fridtjof Nansen (Institute of Marine Research (IMR), Norway-database, survey no: 2018405).
The Indian Ocean (Arabian Sea), is viewed as one of the most productive oceans regarding mesopelagic fish (FAO 2001). Until recently, there was comparatively little research activity on the mesopelagic zone worldwide (Hildago and Browman 2019). In the present study, both morphological and molecular approaches, targeting the mitochondrial cytochrome c oxidase 1 (COI) gene (Ward et al. 2009), were used in parallel for identifying a single egg of D. polystictum from samples collected in the Indian Ocean. Another egg was identified only based on its morphological characteristics. Furthermore, to identify the possible spawning areas, we explored the spatial overlap of adult fish, based on fieldwork and literature review, in relation to the records of eggs from this survey.
Material and methods
Ichthyoplankton samples were taken with the R/V Dr. Fridtjof Nansen ecosystem survey around Sri Lankan waters of the Indian Ocean from 24 June to 16 July 2018 (Krakstad et al. 2018). A Continuous Underway Fish Egg Sampler (CUFES) was used to collect eggs and larval fish in the upper 4 m at 54 stations. Samples were preserved in 96% ethanol onboard and later processed at the laboratory of the National Aquatic Resources Research and Development Agency (NARA), Sri Lanka. The 3735 fish eggs found in the CUFES samples were divided into categories based on their morphological and meristic characteristics following Rodriguez et al. (2017). Among these eggs, only one, collected at 8° 48′ N and 79° 30′E, showed an unusual pattern of conspicuous branched melanophores and size of ca. 2 mm (Table 1a, b). In addition, a Multinet Mammoth (1 m2 – Hydro-Bios) was towed obliquely from 25 to 0 m and 100–0 m respectively with bottom depth close to 30 m and > 100 m at 24 stations. At the station 576 (7° 40′ N, 79° 37′ E, Table 1a, b), a fish egg bearing very similar characteristics to the one collected by the CUFES was retrieved. It was not possible to obtain DNA sequence of this egg as it was subsequently lost after the survey.
Two pelagic trawls (Åkrahamn - mouth opening 8 to 12 m and MultPelt 624 mouth opening 25 to 35 m) and a Gisund Super bottom trawl (18.5 m horizontal opening, 4–5 m vertical opening) were used to catch fish during the same survey (Krakstad et al. 2018). In total, 88 trawl hauls were taken. To identify the D. polystictum adults, we used morphometric and meristic data (Table 2) following Zacharia and Kannan (2012). Temperature and salinity profiles were obtained by a Seabird 911 CTD at the same survey. Further information regarding the sampling strategy can be found in Krakstad et al. (2018). Additional data on the occurrence of this species in the Indian Ocean was obtained from previous studies (Bauchot and Bianchi 1984; Zacharia and Kannan 2012; Deshmukh et al. 2017, reports and online databases).
The egg taken with the CUFES samples was placed in a 1.5 ml Eppendorf tube containing 75 μl of a solution of 5% Chelex 100 Resin (BioRad, CA, USA) and 15 μl of Proteinase K (Qiagen, Germany). The Eppendorf tube was incubated at 56 °C for 1 hour followed by 10 minutes at 96 °C. After a brief centrifugation, the supernatant containing the nucleic acids was transferred into a new Eppendorf tube. DNA isolation and PCR application targeting the mitochondrial COI gene was preformed using methods described by Ivanova et al. (2007) and further modified at the IMR, Norway (Mateos-Rivera pers. com.). Finally, sequencing was performed using 1 μL of M13F primer [0.35 μM] (Messing 1983) at the University of Bergen (http://www.seqlab.uib.no). The resulting sequence was analyzed in Geneious v8.0.5 (Kearse et al. 2012) and used as query for both the Barcode of Life Data System (BOLD; www.boldsystems.org.) and BLASTn (Altschul et al. 1990) in GenBank (www.ncbi.nlm.nih.gov/genbank.) databases to determine its identity. The sequence has been submitted to GenBank under accession number MN117725.
