메뉴 건너뛰기




Volumn 5, Issue , 2015, Pages

Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ANTHOZOA; CLUSTER ANALYSIS; GENETICS; GENOME; GENOME-WIDE ASSOCIATION STUDY; ISLAND (GEOLOGICAL); MOLECULAR EVOLUTION; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84949544765     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep18211     Document Type: Article
Times cited : (50)

References (53)
  • 1
    • 84868152767 scopus 로고    scopus 로고
    • The 27-year decline of coral cover on the great barrier reef and its causes
    • De'ath, G., Fabricius, K. E., Sweatman, H. & Puotinen, M. The 27-year decline of coral cover on the Great Barrier Reef and its causes. Proc Natl Acad Sci USA 109, 17995-17999, doi: 10.1073/pnas.1208909109 (2012).
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 17995-17999
    • De'ath, G.1    Fabricius, K.E.2    Sweatman, H.3    Puotinen, M.4
  • 2
    • 38449123519 scopus 로고    scopus 로고
    • Coral reefs under rapid climate change and ocean acidification
    • Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318, 1737-1742, doi: 10.1126/science.1152509 (2007).
    • (2007) Science , vol.318 , pp. 1737-1742
    • Hoegh-Guldberg, O.1
  • 5
    • 67349287829 scopus 로고    scopus 로고
    • Connectivity, biodiversity conservation and the design of marine reserve networks for coral reefs
    • Almany, G. R. et al. Connectivity, biodiversity conservation and the design of marine reserve networks for coral reefs. Coral Reefs 28, 339-351, doi: 10.1007/S00338-009-0484-X (2009).
    • (2009) Coral Reefs , vol.28 , pp. 339-351
    • Almany, G.R.1
  • 6
    • 44849105162 scopus 로고    scopus 로고
    • A restoration genetics guide for coral reef conservation
    • Baums, I. B. A restoration genetics guide for coral reef conservation. Mol Ecol 17, 2796-2811, doi: 10.1111/j.1365-294X.2008.03787.x (2008).
    • (2008) Mol Ecol , vol.17 , pp. 2796-2811
    • Baums, I.B.1
  • 7
    • 70350031255 scopus 로고    scopus 로고
    • Restoration of coral populations in light of genetic diversity estimates
    • Shearer, T. L., Porto, I. & Zubillaga,. A. L. Restoration of coral populations in light of genetic diversity estimates. Coral Reefs 28, 727-733, doi: 10.1007/s00338-009-0520-x (2009).
    • (2009) Coral Reefs , vol.28 , pp. 727-733
    • Shearer, T.L.1    Porto, I.2    Zubillaga, A.L.3
  • 8
    • 22644452072 scopus 로고    scopus 로고
    • Population structure as a response of coral communities to global change
    • Bak, R. P. M. & Meesters, E. H. Population structure as a response of coral communities to global change. Am Zool 39, 56-65 (1999).
    • (1999) Am Zool , vol.39 , pp. 56-65
    • Bak, R.P.M.1    Meesters, E.H.2
  • 9
    • 0038043576 scopus 로고    scopus 로고
    • Population genetics, demographic connectivity, and the design of marine reserves
    • Palumbi, S. R. Population genetics, demographic connectivity, and the design of marine reserves. Ecol Appl 13, S146-S158 (2003).
    • (2003) Ecol Appl , vol.13 , pp. S146-S158
    • Palumbi, S.R.1
  • 10
    • 0037083646 scopus 로고    scopus 로고
    • Marine biodiversity hotspots and conservation priorities for tropical reefs
    • Roberts, C. M. et al. Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295, 1280-1284, doi: 10.1126/science.1067728 (2002).
    • (2002) Science , vol.295 , pp. 1280-1284
    • Roberts, C.M.1
  • 11
    • 0035091919 scopus 로고    scopus 로고
    • Coral bleaching: The winners and the losers
    • Loya, Y. et al. Coral bleaching: the winners and the losers. Ecol Lett 4, 122-131 (2001).
