메뉴 건너뛰기




Volumn 66, Issue 3, 2017, Pages 399-412

Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants

Author keywords

Hierarchical redundancy; Phylogenetic informativeness; Quartet informativeness; Restriction site associated DNA (RAD) sequencing; Sequencing coverage; Viburnum

Indexed keywords

ANGIOSPERM; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; DNA SEQUENCE; GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

EID: 85019684655     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syw092     Document Type: Article
Times cited : (188)

References (55)
  • 1
    • 84927677447 scopus 로고    scopus 로고
    • Weighted quartets phylogenetics
    • Avni E., Cohen R., Snir S. 2015. Weighted quartets phylogenetics. Syst. Biol. 64:233-242.
    • (2015) Syst. Biol. , vol.64 , pp. 233-242
    • Avni, E.1    Cohen, R.2    Snir, S.3
  • 3
    • 33846839295 scopus 로고    scopus 로고
    • Concordance trees, concordance factors, and the exploration of reticulate genealogy
    • Baum D. A. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56:417-426.
    • (2007) Taxon , vol.56 , pp. 417-426
    • Baum, D.A.1
  • 4
    • 84939184648 scopus 로고    scopus 로고
    • Weighted statistical binning: Enabling statistically consistent genome-scale phylogenetic analyses
    • Bayzid M. S., Mirarab S., Boussau B., Warnow T. 2015. Weighted statistical binning: enabling statistically consistent genome-scale phylogenetic analyses. PLoS ONE 10:e0129183.
    • (2015) PLoS ONE , vol.10 , pp. e0129183
    • Bayzid, M.S.1    Mirarab, S.2    Boussau, B.3    Warnow, T.4
  • 5
    • 0004109091 scopus 로고    scopus 로고
    • release 6.0, Dec. 2012, Accessed: 2015-09-30
    • Bennett M., Leitch I. 2012. Plant DNA C-values database (release 6.0, Dec. 2012). http://www.kew.org/cvalues/. (Accessed: 2015-09-30).
    • (2012) Plant DNA C-values Database
    • Bennett, M.1    Leitch, I.2
  • 6
    • 0001117764 scopus 로고    scopus 로고
    • Inferring evolutionary trees with strong combinatorial evidence
    • Berry V., Gascuel O. 2000. Inferring evolutionary trees with strong combinatorial evidence. Theoret. Computer Sci. 240:271-298.
    • (2000) Theoret. Computer Sci. , vol.240 , pp. 271-298
    • Berry, V.1    Gascuel, O.2
  • 7
    • 84878464979 scopus 로고    scopus 로고
    • Population genomics based on low coverage sequencing: How low should we go?
    • Buerkle A. C., Gompert Z. 2013. Population genomics based on low coverage sequencing: how low should we go? Mol. Ecol. 22:3028-3035.
    • (2013) Mol. Ecol. , vol.22 , pp. 3028-3035
    • Buerkle, A.C.1    Gompert, Z.2
  • 8
    • 84886286947 scopus 로고    scopus 로고
    • Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization
    • Cariou M., Duret L., Charlat S. 2013. Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol. Evol. 3:846-852.
    • (2013) Ecol. Evol. , vol.3 , pp. 846-852
    • Cariou, M.1    Duret, L.2    Charlat, S.3
  • 9
    • 84917697072 scopus 로고    scopus 로고
    • Quartet inference from SNP data under the coalescent model
    • Chifman J., Kubatko L. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30:3317-3324.
    • (2014) Bioinformatics , vol.30 , pp. 3317-3324
    • Chifman, J.1    Kubatko, L.2
  • 10
    • 84904801234 scopus 로고    scopus 로고
    • A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution
    • Clement W. L., Arakaki M., Sweeney P. W., Edwards E. J., Dnoghue M. J. 2014. A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution. Am. J. Botany 101:1029-1049.
