메뉴 건너뛰기




Volumn 65, Issue 3, 2016, Pages 357-365

Unforeseen consequences of excluding missing data from next-generation sequences: Simulation study of rad sequences

Author keywords

Next generation sequencing; Phylogenetic; Phylogeography; RADseq; RADtags; Species delimitation

Indexed keywords

CLASSIFICATION; COMPUTER SIMULATION; DNA SEQUENCE; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; PROCEDURES;

EID: 84978916740     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu046     Document Type: Article
Times cited : (229)

References (40)
  • 1
    • 84878449439 scopus 로고    scopus 로고
    • RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
    • Arnold B., Corbett-Detig R.B., Hartl D., Bomblies K. 2013. RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol. Ecol. 22:3179-3190.
    • (2013) Mol. Ecol , vol.22 , pp. 3179-3190
    • Arnold, B.1    Corbett-Detig, R.B.2    Hartl, D.3    Bomblies, K.4
  • 4
    • 84878464979 scopus 로고    scopus 로고
    • Population genomics based on low coverage sequencing: How low should we go?
    • Buerkle C.A., 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, C.A.1    Gompert, Z.2
  • 6
    • 0029096506 scopus 로고
    • Sampling properties of DNA sequence data in phylogenetic analysis
    • Cummings M.P., Otto S.P., Wakeley J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
    • (1995) Mol. Biol. Evol , vol.12 , pp. 814-822
    • Cummings, M.P.1    Otto, S.P.2    Wakeley, J.3
  • 7
    • 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
  • 9
    • 84859548731 scopus 로고    scopus 로고
    • Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales
    • Faircloth B.C., McCormack J.E., Crawford N.G., Harvey M.G., Brumfield R.T., Glenn T.C. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61:717-726.
    • (2012) Syst. Biol , vol.61 , pp. 717-726
    • Faircloth, B.C.1    McCormack, J.E.2    Crawford, N.G.3    Harvey, M.G.4    Brumfield, R.T.5    Glenn, T.C.6
  • 10
    • 33748204460 scopus 로고    scopus 로고
    • Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and supermatrix analyses of multiple gene data sets
    • Fulton T.L., Strobeck C. 2006. Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets. Mol. Phylogenet. Evol. 41:165-181.
    • (2006) Mol. Phylogenet. Evol , vol.41 , pp. 165-181
    • Fulton, T.L.1    Strobeck, C.2
  • 11
    • 77958059433 scopus 로고    scopus 로고
    • Sources of error for species-Tree estimation: Impact of mutational and coalescent effects on acuracy and implications for choosing among different methods
    • Huang H., He Q., Kubatko L.S., Knowles L.L. 2010. Sources of error for species-Tree estimation: impact of mutational and coalescent effects on acuracy and implications for choosing among different methods. Syst. Biol. 59:573-583.
    • (2010) Syst. Biol , vol.59 , pp. 573-583
    • Huang, H.1    He, Q.2    Kubatko, L.S.3    Knowles, L.L.4
  • 12
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J., DrummondA.J. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570-580.
    • (2010) Mol. Biol. Evol , vol.27 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 13
    • 79959221246 scopus 로고    scopus 로고
    • PRGMATIC: An efficient pipeline for collating genome-enriched second-generation sequencing data using a provisional-reference genome
    • Hird S.M., Brumfield R.T., Carstens B.C. 2011. PRGMATIC: An efficient pipeline for collating genome-enriched second-generation sequencing data using a provisional-reference genome. Mol. Ecol. Resour. 11:743-748.
    • (2011) Mol. Ecol. Resour , vol.11 , pp. 743-748
    • Hird, S.M.1    Brumfield, R.T.2    Carstens, B.C.3
  • 14
    • 84884589326 scopus 로고    scopus 로고
    • Effects of missing data on species tree estimation under the coalescent
    • Hovmöller R., Knowles L.L., Kubatko L.S. 2013. Effects of missing data on species tree estimation under the coalescent. Mol. Phylogenet. Evol. 69:1057-1062.
    • (2013) Mol. Phylogenet. Evol , vol.69 , pp. 1057-1062
    • Hovmöller, R.1    Knowles, L.L.2    Kubatko, L.S.3
  • 15
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a wright-fisher neutral model of genetic variation
    • Hudson R.R. 2002. Generating samples under a wright-fisher neutral model of genetic variation. Bioinformatics 18:337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 16
    • 84866147332 scopus 로고    scopus 로고
    • Full modeling versus summarizing gene-Tree uncertainty:method choice and species-Tree accuracy
    • Knowles L.L., Lanier H., Klimov P.B., He Q. 2012. Full modeling versus summarizing gene-Tree uncertainty:method choice and species-Tree accuracy. Mol. Phylogenet. Evol. 65:501-509.
    • (2012) Mol. Phylogenet. Evol , vol.65 , pp. 501-509
    • Knowles, L.L.1    Lanier, H.2    Klimov, P.B.3    He, Q.4
  • 17
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B., Trapnell C., Pop M., Salzberg S.L. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 18
    • 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
  • 19
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison W.P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
    • (1997) Syst. Biol , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 20
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison W.P., Knowles L.L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
    • (2006) Syst. Biol , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 23
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen R., Paul J.S., Albrechtsen A., Song Y.S. 2011. Genotype and SNP calling from next-generation sequencing data.Nat. Rev. Genet. 12:443-451.