    • (2001) Ecol Lett , vol.4 , pp. 122-131
    • Loya, Y.1
  • 12
    • 84875682389 scopus 로고    scopus 로고
    • Species-specific responses of corals to bleaching events on anthropogenically turbid reefs on Okinawa Island, Japan, over a 15-year period (1995-2009)
    • Hongo, C. & Yamano, H. Species-specific responses of corals to bleaching events on anthropogenically turbid reefs on Okinawa Island, Japan, over a 15-year period (1995-2009). PLoS One 8, e60952, doi: 10.1371/journal.pone.0060952 (2013).
    • (2013) PLoS One , vol.8 , pp. e60952
    • Hongo, C.1    Yamano, H.2
  • 13
    • 79961097637 scopus 로고    scopus 로고
    • Revisiting the winners and the losers a decade after coral bleaching
    • van Woesik, R., Sakai, K., Ganase, A. & Loya, Y. Revisiting the winners and the losers a decade after coral bleaching. Mar Ecol-Prog Ser 434, 67-76, doi: 10.3354/Meps09203 (2011).
    • (2011) Mar Ecol-Prog ser , vol.434 , pp. 67-76
    • Van Woesik, R.1    Sakai, K.2    Ganase, A.3    Loya, Y.4
  • 14
    • 84949562652 scopus 로고    scopus 로고
    • Factors for the annual variation of number of settled acroporid larvae in the west coast of Okinawa Island, southeastern Japan
    • (in Japanese)
    • Iwata, K. & Sakai, K. Factors for the Annual Variation of Number of Settled Acroporid Larvae in the West Coast of Okinawa Island, Southeastern Japan. Biol. Mag. Okinawa 48, 1-10 (2010) (in Japanese).
    • (2010) Biol. Mag. Okinawa , vol.48 , pp. 1-10
    • Iwata, K.1    Sakai, K.2
  • 16
    • 84878427471 scopus 로고    scopus 로고
    • Genotyping-by-sequencing in ecological and conservation genomics
    • Narum, S. R., Buerkle, C. A., Davey, J. W., Miller, M. R. & Hohenlohe, P. A. Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol 22, 2841-2847, doi: 10.1111/mec.12350 (2013).
    • (2013) Mol Ecol , vol.22 , pp. 2841-2847
    • Narum, S.R.1    Buerkle, C.A.2    Davey, J.W.3    Miller, M.R.4    Hohenlohe, P.A.5
  • 17
    • 84907803675 scopus 로고    scopus 로고
    • Ancient human genomes suggest three ancestral populations for present-day europeans
    • Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409-413, doi: 10.1038/nature13673 (2014).
    • (2014) Nature , vol.513 , pp. 409-413
    • Lazaridis, I.1
  • 18
    • 84907279761 scopus 로고    scopus 로고
    • The genetic prehistory of the new world arctic
    • Raghavan, M. et al. The genetic prehistory of the New World Arctic. Science 345, 1255832, doi:10.1126/science.1255832 (2014).
    • (2014) Science , vol.345 , pp. 1255832
    • Raghavan, M.1
  • 19
    • 84911425985 scopus 로고    scopus 로고
    • Population genomics of marine fishes: Next-generation prospects and challenges
    • Hemmer-Hansen, J., Therkildsen, N. O. & Pujolar, J. M. Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges. Biol Bull-Us 227, 117-132 (2014).
    • (2014) Biol Bull-Us , vol.227 , pp. 117-132
    • Hemmer-Hansen, J.1    Therkildsen, N.O.2    Pujolar, J.M.3
  • 20
    • 84885603690 scopus 로고    scopus 로고
    • Genomic divergence between the migratory and stationary ecotypes of Atlantic cod
    • Karlsen, B. O. et al. Genomic divergence between the migratory and stationary ecotypes of Atlantic cod. Mol Ecol 22, 5098-5111, doi: 10.1111/mec.12454 (2013).
    • (2013) Mol Ecol , vol.22 , pp. 5098-5111
    • Karlsen, B.O.1
  • 21
    • 84922343714 scopus 로고    scopus 로고
    • Population genomics reveals seahorses (Hippocampus erectus) of the western mid-Atlantic coast to Be residents rather than vagrants
    • Boehm, J. T., Waldman, J., Robinson, J. D. & Hickerson, M. J. Population Genomics Reveals Seahorses (Hippocampus erectus) of the Western Mid-Atlantic Coast to Be Residents Rather than Vagrants. PLoS One 10, e0116219, doi: 10.1371/journal.pone.0116219 (2015).