    • (2014) Am. J. Botany , vol.101 , pp. 1029-1049
    • Clement, W.L.1    Arakaki, M.2    Sweeney, P.W.3    Edwards, E.J.4    Dnoghue, M.J.5
  • 12
    • 84941254510 scopus 로고    scopus 로고
    • Ddrad-seqphylogenetics basedon nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories
    • DaCosta J. M., Sorenson M. D. 2016. ddRAD-seqphylogenetics basedon nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories. Mol. Phylogenet. Evol. 94:122-135.
    • (2016) Mol. Phylogenet. Evol. , vol.94 , pp. 122-135
    • DaCosta, J.M.1    Sorenson, M.D.2
  • 13
    • 84944157638 scopus 로고    scopus 로고
    • Historical introgression among the American live oaks and the comparative nature of tests for introgression
    • Eaton D. A. R., Hipp A. L., González-Rodríguez A., Cavender-Bares J. 2015. Historical introgression among the American live oaks and the comparative nature of tests for introgression. Evolution 69:2587-2601.
    • (2015) Evolution , vol.69 , pp. 2587-2601
    • Eaton, D.A.R.1    Hipp, A.L.2    González-Rodríguez, A.3    Cavender-Bares, J.4
  • 14
    • 84881616406 scopus 로고    scopus 로고
    • Inferring phylogeny and introgression using RADseq data: An example from flowering plants (Pedicularis: Orobanchaceae)
    • Eaton D. A. R., Ree R. H. 2013. Inferring phylogeny and introgression using RADseq data: An example from flowering plants (Pedicularis: Orobanchaceae). Syst. Biol. 62:689-706.
    • (2013) Syst. Biol. , vol.62 , pp. 689-706
    • Eaton, D.A.R.1    Ree, R.H.2
  • 15
    • 84903726447 scopus 로고    scopus 로고
    • PyRAD: Assembly of de novo RADseq loci for phylogenetic analyses
    • Eaton D. A. R. 2014. PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics 30:1844-1849.
    • (2014) Bioinformatics , vol.30 , pp. 1844-1849
    • Eaton, D.A.R.1
  • 16
    • 84904889067 scopus 로고    scopus 로고
    • Genotyping-bysequencing as a tool to infer phylogeny and ancestral hybridization: A case study in carex (cyperaceae)
    • Escudero M., Eaton D. A., Hahn M., Hipp A. L. 2014. Genotyping-bysequencing as a tool to infer phylogeny and ancestral hybridization: A case study in carex (cyperaceae). Mol. Phylogenet. Evol. 79:359-367.
    • (2014) Mol. Phylogenet. Evol. , vol.79 , pp. 359-367
    • Escudero, M.1    Eaton, D.A.2    Hahn, M.3    Hipp, A.L.4
  • 18
    • 84925246503 scopus 로고    scopus 로고
    • Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents
    • Herrera S., Watanabe H., Shank T. M. 2015. Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents. Mol. Ecol. 24:673-689.
    • (2015) Mol. Ecol. , vol.24 , pp. 673-689
    • Herrera, S.1    Watanabe, H.2    Shank, T.M.3
  • 20
    • 84978916740 scopus 로고    scopus 로고
    • Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation study of RAD Sequences
    • Huang H., Knowles L. L. 2016. Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation study of RAD Sequences. Syst. Biol. 65:357-365.