The phylogenetic tree was made on selected COI gene sequences retrieved in the nucleotide database from NCBI. The tree was reconstructed by using maximum likelihood analysis and the Jukes-Cantor nucleotide substitution model as implemented in MEGA v7 (Kumar et al. 2016). Robustness of the tree was determined using 1000 bootstrap replicates. Sequences were aligned with MUSCLE (Edgar 2004) in MEGA v7. The tree was rooted against the COI gene sequence of an euphausiid (Thysanoessa raschii).
Results and discussion
The two D. polystictum pelagic eggs collected in this study were found in the North-West waters of Sri Lanka in the Central Indian Ocean close to the continental shelf/slope (Table 1b, Fig. 1a). Generally, during the southwest monsoon period when the survey was undertaken, the waters to the east of Sri Lanka are much warmer than to the west (approximately 29 vs 27 °C) (Rathnasuriya et al. submitted). The water temperatures at the two stations (51 and 576) at the time of sampling of D. polystictum eggs, varied from around 27.3 °C at the surface to 19.4 °C at 100 m depth while the salinity varied from 34.96 to 34.87 respectively at surface and 100 m (Table 1b). The temperature and salinity conditions at the two sampling stations mentioned above reflects the overall situation observed along the west coast (Krakstad et al. 2018). During the survey, a cooler temperature signal was identified in the far offshore North West region, reflecting more upwelling and likely associated increase in biological productivity in the region (Krakstad et al. 2018; Rathnasuriya et al. submitted). The high biomass of pelagic and mesopelagic fish was observed in offshore waters is likely due to favorable feeding conditions in the area. Prior to this survey, there were no available data on ichthyoplankton from this region (Krakstad et al. 2018).
The egg of D. polystictum showed a unique pattern of conspicuous branched melanophore scattered over the yolk, anterior to eye and over the head and lateral sides of developing embryo (Fig. 2a). Lateral melanophores on the developing embryo were arranged in several rows from head to tail dorsally on epaxial myomeres, and ventrally on hypaxial myomeres. A transparent chorion was also observed, with narrow perivitelline space, and homogenous yolk with no oil globule present (Fig. 2a, b). This description of the egg agrees with the drawings in Pertseva-Ostroumova and Rass (1973), which to our knowledge is the only previous information about D. polystictum eggs. However, no specimens from that study are available. As the morphological identification of fish eggs for the first time can be tricky, we used DNA barcoding to verify our findings. In addition, we emphasize the need to use molecular analysis, such as DNA barcoding to successfully identify fish eggs as well as to incorporate them into long-term, regional scale ichthyoplankton monitoring programs as has been suggested in recent studies (Lewis et al. 2016; Burrows et al. 2019).
After sequencing and cleaning the COI gene of the egg, we obtained a sequence of 658 bp which was blasted against the GenBank and BOLD databases. Our query sequence showed a high identity (> 99%) with 3 sequences deposited in the GenBank database identified as D. polystictum (accession numbers: MG856425; MG856804 and KF489564; Fig. 3). In addition, the same high sequence identity was obtained with one sequence deposited in the BOLD database (id: MFLE4752) and associated only to the genus Desmodema from an individual collected in the Western part of Jamaica in 2011. Judging from our results, the sequence from the Caribbean would also belong to D. polystictum. However, to our knowledge, none of the above four sequences have been used in any published study so far. In addition, lower identities were obtained with sequences from other species such as D. lorum (accession number: GU440303) or Zu cristatus (accession numbers: KC016059, KU836510, KF930551), among others (Fig. 3).
Among the 88 trawl stations (pelagic and demersal) taken during the R/V Dr. Fridtjof Nansen survey, D. polystictum adults were only observed in offshore waters (> 600 m bottom depth) in 4 stations (Table 1a, b, Fig. 1a, b, Fig. 4). All individuals were caught by pelagic trawls covering the upper 30 m during nighttime (19:00–23:30 local time; data are available at the IMR, Norway-database). Therefore, D. polystictum appear to follow the pattern of other mesopelagic fish, which are known in general to perform diel vertical migration between the deeper waters (~ 200–1000 m), where they hide from predators during the day, and the oceanic surface layer where they feed at night (Aksnes et al. 2017).