    • (2015) PLoS One , vol.10 , pp. e0116219
    • Boehm, J.T.1    Waldman, J.2    Robinson, J.D.3    Hickerson, M.J.4
  • 22
    • 80051936630 scopus 로고    scopus 로고
    • Using the acropora digitifera genome to understand coral responses to environmental change
    • Shinzato, C. et al. Using the Acropora digitifera genome to understand coral responses to environmental change. Nature 476, 320-323, doi: 10.1038/nature10249 (2011).
    • (2011) Nature , vol.476 , pp. 320-323
    • Shinzato, C.1
  • 23
    • 20044395284 scopus 로고    scopus 로고
    • Settlement-competency period of planulae and genetic differentiation of the scleractinian coral acropora digitifera
    • Nishikawa, A. & Sakai, K. Settlement-competency period of planulae and genetic differentiation of the scleractinian coral Acropora digitifera. Zoolog Sci 22, 391-399 (2005).
    • (2005) Zoolog Sci , vol.22 , pp. 391-399
    • Nishikawa, A.1    Sakai, K.2
  • 24
    • 20044393319 scopus 로고    scopus 로고
    • Larval tracking using small drifters and larval settlement experiments to examine long-distance larval transport of corals
    • (in Japanese)
    • Nadaoka, K. et al. Larval Tracking Using Small Drifters and Larval Settlement Experiments to Examine Long-Distance Larval Transport of Corals. JSCE 49, 366-370 (2002) (in Japanese).
    • (2002) JSCE , vol.49 , pp. 366-370
    • Nadaoka, K.1
  • 25
    • 77955302343 scopus 로고    scopus 로고
    • Gene flow and genetic diversity of a broadcast-spawning coral in northern peripheral populations
    • Nakajima, Y., Nishikawa, A., Iguchi, A. & Sakai, K. Gene flow and genetic diversity of a broadcast-spawning coral in northern peripheral populations. PLoS One 5, e11149, doi: 10.1371/journal.pone.0011149 (2010).
    • (2010) PLoS One , vol.5 , pp. e11149
    • Nakajima, Y.1    Nishikawa, A.2    Iguchi, A.3    Sakai, K.4
  • 26
    • 69749099417 scopus 로고    scopus 로고
    • Fast model-based estimation of ancestry in unrelated individuals
    • Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19, 1655-1664, doi: 10.1101/gr.094052.109 (2009).
    • (2009) Genome Res , vol.19 , pp. 1655-1664
    • Alexander, D.H.1    Novembre, J.2    Lange, K.3
  • 27
    • 84902485214 scopus 로고    scopus 로고
    • FastSTRUCTURE: Variational inference of population structure in large SNP data sets
    • Raj, A., Stephens, M. & Pritchard, J. K. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197, 573-589, doi: 10.1534/genetics.114.164350 (2014).
    • (2014) Genetics , vol.197 , pp. 573-589
    • Raj, A.1    Stephens, M.2    Pritchard, J.K.3
  • 28
    • 84869173901 scopus 로고    scopus 로고
    • Regional genetic differentiation among northern high-latitude island populations of a broadcast-spawning coral
    • Nakajima, Y., Nishikawa, A., Iguchi, A. & Sakai, K. Regional genetic differentiation among northern high-latitude island populations of a broadcast-spawning coral. Coral Reefs 31, 1125-1133, doi: 10.1007/S00338-012-0932-X (2012).
    • (2012) Coral Reefs , vol.31 , pp. 1125-1133
    • Nakajima, Y.1    Nishikawa, A.2    Iguchi, A.3    Sakai, K.4
  • 29
    • 33846920153 scopus 로고    scopus 로고
    • Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching
    • Underwood, J. N., Smith, L. D., Van Oppen, M. J. & Gilmour, J. P. Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching. Mol Ecol 16, 771-784, doi: 10.1111/j.1365-294X.2006.03187.x (2007).
