메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

Hybrid-Lambda: Simulation of multiple merger and Kingman gene genealogies in species networks and species trees

Author keywords

Coalescent; FST< inf>; Gene tree; Hybrid lambda; Hybridization; Infinite sites model; Multiple merger; Skewed offspring distribution

Indexed keywords

FORESTRY; GENES; HISTORY; MERGING; POPULATION STATISTICS;

EID: 84941631015     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0721-y     Document Type: Article
Times cited : (30)

References (46)
  • 1
    • 2442502566 scopus 로고    scopus 로고
    • Mitochondrial cytochrome b variation in the high-fecundity Atlantic cod: trans-Atlantic clines and shallow gene genealogy
    • Árnason E. Mitochondrial cytochrome b variation in the high-fecundity Atlantic cod: trans-Atlantic clines and shallow gene genealogy. Genetics. 2004; 166:1871-85.
    • (2004) Genetics , vol.166 , pp. 1871-1885
    • Árnason, E.1
  • 2
    • 84926471520 scopus 로고    scopus 로고
    • Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
    • e786
    • Árnason E, Halldórsdóttir K.Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models. PeerJ. 2015; e786:3. doi: 10.7717/peerj.786 .
    • (2015) PeerJ , pp. 3
    • Árnason, E.1    Halldórsdóttir, K.2
  • 3
    • 84873147574 scopus 로고    scopus 로고
    • Time to a single hybridization event in a group of species with unknown ancestral history
    • Bartoszek K, Jones G, Oxelman B, Sagitov S. Time to a single hybridization event in a group of species with unknown ancestral history. J Theor Biol. 2004; 322:1-6.
    • (2004) J Theor Biol , vol.322 , pp. 1-6
    • Bartoszek, K.1    Jones, G.2    Oxelman, B.3    Sagitov, S.4
  • 4
    • 0013327863 scopus 로고
    • Mitochondrial haplotype frequencies in oysters: neutral alternatives to selection models, Non-neutral Evolution
    • In: (Golding B, editor). New York: Chapman & Hall
    • Beckenbach AT. In: (Golding B, editor.)Mitochondrial haplotype frequencies in oysters: neutral alternatives to selection models, Non-neutral Evolution. New York: Chapman & Hall; 1994, pp. 188-98.
    • (1994) , pp. 188-198
    • Beckenbach, A.T.1
  • 5
    • 58249119586 scopus 로고    scopus 로고
    • Extended Newick: it is time for a standard representation of phylogenetic networks
    • Cardona G, Rossell F, Valiente G. Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinform. 2008; 9:532.
    • (2008) BMC Bioinform , vol.9 , pp. 532
    • Cardona, G.1    Rossell, F.2    Valiente, G.3
  • 6
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • Degnan JH, Salter LA. Gene tree distributions under the coalescent process. Evolution. 2005; 59:24-37.
    • (2005) Evolution , vol.59 , pp. 24-37
    • Degnan, J.H.1    Salter, L.A.2
  • 7
    • 52949134472 scopus 로고    scopus 로고
    • Asymptotic results on the length of coalescent trees
    • Delmas JF, Dhersin JS, Siri-Jegousse A. Asymptotic results on the length of coalescent trees. Ann Appl Prob. 2008; 18:997-1025.
    • (2008) Ann Appl Prob , vol.18 , pp. 997-1025
    • Delmas, J.F.1    Dhersin, J.S.2    Siri-Jegousse, A.3
  • 8
    • 0033243134 scopus 로고    scopus 로고
    • Particle representations for measure-valued population models
    • Donnelly P, Kurtz TG. Particle representations for measure-valued population models. Ann Probab. 1999; 27:166-205.
    • (1999) Ann Probab , vol.27 , pp. 166-205
    • Donnelly, P.1    Kurtz, T.G.2
  • 9
    • 33646168295 scopus 로고    scopus 로고
    • Coalesent processes when the distribution of offspring number among individuals is highly skewed
    • Eldon B, Wakeley J. Coalesent processes when the distribution of offspring number among individuals is highly skewed. Genetics. 2006; 172:2621-33.
    • (2006) Genetics , vol.172 , pp. 2621-2633
    • Eldon, B.1    Wakeley, J.2