    • (2016) Syst. Biol. , vol.65 , pp. 357-365
    • Huang, H.1    Knowles, L.L.2
  • 21
    • 84917708482 scopus 로고    scopus 로고
    • Wholegenome analyses resolve early branches in the tree of life of modern birds
    • Jarvis E. D., Mirarab S., Aberer A. J., Li B., Houde P., Li C., Ho S. Y. W., Faircloth B. C., Nabholz B., Howard J. T., Suh A., Weber C. C., Fonseca R. R.d., Li J., Zhang F., Li H., Zhou L., Narula N., Liu L., Ganapathy G., Boussau B., Bayzid M. S., Zavidovych V., Subramanian S., Gabaldón T., Capella-Gutiérrez S., Huerta-Cepas J., Rekepalli B., Munch K., Schierup M., Lindow B., Warren W. C., Ray D., Green R. E., Bruford M. W., Zhan X., Dixon A., Li S., Li N., Huang Y., Derryberry E. P., Bertelsen M. F., Sheldon F. H., Brumfield R. T., Mello C. V., Lovell P. V., Wirthlin M., Schneider M. P. C., Prosdocimi F., Samaniego J. A., Velazquez A. M. V., Alfaro-Núñez A., Campos P. F., Petersen B., Sicheritz-Ponten T., Pas A., Bailey T., Scofield P., Bunce M., Lambert D. M., Zhou Q., Perelman P., Driskell A. C., Shapiro B., Xiong Z., Zeng Y., Liu S., Li Z., Liu B., Wu K., Xiao J., Yinqi X., Zheng Q., Zhang Y., Yang H., Wang J., Smeds L., Rheindt F. E., Braun M., Fjeldsa J., Orlando L., Barker F. K., Jønsson K. A., Johnson W., Koepfli K. P., O'Brien S., Haussler D., Ryder O. A., Rahbek C., Willerslev E., Graves G. R., Glenn T. C., Mc Cormack J., Burt D., Ellegren H., Alström P., Edwards S. V., Stamatakis A., Mindell D. P., Cracraft J., Braun E. L., Warnow T., Jun. W., Gilbert M. T. P., Zhang G. 2014. Wholegenome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331.
    • (2014) Science , vol.346 , pp. 1320-1331
    • Jarvis, E.D.1    Mirarab, S.2    Aberer, A.J.3    Li, B.4    Houde, P.5    Li, C.6    Ho, S.Y.W.7    Faircloth, B.C.8    Nabholz, B.9    Howard, J.T.10    Suh, A.11    Weber, C.C.12    Fonseca, R.R.D.13    Li, J.14    Zhang, F.15    Li, H.16    Zhou, L.17    Narula, N.18    Liu, L.19    Ganapathy, G.20    more..
  • 22
    • 84964312527 scopus 로고    scopus 로고
    • Correcting for sequencing error in maximum likelihood phylogeny inference
    • Kuhner M. K., Mc Gill J. 2014. Correcting for sequencing error in maximum likelihood phylogeny inference. G3: Genes|Genomes|Genetics 4:2545-2552.
    • (2014) G3: Genes|Genomes|Genetics , vol.4 , pp. 2545-2552
    • Kuhner, M.K.1    Gill, J.M.2
  • 23
    • 78149256307 scopus 로고    scopus 로고
    • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
    • Larget B. R., Kotha S. K., Dewey C. N., Ané C. 2010. BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26:2910-2911.
    • (2010) Bioinformatics , vol.26 , pp. 2910-2911
    • Larget, B.R.1    Kotha, S.K.2    Dewey, C.N.3    Ané, C.4
  • 24
    • 84936771254 scopus 로고    scopus 로고
    • Phylogenomics of phrynosomatid lizards: Conflicting signals from sequence capture versus restriction site associated DNA sequencing
    • Leaché A. D., Chavez A. S., Jones L. N., Grummer J. A., Gottscho A. D., Linkem C. W. 2015. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biol. Evol. 7:706-719.
    • (2015) Genome Biol. Evol. , vol.7 , pp. 706-719
    • Leaché, A.D.1    Chavez, A.S.2    Jones, L.N.3    Grummer, J.A.4    Gottscho, A.D.5    Linkem, C.W.6
  • 26
    • 84865266483 scopus 로고    scopus 로고
    • Anchored hybrid enrichment for massively high-throughput phylogenomics
    • Lemmon A. R., Emme S. A., Lemmon E. M. (2012). Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol. 61:727-744.