    • (2007) Mol Ecol , vol.16 , pp. 771-784
    • Underwood, J.N.1    Smith, L.D.2    Van Oppen, M.J.3    Gilmour, J.P.4
  • 30
    • 72749109848 scopus 로고    scopus 로고
    • Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution
    • Noreen, A. M., Harrison, P. L. & Van Oppen, M. J. Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution. Proc Biol Sci 276, 3927-3935, doi: 10.1098/rspb.2009.1050 (2009).
    • (2009) Proc Biol Sci , vol.276 , pp. 3927-3935
    • Noreen, A.M.1    Harrison, P.L.2    Van Oppen, M.J.3
  • 31
    • 44849139420 scopus 로고    scopus 로고
    • Population structure is not a simple function of reproductive mode and larval type: Insights from tropical corals
    • Miller, K., J. & Ayre, D. J. Population structure is not a simple function of reproductive mode and larval type: insights from tropical corals. J Anim Ecol 77, 713-724 (2008).
    • (2008) J Anim Ecol , vol.77 , pp. 713-724
    • Miller, K.J.1    Ayre, D.J.2
  • 32
    • 84897591951 scopus 로고    scopus 로고
    • Regional population structure of montipora capitata across the hawaiian archipelago
    • Concepcion, G. T., Baums, I. B. & Toonen, R. J. Regional population structure of Montipora capitata across the Hawaiian Archipelago. B Mar Sci 90, 257-275, doi: 10.5343/bms.2012.1109 (2014).
    • (2014) B Mar Sci , vol.90 , pp. 257-275
    • Concepcion, G.T.1    Baums, I.B.2    Toonen, R.J.3
  • 33
    • 0000368547 scopus 로고    scopus 로고
    • Changes in living coral coverage before and after the 1998 bleaching event on coral reef flats of ishigaki island, ryukyu islands
    • (in Japanese)
    • Kayanne, H. et al. Changes in living coral coverage before and after the 1998 bleaching event on coral reef flats of Ishigaki Island, Ryukyu Islands. Galaxea 1, 73-82 (1999) (in Japanese).
    • (1999) Galaxea , vol.1 , pp. 73-82
    • Kayanne, H.1
  • 34
    • 67649221238 scopus 로고    scopus 로고
    • Doom and boom on a resilient reef: Climate change, algal overgrowth and coral recovery
    • Diaz-Pulido, G. et al. Doom and boom on a resilient reef: climate change, algal overgrowth and coral recovery. PLoS One 4, e5239, doi: 10.1371/journal.pone.0005239 (2009).
    • (2009) PLoS One , vol.4 , pp. e5239
    • Diaz-Pulido, G.1
  • 35
    • 84937850644 scopus 로고    scopus 로고
    • A population genetic assessment of coral recovery on highly disturbed reefs of the keppel island archipelago in the southern great barrier reef
    • van Oppen, M. J., Lukoschek, V., Berkelmans, R., Peplow, L. M. & Jones, A. M. A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef. PeerJ 3, e1092, doi: 10.7717/peerj.1092 (2015).
    • (2015) PeerJ , vol.3 , pp. e1092
    • Van Oppen, M.J.1    Lukoschek, V.2    Berkelmans, R.3    Peplow, L.M.4    Jones, A.M.5
  • 36
    • 79954999839 scopus 로고    scopus 로고
    • RADSeq: Next-generation population genetics
    • Davey, J. W. & Blaxter, M. L. RADSeq: next-generation population genetics. Brief Funct Genomics 9, 416-423, doi: 10.1093/bfgp/elq031 (2010).
    • (2010) Brief Funct Genomics , vol.9 , pp. 416-423
    • Davey, J.W.1    Blaxter, M.L.2
  • 37
    • 84929166324 scopus 로고    scopus 로고
    • Trans-pacific RAD-seq population genomics confirms introgressive hybridization in eastern pacific pocillopora corals
    • Combosch, D. J. & Vollmer, S. V. Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals. Mol Phylogenet Evol 88, 154-162, doi: 10.1016/j.ympev.2015.03.022 (2015).