  • 10
    • 62449248724 scopus 로고    scopus 로고
    • Coalescence times and FST under a skewed offspring distribution among individuals in a population
    • Eldon B, Wakeley J. Coalescence times and F ST under a skewed offspring distribution among individuals in a population. Genetics. 2009; 181:615-29.
    • (2009) Genetics , vol.181 , pp. 615-629
    • Eldon, B.1    Wakeley, J.2
  • 11
    • 79959378608 scopus 로고    scopus 로고
    • Estimation of parameters in large offspring number models and ratios of coalescence times
    • Eldon B. Estimation of parameters in large offspring number models and ratios of coalescence times. Theor Popul Biol. 2011; 80:16-28.
    • (2011) Theor Popul Biol , vol.80 , pp. 16-28
    • Eldon, B.1
  • 12
    • 84863882958 scopus 로고    scopus 로고
    • Multiple merger gene genealogies in two species: monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents
    • Eldon B, Degnan JH. Multiple merger gene genealogies in two species: monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents. Theor Popul Biol. 2012; 82:117-30.
    • (2012) Theor Popul Biol , vol.82 , pp. 117-130
    • Eldon, B.1    Degnan, J.H.2
  • 13
    • 84925002635 scopus 로고    scopus 로고
    • Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents
    • Eldon B, Birkner M, Blath J, Freund F. Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger CoalescentsGenetics. 2015; 199:841-56.
    • (2015) Genetics , vol.199 , pp. 841-856
    • Eldon, B.1    Birkner, M.2    Blath, J.3    Freund, F.4
  • 14
    • 77955381733 scopus 로고    scopus 로고
    • MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus
    • Ewing G, Hermisson J. MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics. 2010; 26:2064-65.
    • (2010) Bioinformatics , vol.26 , pp. 2064-2065
    • Ewing, G.1    Hermisson, J.2
  • 15
    • 84926358875 scopus 로고    scopus 로고
    • Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
    • Excoffier L, Foll M. Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics. 2011; 27:9.
    • (2011) Bioinformatics , vol.27 , pp. 9
    • Excoffier, L.1    Foll, M.2
  • 16
    • 33748607987 scopus 로고    scopus 로고
    • Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand
    • Goldstien SJ, Schiel DR, Gemmell NJ. Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand. Mol Ecol. 2009; 15:3259-68.
    • (2009) Mol Ecol , vol.15 , pp. 3259-3268
    • Goldstien, S.J.1    Schiel, D.R.2    Gemmell, N.J.3
  • 17
    • 0002761623 scopus 로고
    • Does variance in reproductive success limit effective population sizes of marine organisms? Genetics and Evolution of Aquatic Organisms
    • In: (Beaumont A, editor.). London: Chapman and Hall
    • Hedgecock D. In: (Beaumont A, editor.)Does variance in reproductive success limit effective population sizes of marine organisms? Genetics and Evolution of Aquatic Organisms. London: Chapman and Hall; 1994, pp. 1222-344.
    • (1994) , pp. 1222-1344
    • Hedgecock, D.1
  • 18
    • 0000703578 scopus 로고
    • In: (Abele LG, editor.)Genetics, The Biology of Crustacea. New York: Academic Press
    • Hedgecock D, Tracey M, Nelson K. In: (Abele LG, editor.)Genetics, The Biology of Crustacea vol. 2. New York: Academic Press; 1982, pp. 297-403.
    • (1982) , vol.2 , pp. 297-403
    • Hedgecock, D.1    Tracey, M.2    Nelson, K.3
  • 19
    • 80054114829 scopus 로고    scopus 로고
    • Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary
    • Hedgecock D, Pudovkin AI. Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bull Mar Sci. 2011; 87:971-1002.
    • (2011) Bull Mar Sci , vol.87 , pp. 971-1002
    • Hedgecock, D.1    Pudovkin, A.I.2
  • 21
    • 33847273741 scopus 로고    scopus 로고
    • msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
    • Hellenthal G, Stephens M. msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics. 2007; 23:520-21.