The majority of the adults were collected at stations 80 and 87 (57 and 42 individuals), respectively; Table 1(b). While, in the other two stations, 65 and 81, the number was considerably lower (2 and 1, respectively). In fact, D. polystictum is a rare, deep dwelling species (Smith-Vaniz 2015), which can be confirmed by the little information available about this species. Indeed, to our knowledge, only few individuals have been previously reported in the Indian Ocean (Bauchot and Bianchi 1984; Zacharia and Kannan 2012; Deshmukh et al. 2017, reports and online databases).
The western region of the Indian Ocean close to Sri Lanka is a highly productive area (Yapa 2012), making this zone attractive as a feeding ground for fish. Good feeding conditions (e.g. high biomass of mesozooplankton) likely attracts early larval stages into the inner shelf regions (Krakstad et al. 2018). Though sparse, records of eggs close to the continental shelf /slope may imply that this pattern is also likely adapted by D. polystictum. Eggs of some species may occur both on the continental shelf and over deep ocean waters while other species may restrict their spawning to the continental break (Burrows et al. 2019). The eggs recorded near the shelf break and shelf in our study seem to indicate that these could be dispersed from offshore waters (where adults were abundant) with the near surface northward flowing currents closer to the shelf (Krakstad et al. 2018). It is likely that spawning of D. polystictum coincided with the southwest monsoon where high plankton production occurred (Rathnasuriya et al. submitted) in the southern and western regions off Sri Lanka. The high density of adults found in two of the sampling sites could indicate seasonality or a coordinated reproductive event, given the suitable environmental conditions. This could be a strategy of adults to provide good feeding conditions and high survival rates for larval fish. It is noteworthy that all adults of D. polystictum reported to date are from the western Indian Ocean, west side of India and Sri Lanka (Fig. 1b). The geographical overlap of eggs and adults in the Indian Ocean (North West region off Sri Lanka) indicates that this area could be an important spawning ground of D. polystictum.
This study contains novel findings of a rare mesopelagic species that is distributed circumglobally in tropical and temperate regions. Our findings verify for the first time, the eggs of D. polystictum through morphological and DNA barcoding approaches. We observed significantly higher number of adults than previously reported from the Indian Ocean. The high density of adults found in the western region may indicate spawning aggregations in an area with favourable environmental conditions for their offspring. Eggs in the proximity of numerous adults indicate that the Central Indian Ocean is likely an important spawning ground of D. polystictum.
Availability of data and materials
All data generated or analyzed during this study are included in this published article.
Aksnes DL, Røstad A, Kaartvedt S, Martinez U, Duarte CM, Irigoien X. Light penetration structures the deep acoustic scattering layers in the global ocean. Sci Adv. 2017;3(5):e1602468. https://doi.org/10.1126/sciadv.1602468.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Angulo A, López-Sánchez MI. New records of lampriform fishes (Teleostei: Lampriformes) from the Pacific coast of lower Central America, with comments on the diversity, taxonomy and distribution of the Lampriformes in the eastern Pacific Ocean. Zootaxa. 2017;4236(3):573–91.
Bauchot M, Bianchi G. First record of Desmodema polystictum (Ogilby, 1897) in the North Indian Ocean. Cybium. 1984;8:96–8.
Burrows M, Browning JS, Breitbart M, Murawski SA, Peebles EB. DNA barcoding reveals clear delineation between spawning sites for neritic versus oceanic fishes in the Gulf of Mexico. Fish Oceanogr. 2019;28(2):228–39.
Deshmukh A, Dragičević B, Paidi CK, Muniraj K. New record of Desmodema polystictum from northwestern Indian Ocean. Cybium. 2017;41(4):379–80.
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7.
Fanning LP, Khan MW, Kidwai S, Macauley GJ. Surveys of the offshore fisheries resources of Pakistan – 2010. FAO Fisheries and Aquaculture Circular. 2011 (C1065): I.
FAO. Report of the trilateral workshop on lanternfish in the Gulf of Oman. Rome: FAO Fisheries Report No. 665; 2001.