    • (2011) Nat. Rev. Genet , vol.12 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 24
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo P., Ne M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
    • (1988) Mol. Biol. Evol , vol.5 , pp. 568-583
    • Pamilo, P.1    Ne, M.2
  • 25
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A., Grassly N.C. 1997. Seq-gen: An application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 26
    • 0030889065 scopus 로고    scopus 로고
    • Differences inDNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms
    • Reyna-Lopez G.E., Simpson J., Ruiz-Herrera J. 1997. Differences inDNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol. Gen. Genet. 253:703-710.
    • (1997) Mol. Gen. Genet , vol.253 , pp. 703-710
    • Reyna-Lopez, G.E.1    Simpson, J.2    Ruiz-Herrera, J.3
  • 27
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson D.F., Foulds L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
    • (1981) Math. Biosci , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 28
    • 84871842306 scopus 로고    scopus 로고
    • Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
    • Roure B., Baurain D., Philippe H. 2013. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol. Biol. Evol. 30:197-214.
    • (2013) Mol. Biol. Evol , vol.30 , pp. 197-214
    • Roure, B.1    Baurain, D.2    Philippe, H.3
  • 29
    • 84859516080 scopus 로고    scopus 로고
    • Inferring phylogenies from RAD sequence data
    • Rubin B.E., 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.1    Ree, R.H.2    Moreau, C.S.3
  • 30
    • 84891531569 scopus 로고    scopus 로고
    • Target capture and massivel parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales
    • Smith B.T., Harvey M.G., Faircloth B.C., Glenn T.C., Brumfield R.T. 2014. Target capture and massivel parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst. Biol. 63:83-95.
    • (2014) Syst. Biol , vol.63 , pp. 83-95
    • Smith, B.T.1    Harvey, M.G.2    Faircloth, B.C.3    Glenn, T.C.4    Brumfield, R.T.5
  • 31
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML web servers
    • Stamatakis A., Hoover P., Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57: 758-771.
    • (2008) Syst. Biol , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 32
    • 0024713112 scopus 로고
    • Gene genealogy in 3 related populations-consistency probability between gene and population trees
    • Takahata N. 1989. Gene genealogy in 3 related populations-consistency probability between gene and population trees. Genetics 122:957-966.
    • (1989) Genetics , vol.122 , pp. 957-966
    • Takahata, N.1
  • 33
    • 3242795999 scopus 로고    scopus 로고
    • An assessment of accuracy error, and conflict with support values from genome-scale phylogenetic data 21 1534 2004
    • Taylor D.J., Piel W.H. 2004. An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data (Vol. 21, p. 1534, 2004). Mol. Biol. Evol. 21:1812-1812.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 1812
    • Taylor, D.J.1    Piel, W.H.2
  • 34
    • 84872480881 scopus 로고    scopus 로고
    • Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
    • Wagner C.E., Keller I., Wittwer S., Selz O.M., Mwaiko S., Greuter L., Sivasundar A., Seehausen O. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol. Ecol. 22:787-798.
    • (2013) Mol. Ecol , vol.22 , pp. 787-798
    • Wagner, C.E.1    Keller, I.2    Wittwer, S.3    Selz, O.M.4    Mwaiko, S.5    Greuter, L.6    Sivasundar, A.7    Seehausen, O.8
  • 35
    • 84881616937 scopus 로고    scopus 로고
    • Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) usingRADsequencing
    • Wang X.Q., Zhao L., Eaton D.A., Li D.Z., Guo Z.H. 2013. Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) usingRADsequencing. Mol. Ecol.Resour. 13:938-945.
    • (2013) Mol. Ecol.Resour , vol.13 , pp. 938-945
    • Wang, X.Q.1    Zhao, L.2    Eaton, D.A.3    Li, D.Z.4    Guo, Z.H.5
  • 36
    • 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
  • 37
    • 31344471014 scopus 로고    scopus 로고
    • Missing data and the design of phylogenetic analyses
    • Wiens J.J. 2006. Missing data and the design of phylogenetic analyses. J. Biomed. Inform. 39:34-42.
    • (2006) J. Biomed. Inform , vol.39 , pp. 34-42
    • Wiens, J.J.1
  • 38
    • 0029498439 scopus 로고
    • Coping with missing entries in phylogenetic inference using parsimony
    • Wilkinson M. 1995. Coping with missing entries in phylogenetic inference using parsimony. Syst. Biol. 44:501-514.
    • (1995) Syst. Biol , vol.44 , pp. 501-514
    • Wilkinson, M.1
  • 39
    • 80955136714 scopus 로고    scopus 로고
    • Algorithms for MDC-based multilocus phylogeny inference: Beyond rooted binary gene trees on single alleles
    • Yu Y., Warnow T., Nakhleh L. 2011. Algorithms for MDC-based multilocus phylogeny inference: beyond rooted binary gene trees on single alleles. J. Comput. Biol. 18:1543-1559.
    • (2011) J. Comput. Biol , vol.18 , pp. 1543-1559
    • Yu, Y.1    Warnow, T.2    Nakhleh, L.3
  • 40
    • 84865263760 scopus 로고    scopus 로고
    • Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata
    • Zellmer A.J., Hanes M.M., Hird S.M., Carstens B.C. 2012. Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata. Syst. Biol. 61:763-777.
    • (2012) Syst. Biol , vol.61 , pp. 763-777
    • Zellmer, A.J.1    Hanes, M.M.2    Hird, S.M.3    Carstens, B.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.