    • (2007) Bioinformatics , vol.23 , pp. 520-521
    • Hellenthal, G.1    Stephens, M.2
  • 23
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • Hudson RR. Gene genealogies and the coalescent process. Oxford Surv Evol Biol. 1990; 7:1-44.
    • (1990) Oxford Surv Evol Biol , vol.7 , pp. 1-44
    • Hudson, R.R.1
  • 24
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model
    • Hudson RR. Generating samples under a Wright-Fisher neutral model. Bioinformatics. 2002; 18:337-38.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 25
    • 84924456174 scopus 로고    scopus 로고
    • Phylogenetic Networks: Concepts, Algorithms and Applications: Cambridge University Press
    • Huson D, Rupp R, Scornavacca C. Phylogenetic Networks: Concepts, Algorithms and Applications: Cambridge University Press; 2010.
    • (2010)
    • Huson, D.1    Rupp, R.2    Scornavacca, C.3
  • 26
    • 84876251356 scopus 로고    scopus 로고
    • Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting
    • Jones G, Sagitov S, Oxelman B. Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Syst Biol. 2013; 62:467-78.
    • (2013) Syst Biol , vol.62 , pp. 467-478
    • Jones, G.1    Sagitov, S.2    Oxelman, B.3
  • 27
    • 0002556819 scopus 로고
    • On the genealogy of large populations
    • Kingman JFC. On the genealogy of large populations. J App Probab. 1982; 19A:27-43.
    • (1982) J App Probab , vol.19A , pp. 27-43
    • Kingman, J.F.C.1
  • 28
    • 70450277249 scopus 로고    scopus 로고
    • Identifying hybridization events in the presence of coalescence via model selection
    • Kubatko LS. Identifying hybridization events in the presence of coalescence via model selection. Syst Biol. 2009; 58:478-88.
    • (2009) Syst Biol , vol.58 , pp. 478-488
    • Kubatko, L.S.1
  • 29
    • 7244221627 scopus 로고    scopus 로고
    • SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
    • Laval G, Excoffier L. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics. 2004; 20:2485-87.
    • (2004) Bioinformatics , vol.20 , pp. 2485-2487
    • Laval, G.1    Excoffier, L.2
  • 30
    • 34547830810 scopus 로고    scopus 로고
    • GENOME: a rapid coalescent-based whole genome simulator
    • Liang L, Zöllner S, Abecasis GR. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics. 2007; 23:1565-67.
    • (2007) Bioinformatics , vol.23 , pp. 1565-1567
    • Liang, L.1    Zöllner, S.2    Abecasis, G.R.3
  • 31
    • 58249136809 scopus 로고    scopus 로고
    • Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model
    • Meng C, Kubatko LS. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. Theor Popul Biol. 2009; 75:35-45.
    • (2009) Theor Popul Biol , vol.75 , pp. 35-45
    • Meng, C.1    Kubatko, L.S.2
  • 33
    • 84883517554 scopus 로고
    • Gary Olsen's interpretation of the "Newick's 8:45" tree format standard
    • Access date 2/Sep/2015
    • Olsen G. Gary Olsen's interpretation of the "Newick's 8:45" tree format standard. 1990. http://evolution.genetics.washington.edu/phylip/newick_doc.html . Access date 2/Sep/2015.
    • (1990)
    • Olsen, G.1
  • 34
    • 3242679961 scopus 로고    scopus 로고
    • Effects of hydrographic barriers on population genetic structure of the sea star Coscinasterias muricata (Echinodermata, Asteroidea) in the New Zealand fiords
    • Perrin C, Wing SR, Roy MS. Effects of hydrographic barriers on population genetic structure of the sea star Coscinasterias muricata (Echinodermata, Asteroidea) in the New Zealand fiords. Mol Ecol. 2004; 13:2183-95.
    • (2004) Mol Ecol , vol.13 , pp. 2183-2195
    • Perrin, C.1    Wing, S.R.2    Roy, M.S.3
  • 35
    • 0033233681 scopus 로고    scopus 로고
    • Coalescents with multiple collisions
    • Pitman J. Coalescents with multiple collisions. Ann Probab. 1999; 27:1870-902.