Froese R, Pauly D. FishBase. World Wide Web electronic publication. 2019. www.fishbase.org. .
Hildago M, Browman H. Developing the knowledge base needed to sustainably manage mesopelagic resources. ICES J Mar Sci. 2019;76:609–15.
Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes. 2007;7(4):544–8.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9.
Krakstad JO, Jayasinghe P, Totland A, Dalpadado P, Søiland H, Cervantes D, et al. Survey of regional resources and ecosystems of the Bay of Bengal: Part 1 Sri Lanka, 24 June- 16 July 2018. NORAD-FAO programme GCP/GLO/690/NOR, Cruise reports Dr. FRIDTJOF NANSEN, EAF-Nansen/CR/2018/8 pp. 162. 2018.
Kumar S, Stecher G, Tamura K. Mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.
Lewis LA, Richardson DE, Zakharov EV, Hanner R. Integrating DNA barcoding of fish eggs into ichthyoplankton monitoring programs. Fish Bull. 2016;114:153–65. https://doi.org/10.7755/FB.114.2.3.
Martin JM. Phylogeny, Ontogeny and Distribution of the Ribbonfishes (Lampridiformes: Trachipteridae). The Faculty of the School of Marine Science, The College of William & Mary in Virginia, USA, 2015. Pp.1–215 Retrieved from https://scholarworks.wm.edu/etd/1539616922/. .
Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78.
Pertseva-Ostroumova TA, Rass TS. Ichthyoplankton of the southeastern Pacific Ocean. Trudy Inst Okeanol Acad Nauk SSSR. 1973;94:7–70 (In Russian, translated by Dept Secretary of State of Canada Translation Series No. 4097).
Rodriguez JM, Alemany F, Garcia A. A guide to the eggs and larvae of 100 common Western Mediterranean Sea bony fish species. Rome, Italy: FAO; 2017.
Smith-Vaniz WF. Desmodema polystictum. In The IUCN Red List of Threatened Species 2015. Available at https://www.iucnredlist.org/species/190073/21909640. .
Ward RD, Hanner R, Hebert PD. The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol. 2009;74(2):329–56. https://doi.org/10.1111/j.1095-8649.2008_02080_x.
Yapa KKAS. Effect of surface wind and wind vectors on sea surface chlorophyll a distribution in the ocean waters surrounding Sri Lanka for the period 1999–2003. Journal of National Science Foundation of Sri Lanka. 2012;40(3):221–9.
Zacharia PU, Kannan K. First record of polka-dot ribbonfish Desmodema polystictum (Pisces: Trachipteridae) from Indian waters. Marine Biodivers Rec. 2012;5(8):1–4.
This paper/report uses data collected through the scientific surveys with the R/V Dr. Fridtjof Nansen as part of the collaboration between the EAF-Nansen Programme and government of Sri Lanka. The EAF-Nansen Programme is a partnership between the Food and Agriculture Organization of the United Nations (FAO), the Norwegian Agency for Development Cooperation (Norad), the Institute of Marine Research (IMR), Norway and partner countries, in support of the application of the ecosystem approach to fisheries considering climate and pollution impacts. We greatly appreciate the support given by the National Aquatic Resources Research and Development Agency (NARA), Sri Lanka and the Institute of Marine Research (IMR), Norway and the Ocean University of Sri Lanka for their support.
This research was funded by EAF Nansen program of the Food and Agriculture Organization (FAO), the Norwegian Agency for Development Cooperation (Norad) and the Government of Sri Lanka (Grant number 15113–39).
All animals we have used in this study are collected from sea, in their natural environment in accordance with the national and international regulations.
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Rathnasuriya, M.I.G., Mateos-Rivera, A., Bandara, A.G.G.C. et al. DNA barcoding confirms the first record of a Desmodema polystictum (Ogilby, 1898) egg and all-time high adult catches in the Indian Ocean. Mar Biodivers Rec 12, 22 (2019). https://doi.org/10.1186/s41200-019-0180-7
- Central Indian Ocean
- COI gene
- Fish egg
- Mesopelagic fish