    • (2015) Mol Phylogenet Evol , vol.88 , pp. 154-162
    • Combosch, D.J.1    Vollmer, S.V.2
  • 38
    • 84864443173 scopus 로고    scopus 로고
    • 2b-RAD: A simple and flexible method for genome-wide genotyping
    • Wang, S., Meyer, E., McKay, J. K. & Matz, M. V. 2b-RAD: a simple and flexible method for genome-wide genotyping. Nature methods 9, 808-810, doi: 10.1038/nmeth.2023 (2012).
    • (2012) Nature Methods , vol.9 , pp. 808-810
    • Wang, S.1    Meyer, E.2    McKay, J.K.3    Matz, M.V.4
  • 39
    • 0034336914 scopus 로고    scopus 로고
    • Phylogenetic relationships in the coral family acroporidae, reassessed by inference from mitochondrial genes
    • Fukami, H., Omori, M. & Hatta, M. Phylogenetic relationships in the coral family acroporidae, reassessed by inference from mitochondrial genes. Zoolog Sci 17, 689-696, doi: 10.2108/zsj.15.689 (2000).
    • (2000) Zoolog Sci , vol.17 , pp. 689-696
    • Fukami, H.1    Omori, M.2    Hatta, M.3
  • 41
    • 75149155568 scopus 로고    scopus 로고
    • The sequence and de novo assembly of the giant panda genome
    • Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317, doi: 10.1038/nature08696 (2010).
    • (2010) Nature , vol.463 , pp. 311-317
    • Li, R.1
  • 42
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrows-wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760, doi: 10.1093/bioinformatics/btp324 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 43
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/Map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079, doi: 10.1093/bioinformatics/btp352 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 44
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297-1303, doi: 10.1101/gr.107524.110 (2010).
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1
  • 45
    • 78651100696 scopus 로고    scopus 로고
    • Data quality control in genetic case-control association studies
    • Anderson, C. A. et al. Data quality control in genetic case-control association studies. Nature protocols 5, 1564-1573, doi: 10.1038/nprot.2010.116 (2010).
    • (2010) Nature Protocols , vol.5 , pp. 1564-1573
    • Anderson, C.A.1
  • 46
    • 34548292504 scopus 로고    scopus 로고
    • PLINK: A tool set for whole-genome association and population-based linkage analyses
    • Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. American journal of human genetics 81, 559-575, doi: 10.1086/519795 (2007).
    • (2007) American Journal of Human Genetics , vol.81 , pp. 559-575
    • Purcell, S.1
  • 47
    • 33846006923 scopus 로고    scopus 로고
    • Population structure and eigenanalysis
    • Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet 2, e190, doi: 10.1371/journal.pgen.0020190 (2006).
    • (2006) PLoS Genet , vol.2 , pp. e190
    • Patterson, N.1    Price, A.L.2    Reich, D.3
  • 48
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nature genetics 38, 904-909, doi: 10.1038/ng1847 (2006).
    • (2006) Nature Genetics , vol.38 , pp. 904-909
    • Price, A.L.1
  • 49
    • 79960405019 scopus 로고    scopus 로고
    • The variant call format and VCFtools
    • Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158, doi: 10.1093/bioinformatics/btr330 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2156-2158
    • Danecek, P.1
  • 51
    • 84869026948 scopus 로고    scopus 로고
    • Inference of population splits and mixtures from genome-wide allele frequency data
    • Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8, e1002967, doi: 10.1371/journal.pgen.1002967 (2012).
    • (2012) PLoS Genet , vol.8 , pp. e1002967
    • Pickrell, J.K.1    Pritchard, J.K.2
  • 52
    • 84869057650 scopus 로고    scopus 로고
    • Ancient admixture in human history
    • Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065-1093, doi: 10.1534/genetics.112.145037 (2012).
    • (2012) Genetics , vol.192 , pp. 1065-1093
    • Patterson, N.1
  • 53
    • 70349472875 scopus 로고    scopus 로고
    • Reconstructing Indian population history
    • Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature 461, 489-494, doi: 10.1038/nature08365 (2009).
    • (2009) Nature , vol.461 , pp. 489-494
    • Reich, D.1    Thangaraj, K.2    Patterson, N.3    Price, A.L.4    Singh, L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.