    • (1999) Ann Probab , vol.27 , pp. 1870-1902
    • Pitman, J.1
  • 36
    • 0033233843 scopus 로고    scopus 로고
    • The general coalescent with asynchronous mergers of ancestral lines
    • Sagitov S. The general coalescent with asynchronous mergers of ancestral lines. J Appl Probab. 1999; 36:1116-125.
    • (1999) J Appl Probab , vol.36 , pp. 1116-1125
    • Sagitov, S.1
  • 37
    • 78650649545 scopus 로고    scopus 로고
    • R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
    • R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2015. http://www.R-project.org/ .
    • (2015)
  • 38
    • 46449135597 scopus 로고    scopus 로고
    • A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms
    • Sargsyan O, Wakeley J. A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms. Theor Popul Biol. 2008; 74:104-114.
    • (2008) Theor Popul Biol , vol.74 , pp. 104-114
    • Sargsyan, O.1    Wakeley, J.2
  • 39
    • 0037843651 scopus 로고    scopus 로고
    • Coalescent processes obtained from supercritical Galton-Watson processes
    • Schweinsberg J. Coalescent processes obtained from supercritical Galton-Watson processes. Stoch Proc Appl. 2003; 106:107-39.
    • (2003) Stoch Proc Appl , vol.106 , pp. 107-139
    • Schweinsberg, J.1
  • 40
    • 0026050476 scopus 로고
    • Inbreeding coefficients and coalescence times
    • Slatkin M. Inbreeding coefficients and coalescence times. Genet. Res. 1991; 58:167-175.
    • (1991) Genet. Res. , vol.58 , pp. 167-175
    • Slatkin, M.1
  • 41
    • 84929624753 scopus 로고    scopus 로고
    • Scrm: efficiently simulating long sequences using the approximated coalescent with recombination
    • Staab PR, Zhu S, Metzler D, Lunter G. Scrm: efficiently simulating long sequences using the approximated coalescent with recombination. Bioinformatics. 2015; 31(10):1680-82.
    • (2015) Bioinformatics , vol.31 , Issue.10 , pp. 1680-1682
    • Staab, P.R.1    Zhu, S.2    Metzler, D.3    Lunter, G.4
  • 42
    • 84901481068 scopus 로고    scopus 로고
    • Coalescence 2.0: a multiple branching of recent theoretical developments and their applications
    • Tellier A, Lemaire C.Coalescence 2.0: a multiple branching of recent theoretical developments and their applications. Mol Ecol. 2014; 23:2637-52.
    • (2014) Mol Ecol , vol.23 , pp. 2637-2652
    • Tellier, A.1    Lemaire, C.2
  • 43
    • 51349098340 scopus 로고    scopus 로고
    • PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
    • Than C, Ruths D, Nakhleh L. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinforma. 2008; 9:322. doi: 10.1186/1471-2105-9-322 .
    • (2008) BMC Bioinforma , vol.9 , pp. 322
    • Than, C.1    Ruths, D.2    Nakhleh, L.3
  • 44
    • 4344610360 scopus 로고    scopus 로고
    • Phylogeography of a high-dispersal New Zealand sea-star: does upwelling block gene-flow
    • Waters JM, Roy MS. Phylogeography of a high-dispersal New Zealand sea-star: does upwelling block gene-flowMol Ecol. 2004; 13:2797-806.
    • (2004) Mol Ecol , vol.13 , pp. 2797-2806
    • Waters, J.M.1    Roy, M.S.2
  • 45
    • 79951575208 scopus 로고    scopus 로고
    • Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting
    • Yu Y, Than C, Degnan JH, Nakhleh L. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst Biol. 2011; 60:138-49.
    • (2011) Syst Biol , vol.60 , pp. 138-149
    • Yu, Y.1    Than, C.2    Degnan, J.H.3    Nakhleh, L.4
  • 46
    • 84860577768 scopus 로고    scopus 로고
    • The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection
    • e1002660
    • Yu Y, Degnan JH, Nakhleh L. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genet. 2012; e1002660:8. doi: 10.1371/journal.pgen.1002660 .
    • (2012) PLoS Genet , pp. 8
    • Yu, Y.1    Degnan, J.H.2    Nakhleh, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.