    • (2012) Syst. Biol. , vol.61 , pp. 727-744
    • Lemmon, A.R.1    Emme, S.A.2    Lemmon, E.M.3
  • 29
    • 77957686501 scopus 로고    scopus 로고
    • A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
    • Liu L., Yu L., Edwards S. V. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 10:1-18.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 1-18
    • Liu, L.1    Yu, L.2    Edwards, S.V.3
  • 30
    • 84982182287 scopus 로고    scopus 로고
    • Phylogeny of zebrafish, a "model species", within danio, a "model genus"
    • Mc Cluskey B. M., Postlethwait J. H. (2015). Phylogeny of Zebrafish, a "Model Species", within Danio, a "Model Genus". Mol. Biol. Evol. 32:635-652.
    • (2015) Mol. Biol. Evol. , vol.32 , pp. 635-652
    • Cluskey, B.M.M.1    Postlethwait, J.H.2
  • 31
    • 84859530730 scopus 로고    scopus 로고
    • Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
    • Mc Cormack J. E., Faircloth B. C., Crawford N. G., Gowaty P. A., Brumfield R. T., Glenn T. C. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 22:746-754.
    • (2012) Genome Res. , vol.22 , pp. 746-754
    • Cormack, J.E.M.1    Faircloth, B.C.2    Crawford, N.G.3    Gowaty, P.A.4    Brumfield, R.T.5    Glenn, T.C.6
  • 32
    • 33846874137 scopus 로고    scopus 로고
    • Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
    • Miller M. R., Dunham J. P., Amores A., Cresko W. A., Johnson E. A. 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 17:240-248.
    • (2007) Genome Res. , vol.17 , pp. 240-248
    • Miller, M.R.1    Dunham, J.P.2    Amores, A.3    Cresko, W.A.4    Johnson, E.A.5
  • 33
    • 84917708481 scopus 로고    scopus 로고
    • Statistical binning enablesanaccuratecoalescent-basedestimationoftheavian tree
    • Mirarab S., Bayzid M. S., Boussau B., Warnow T. 2014a. Statistical binning enablesanaccuratecoalescent-basedestimationoftheavian tree. Science 346 (6215).
    • (2014) Science , vol.346 , Issue.6215
    • Mirarab, S.1    Bayzid, M.S.2    Boussau, B.3    Warnow, T.4
  • 35
    • 84859499806 scopus 로고    scopus 로고
    • EggLib: Processing, analysis and simulation tools for population genetics and genomics
    • Mita S. D., Siol M. 2012. EggLib: processing, analysis and simulation tools for population genetics and genomics. BMC Genetics 13:27.
    • (2012) BMC Genetics , vol.13 , pp. 27
    • Mita, S.D.1    Siol, M.2
  • 37
    • 84861691274 scopus 로고    scopus 로고
    • Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species
    • Peterson B. K., Weber J. N., Kay E. H., Fisher H. S., Hoekstra H. E. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS One 7:e37135.
    • (2012) PloS One , vol.7 , pp. e37135
    • Peterson, B.K.1    Weber, J.N.2    Kay, E.H.3    Fisher, H.S.4    Hoekstra, H.E.5
  • 38
    • 33847259379 scopus 로고    scopus 로고
    • Nlme: Linear and Nonlinear Mixed Effects Models
    • Pinheiro J., Bates D., Deb Roy S., Sarkar D., R Core Team 2016. nlme: Linear and Nonlinear Mixed Effects Models. R package version 3. 1-128.
    • (2016) R Package Version , vol.3 , pp. 1-128
    • Pinheiro, J.1    Bates, D.2    Roy, S.D.3    Sarkar, D.4
  • 39
  • 40
    • 33845627286 scopus 로고    scopus 로고
    • The supermatrix approachtosystematics
    • de Queiroz A., Gatesy J. 2007. The supermatrix approachtosystematics. Trend Ecol. Evol. 22:34-41.
    • (2007) Trend Ecol. Evol. , vol.22 , pp. 34-41
    • De Queiroz, A.1    Gatesy, J.2
  • 41
    • 84968762213 scopus 로고    scopus 로고
    • Inferring phylogenetic history from restriction site associated DNA (RADseq)
    • Hörandl E., AppelhansM., editors, International Association for Plant Taxonomy IAPT, chap. 6
    • Ree R. H., Hipp A. L. 2015. Inferring phylogenetic history from restriction site associated DNA (RADseq). In: (Hörandl E., AppelhansM., editors. Next-generation sequencing inplantsystematics, International Association for Plant Taxonomy (IAPT), chap. 6.
