Beyond biodiversity: Fish metagenomes

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Ardura, Alba ^a   Planes, Serge ^b,c   Garcia Vazquez, Eva ^a  

^a UNIVERSITY OF OVIEDO   (Spain)

^b UNIVERSITÉ DE PERPIGNAN   (France)

^c Centre de Biologie et d Ecologie Tropicale et Méditerranéenne   (French Polynesia)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL COMMUNITY; ARTICLE; BIODIVERSITY; DNA BARCODING; ENVIRONMENTAL EXPLOITATION; FISH; FRESHWATER ENVIRONMENT; GENE TARGETING; GENETIC ANALYSIS; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; INTRASPECIFIC VARIATION; MARINE ENVIRONMENT; METAGENOME; METAGENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; ANIMAL; CLASSIFICATION; GENETICS; GENOME;

ANIMALIA; EUKARYOTA; PROKARYOTA;

ANIMALS; BIODIVERSITY; FISHES; GENOME;

EID: 79961138275     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022592     Document Type: Article

References (37)

1. Frankham R, (1995) Conservation genetics. Ann Rev Genet 29: 305-327.
2. Hedrick PW, (2001) Conservation genetics: where are we now? Trends Ecol Evol 16 (11): 629-636.
3. Wang SZ, Hard JJ, Utter F, (2002) Genetic variation and fitness in salmonids. Conserv Genet 3 (3): 321-333.
4. Lankau RA, Strauss SY, (2007) Mutual feedbacks maintain both genetic and species diversity in a plant community. Science 317: 1561-1563.
5. Kennedy J, Marchesi JR, Dobson ADW, (2008) Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 7: 27.
6. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. Plos Biology 5 (3): e77 doi:10.1371/journal.pbio.0050077.
7. Singh B, Gautam SK, Verma V, Kumar M, Singh B, (2008) Metagenomics in animal gastrointestinal ecosystem: Potential biotechnological prospects. Anaerobe 14 (3): 138-144.
8. Landgridge G, (2009) Testing the water: marine metagenomics. Nat Rev Microbiol 7: 552.
9. Fonseca VG, Carvalho GR, Sung W, Jonson HF, Power DM, et al. (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Comm 1: 98.
10. Hebert P, Cywinska A, Ball S, deWaard J, (2003) Biological identification through DNA barcodes. P Roy Soc B-Bio Sci 270: 313-321.
11. Ward RD, Hanner R, Hebert PDN, (2009) The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74: 329-356.
12. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA, (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 23 (4): 167-172.
13. Worm B, Barbier EB, Beaumont N, Duffy JE, Folke C, et al. (2006) Impacts of Biodiversity Loss on Ocean Ecosystem Services. Science 314: 787-790.
14. Myers R, Worm B, (2003) Rapid worldwide depletion of predatory fish communities. Nature 423: 280-283.
15. Myers RA, Worm B, (2005) Extinction, survival or recovery of large predatory fishes. Philos Transactions of the Roy Soc B 360 (1453): 13-20.
16. Law R, (2000) Fishing, selection, and phenotypic evolution. Ices J Mar Sci 57 (3): 659-668.
17. Brown CJ, Hobday AJ, Ziegler PE, Welsford DC, (2008) Darwinian fisheries science needs to consider realistic fishing pressures over evolutionary time scales. Mar Ecol-Prog Ser 369: 257-266.
18. Agostinho AA, Thomaz SM, Gomes LC, (2005) Conservation of the Biodiversity of Brazil's Inland Waters. Cons Biol 19 (3): 646-652.
19. Ardura A, Linde AR, Moreira JC, Garcia-Vazquez E, (2010) DNA Barcoding for conservation and management of Amazonian commercial fish. Biol Cons 143: 1438-1443.
20. Garcia A, Tello S, Vargas G, Duponchelle F, (2009) Patterns of commercial fish landings in the Loreto region (Peruvian Amazon) between 1984 and 2006. Fish Physiol Biochem 35: 53-67.
21. Bearzi G, Politi E, Agazzi S, Azzellino A, (2006) Prey depletion caused by overfishing and the decline of marine megafauna in eastern Ionian Sea coastal waters (central Mediterranean). Biol Conserv 127 (4): 373-382.
22. Ferretti F, Myers RA, Serena F, Lotze HK, (2008) Loss of Large Predatory Sharks from the Mediterranean Sea. Conserv Biol 22 (4): 952-964.
23. Borsa P, (2002) Allozyme, mitochondrial-DNA, and morphometric variability indicate cryptic species of anchovy (Engraulis encrasicolus). Biol J Linn Soc 75 (2): 261-269.
24. Moritz C, Cicero C, (2004) DNA barcoding: Promise and pitfalls. Plos Biol 2 (10): 1529-1531.
25. Pauly D, Christensen V, Dalsgaard J, Froese R, Torres F Jr, (1998) Fishing down marine food webs. Science 279 (5352): 870-873.
26. DeWoody JA, Avise JC, (2000) Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J Fish Biol 56 (3): 461-473.
27. Carr MH, Neigel JE, Estes JA, Andelman S, Warner RR, Largier JL, (2003) Comparing marine and terrestrial ecosystems: implications for the design of coastal marine reserves. Ecol Appl 13 (1): S90-S107.
28. Schweiger O, Klotz S, Durka W, Kuhn IA, (2008) A comparative test of phylogenetic diversity indices. Oecologia 157 (3): 485-495.
29. Ward RD, Zemlak TS, Innes BH, Last PD, Hebert PDN, (2005) DNA barcoding Australia's fish species. P Roy Soc B-Biol Sci 360: 1847-1857.
30. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids S 41: 95-98.
31. Thompson JD, Higgins DG, Gibson TJ, (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.
32. Librado P, Rozas J, (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
33. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
34. Abascal F, Zardoya R, Posada D, (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
35. Posada D, (2008) jModelTest: Phylogenetic model averaging. Mol Biol Evol 25 (7): 1253-1256.
36. Jones DT, Taylor WR, Thornton JM, (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosc 8 (3): 275-282 (1992).
37. Tamura K, Nei M, (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526.