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DNA barcodes and species identifications in Ross Sea and Southern Ocean fishes

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Abstract

The Southern Ocean occupies about 10 % of the world’s oceans but has low species richness with only ~1.5 % of the marine fishes. Within the Southern Ocean, the Ross Sea region is one of the least exploited sea areas in the world, but is subject to commercial fishing. The fauna are not well known, and preliminary IPY molecular studies have indicated that species diversity has been underestimated in this region. DNA barcodes of fishes from the Ross Sea region were compared with barcodes of fishes from the Atlantic and Indian Ocean sectors of the Southern Ocean. Barcoding resolved 87.5 % of 112 species that typically exhibited high inter-specific divergences. Intra-specific divergence was usually low with shared haplotypes among regions. The Zoarcid Ophthalmolycus amberensis showed shallow divergences (0.1 %) within the Ross Sea and Australian Antarctic Territory but high inter-region divergence (2 %), indicative of cryptic species. Other potential cryptic species with high intra-specific divergences were found in Notolepis coatsi and Gymnoscopelus bolini. In contrast, several taxa showed low inter-specific divergences and shared haplotypes among morphological species. COI provided limited phylogenetic resolution of the genera Pogonophryne and Bathydraco. Trematomus loennbergii and T. lepidorhinus shared COI haplotypes, as previously noted in other regions, as did Cryodraco antarcticus and C. atkinsoni. There was a marked lack of congruence between morphological descriptions and COI divergences among the Ross Sea liparids with shallow or zero divergences among recently described species. Barcodes for the Ross Sea fishes highlighted several initial misidentifications that were corrected when specimens were re-examined.

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Acknowledgments

We are grateful to the New Zealand Ministry of Fisheries and CCAMLR Scientific Observers, and to the Australian Fisheries Management Authority observers for the collection of specimens in the commercial fisheries in the Ross Sea region, the Australian Antarctic Territory, and the Indian Ocean. Additional Ross Sea IPY specimens were collected and identified by Peter McMillan and Andrew Stewart aboard the NIWA Research vessel Tangaroa. Peter Smith, Peter McMillan, and Andrew Stewart were supported by the New Zealand Government under the NZ International Polar Year-Census of Antarctic Marine Life Project and acknowledge the Ministry of Fisheries Science Team and Ocean Survey 20/20 CAML Advisory Group (Land Information New Zealand, Ministry of Fisheries, Antarctica New Zealand, Ministry of Foreign Affairs and Trade, and National Institute of Water and Atmospheric Research Ltd.). D. Steinke and laboratory analyses of sequences generated at the Canadian Centre for DNA Barcoding (CCDB) were supported by funding of the Alfred P. Sloan Foundation to MarBOL and by the Government of Canada through Genome Canada, through the Ontario Genomics Institute (2008-0GI-ICI-03). Preservation and storage costs for voucher specimens from the Ross Sea registered into the Museum of New Zealand Te Papa Tongarewa were provided by the Te Papa Collection Development programme. The collection and study of the East Antarctic specimens from the CAML-CEAMARC cruises of the RSV Aurora Australis and the TRV Umitaka Maru (IPY project no. 53) were supported by the Australian Antarctic Division, the Japanese Science Foundation, the French polar institute IPEV (ICOTA and REVOLTA programs), the CNRS, the MNHN, and the ANR (White Project ANTFLOCKs USAR no. 07-BLAN-0213-01 directed by Guillaume Lecointre). We are grateful to Anton Van de Putte (Leuven, Belgium), Olly Berry, and Sharon Appleyard (Hobart, Australia), and two anonymous referees for constructive comments on the manuscript.

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Authors and Affiliations

  1. National Museum Victoria, GPO Box 666, Melbourne, VIC, 3001, Australia

    P. J. Smith

  2. Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada

    D. Steinke

  3. Muséum national d‘Histoire naturelle, Département Systématique et Evolution, UMR 7138, CP 26, 43, rue Cuvier, 75231, Paris, Cedex 05, France

    A. Dettai

  4. National Institute of Water and Atmospheric Research Ltd., Private Bag 14 901, Wellington, New Zealand

    P. McMillan

  5. Australian Antarctic Division, 203 Channel Highway, Kingston, TAS, 7050, Australia

    D. Welsford

  6. Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand

    A. Stewart

  7. Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, TAS, 7001, Australia

    R. D. Ward

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Electronic supplementary material

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300_2012_1173_MOESM1_ESM.xls

Appendix 1 Southern Ocean fishes barcoded listed by Species, Specimen Reference Number, GenBank Accession Number, Bold Process Number, and Institute storing specimens. The list excludes published data on Macrourus, available in Smith et al. (2011) (XLS 240 kb)

300_2012_1173_MOESM2_ESM.pdf

Appendix 2 COI relationships among the Artedidraconidae (154 specimens, including those identified to genus level only) from the Southern Ocean; unrooted ML tree. The scale bar represents an interval of the K2P model; numbers at nodes are bootstrap percentages (>75%). Sequence numbers represent BOLD Process Number, GenBank Accession Number, followed by Registration Number, and species name (PDF 37 kb)

300_2012_1173_MOESM3_ESM.pdf

Appendix 3 COI relationships among Trematomus specimens (181 specimens, including those identified to genus level only); unrooted ML tree. The scale bar represents an interval of the K2P model; numbers at nodes are bootstrap percentages (>75%). Sequence numbers represent BOLD Process Number, GenBank Accession Number, followed by Registration Number, and species name (PDF 42 kb)

300_2012_1173_MOESM4_ESM.pdf

Appendix 4 COI relationships among the Bathydraconidae (168 specimens, including those identified to genus level only) from the Southern Ocean; unrooted ML tree. The scale bar represents an interval of the K2P +G model; numbers at nodes are bootstrap percentages (>75%). Sequence numbers represent BOLD Process Number, GenBank Accession Number, followed by Registration Number, and species name (PDF 39 kb)

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Smith, P.J., Steinke, D., Dettai, A. et al. DNA barcodes and species identifications in Ross Sea and Southern Ocean fishes. Polar Biol 35, 1297–1310 (2012). https://doi.org/10.1007/s00300-012-1173-8

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