    • (2015) Next-generation Sequencing Inplantsystematics
    • Ree, R.H.1    Hipp, A.L.2
  • 42
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F., Huelsenbeck J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 43
    • 84859516080 scopus 로고    scopus 로고
    • Inferring phylogenies from RAD sequence data
    • Rubin B. E. R., Ree R. H., Moreau C. S. 2012. Inferring phylogenies from RAD sequence data. PLoS ONE 7:e33394.
    • (2012) PLoS ONE , vol.7 , pp. e33394
    • Rubin, B.E.R.1    Ree, R.H.2    Moreau, C.S.3
  • 44
    • 84878113118 scopus 로고    scopus 로고
    • Inferring ancient divergences requires genes with strong phylogenetic signals
    • Salichos L., Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327-331.
    • (2013) Nature , vol.497 , pp. 327-331
    • Salichos, L.1    Rokas, A.2
  • 46
    • 79960670940 scopus 로고    scopus 로고
    • Terraces in phylogenetic tree space
    • Sanderson M. J., Mc Mahon M. M., Steel M. 2011. Terraces in phylogenetic tree space. Science 333:448-450.
    • (2011) Science , vol.333 , pp. 448-450
    • Sanderson, M.J.1    Mahon, M.M.M.2    Steel, M.3
  • 47
    • 0032030505 scopus 로고    scopus 로고
    • Phylogenetic supertrees: Assembling the trees of life
    • Sanderson M. J., Purvis A., Henze C. 1998. Phylogenetic supertrees: Assembling the trees of life. Trend Ecol. Evol. 13:105-109.
    • (1998) Trend Ecol. Evol. , vol.13 , pp. 105-109
    • Sanderson, M.J.1    Purvis, A.2    Henze, C.3
  • 49
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 51
    • 84940397165 scopus 로고    scopus 로고
    • A RAD-based phylogenetics for Orestias fishes from Lake Titicaca
    • Takahashi T., Moreno E. 2015. A RAD-based phylogenetics for Orestias fishes from Lake Titicaca. Mol. Phylogenet. Evol. 93:307-317.
    • (2015) Mol. Phylogenet. Evol. , vol.93 , pp. 307-317
    • Takahashi, T.1    Moreno, E.2
  • 52
    • 84906719626 scopus 로고    scopus 로고
    • Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock
    • Takahashi T., Nagata N., Sota T. 2014. Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock. Mol. Phylogenet. Evol. 80:137-144.
    • (2014) Mol. Phylogenet. Evol. , vol.80 , pp. 137-144
    • Takahashi, T.1    Nagata, N.2    Sota, T.3
  • 53
    • 84929590793 scopus 로고    scopus 로고
    • Quantifying MCMC exploration of phylogenetic tree space
    • Whidden C., Matsen F. A. 2015. Quantifying MCMC exploration of phylogenetic tree space. Syst. Biol. 64:472-491.
    • (2015) Syst. Biol. , vol.64 , pp. 472-491
    • Whidden, C.1    Matsen, F.A.2
  • 54
    • 0042905752 scopus 로고    scopus 로고
    • Missing data, incomplete taxa, and phylogenetic accuracy
    • Wiens J. J. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-538.
    • (2003) Syst. Biol. , vol.52 , pp. 528-538
    • Wiens, J.J.1
  • 55
    • 84934296789 scopus 로고    scopus 로고
    • Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
    • Xi Z., Liu L., Davis C. C. 2015. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased. Mol. Phylogenet. Evol. 92:63-71.
    • (2015) Mol. Phylogenet. Evol. , vol.92 , pp. 63-71
    • Xi, Z.1    Liu, L.2    Davis, C.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.