TY - JOUR AU - Otto, S. P. AU - Whitton, J. PY - 2000 DA - 2000// TI - Polyploid incidence and evolution JO - Annu Rev Genet VL - 34 UR - https://doi.org/10.1146/annurev.genet.34.1.401 DO - 10.1146/annurev.genet.34.1.401 ID - Otto2000 ER - TY - JOUR AU - Adams, K. L. AU - Wendel, J. F. PY - 2005 DA - 2005// TI - Polyploidy and genome evolution in plants JO - Curr Opin Plant Biol VL - 8 UR - https://doi.org/10.1016/j.pbi.2005.01.001 DO - 10.1016/j.pbi.2005.01.001 ID - Adams2005 ER - TY - JOUR AU - Madlung, A. PY - 2013 DA - 2013// TI - Polyploidy and its effect on evolutionary success: old questions revisited with new tools JO - Heredity VL - 110 UR - https://doi.org/10.1038/hdy.2012.79 DO - 10.1038/hdy.2012.79 ID - Madlung2013 ER - TY - JOUR AU - Blomme, T. AU - Vandepoele, K. AU - Bodt, S. AU - Simillion, C. AU - Maere, S. AU - Peer, Y. PY - 2006 DA - 2006// TI - The gain and loss of genes during 600 million years of vertebrate evolution JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-5-r43 DO - 10.1186/gb-2006-7-5-r43 ID - Blomme2006 ER - TY - JOUR AU - Jiao, Y. AU - Wickett, N. J. AU - Ayyampalayam, S. AU - Chanderbali, A. S. AU - Landherr, L. AU - Ralph, P. E. PY - 2011 DA - 2011// TI - Ancestral polyploidy in seed plants and angiosperms JO - Nature VL - 473 UR - https://doi.org/10.1038/nature09916 DO - 10.1038/nature09916 ID - Jiao2011 ER - TY - JOUR AU - Mallet, J. PY - 2007 DA - 2007// TI - Hybrid speciation JO - Nature VL - 446 UR - https://doi.org/10.1038/nature05706 DO - 10.1038/nature05706 ID - Mallet2007 ER - TY - JOUR AU - Chester, M. AU - Gallagher, J. P. AU - Symonds, V. V. AU - Cruz da Silva, A. V. AU - Mavrodiev, E. V. AU - Leitch, A. R. PY - 2012 DA - 2012// TI - Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae) JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1112041109 DO - 10.1073/pnas.1112041109 ID - Chester2012 ER - TY - JOUR AU - Soltis, D. E. AU - Mavrodiev, E. V. AU - Meyers, S. C. AU - Severns, P. M. AU - Zhang, L. AU - Gitzendanner, M. A. PY - 2012 DA - 2012// TI - Additional origins of Ownbey’s Tragopogon mirus JO - Bot J Linn Soc VL - 169 UR - https://doi.org/10.1111/j.1095-8339.2012.01244.x DO - 10.1111/j.1095-8339.2012.01244.x ID - Soltis2012 ER - TY - JOUR AU - Arkhipova, I. R. AU - Rodriguez, F. PY - 2013 DA - 2013// TI - Genetic and epigenetic changes involving (retro) transposons in animal hybrids and polyploids JO - Cytogenet Genome Res VL - 140 UR - https://doi.org/10.1159/000352069 DO - 10.1159/000352069 ID - Arkhipova2013 ER - TY - JOUR AU - Vallejo-Marín, M. AU - Buggs, R. J. A. AU - Cooley, A. M. AU - Puzey, J. R. PY - 2015 DA - 2015// TI - Speciation by genome duplication: repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus JO - Evolution VL - 69 UR - https://doi.org/10.1111/evo.12678 DO - 10.1111/evo.12678 ID - Vallejo-Marín2015 ER - TY - STD TI - Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH. The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A. 2009;106:13875–9. ID - ref11 ER - TY - STD TI - Weiss-Schneeweiss H, Emadzade K, Jang T-S, Schneeweiss GM. Evolutionary consequences, constraints and potential of polyploidy in plants. Cytogenet Genome Res. 2013;140:137-50. ID - ref12 ER - TY - JOUR AU - Otto, S. P. PY - 2007 DA - 2007// TI - The evolutionary consequences of polyploidy JO - Cell VL - 131 UR - https://doi.org/10.1016/j.cell.2007.10.022 DO - 10.1016/j.cell.2007.10.022 ID - Otto2007 ER - TY - JOUR AU - Mayrose, I. AU - Zhan, S. H. AU - Rothfels, C. J. AU - Magnuson-Ford, K. AU - Barker, M. S. AU - Rieseberg, L. H. PY - 2011 DA - 2011// TI - Recently formed polyploid plants diversify at lower rates JO - Science VL - 333 UR - https://doi.org/10.1126/science.1207205 DO - 10.1126/science.1207205 ID - Mayrose2011 ER - TY - JOUR AU - Soltis, D. E. AU - Segovia-Salcedo, M. C. AU - Jordon-Thaden, I. AU - Majure, L. AU - Miles, N. M. AU - Mavrodiev, E. V. PY - 2014 DA - 2014// TI - Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al. (2011) JO - New Phytol VL - 202 UR - https://doi.org/10.1111/nph.12756 DO - 10.1111/nph.12756 ID - Soltis2014 ER - TY - STD TI - Fawcett JA, Maere S, Van de Peer Y. Plants with double genomes might have had a better chance to survive the Cretaceous–Tertiary extinction event. Proc Natl Acad Sci U S A. 2009;106:5737–42. ID - ref16 ER - TY - STD TI - Vanneste K, Baele G, Maere S, Van de Peer Y. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res. 2014;24:1334-47. ID - ref17 ER - TY - JOUR AU - Leitch, A. R. AU - Leitch, I. J. PY - 2008 DA - 2008// TI - Genomic plasticity and the diversity of polyploid plants JO - Science VL - 320 UR - https://doi.org/10.1126/science.1153585 DO - 10.1126/science.1153585 ID - Leitch2008 ER - TY - STD TI - Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, et al. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun. 2014;5:3930. ID - ref19 ER - TY - JOUR AU - Moghe, G. D. AU - Shiu, S. -. H. PY - 2014 DA - 2014// TI - The causes and molecular consequences of polyploidy in flowering plants JO - Ann N Y Acad Sci VL - 1320 UR - https://doi.org/10.1111/nyas.12466 DO - 10.1111/nyas.12466 ID - Moghe2014 ER - TY - JOUR AU - Renny-Byfield, S. AU - Wendel, J. F. PY - 2014 DA - 2014// TI - Doubling down on genomes: polyploidy and crop plants JO - Am J Bot VL - 101 UR - https://doi.org/10.3732/ajb.1400119 DO - 10.3732/ajb.1400119 ID - Renny-Byfield2014 ER - TY - STD TI - Gregory TR, Mable BK. Polyploidy in animals. In: TR Gregory, ed. The Evolution of the Genome. Burlington, MA: Academic Press; 2011. pp. 427–517. ID - ref22 ER - TY - JOUR AU - Thompson, J. D. AU - Lumaret, R. PY - 1992 DA - 1992// TI - The evolutionary dynamics of polyploid plants: origins, establishment and persistence JO - Trends Ecol Evol VL - 7 UR - https://doi.org/10.1016/0169-5347(92)90228-4 DO - 10.1016/0169-5347(92)90228-4 ID - Thompson1992 ER - TY - JOUR AU - Ramsey, J. AU - Schemske, D. W. PY - 1998 DA - 1998// TI - Pathways, mechanisms, and rates of polyploid formation in flowering plants JO - Annu Rev Ecol Syst VL - 29 UR - https://doi.org/10.1146/annurev.ecolsys.29.1.467 DO - 10.1146/annurev.ecolsys.29.1.467 ID - Ramsey1998 ER - TY - JOUR AU - Ramsey, J. AU - Schemske, D. W. PY - 2002 DA - 2002// TI - Neopolyploidy in flowering plants JO - Annu Rev Ecol Syst VL - 33 UR - https://doi.org/10.1146/annurev.ecolsys.33.010802.150437 DO - 10.1146/annurev.ecolsys.33.010802.150437 ID - Ramsey2002 ER - TY - STD TI - Giraud T, Refrégier G, Le Gac M, de Vienne DM, Hood ME. Speciation in fungi. Fungal Genet Biol. 2008;45:791–802. ID - ref26 ER - TY - STD TI - Kim S-T, Sultan SE, Donoghue MJ. Allopolyploid speciation in Persicaria (Polygonaceae): insights from a low-copy nuclear region. Proc Natl Acad Sci U S A. 2008;105:12370–5. ID - ref27 ER - TY - STD TI - Ainouche ML, Wendel JF. Polyploid speciation and genome evolution: lessons from recent allopolyploids. In: P Pontarotti, ed. Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life. New York City: Springer; 2014. pp. 87–113. ID - ref28 ER - TY - JOUR AU - Marcussen, T. AU - Sandve, S. R. AU - Heier, L. AU - Spannagl, M. AU - Pfeifer, M. PY - 2014 DA - 2014// TI - Ancient hybridizations among the ancestral genomes of bread wheat JO - Science VL - 345 UR - https://doi.org/10.1126/science.1250092 DO - 10.1126/science.1250092 ID - Marcussen2014 ER - TY - JOUR AU - Tennessen, J. A. AU - Govindarajulu, R. AU - Ashman, T. -. L. AU - Liston, A. PY - 2014 DA - 2014// TI - Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps JO - Genome Biol Evol VL - 6 UR - https://doi.org/10.1093/gbe/evu261 DO - 10.1093/gbe/evu261 ID - Tennessen2014 ER - TY - STD TI - Marcussen T, Heier L, Brysting AK, Oxelman B, Jakobsen KS. From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae). Syst Biol. 2015;64:84–101. ID - ref31 ER - TY - JOUR AU - McBreen, K. AU - Lockhart, P. J. PY - 2006 DA - 2006// TI - Reconstructing reticulate evolutionary histories of plants JO - Trends Plant Sci VL - 11 UR - https://doi.org/10.1016/j.tplants.2006.06.004 DO - 10.1016/j.tplants.2006.06.004 ID - McBreen2006 ER - TY - JOUR AU - Linder, C. R. AU - Rieseberg, L. H. PY - 2004 DA - 2004// TI - Reconstructing patterns of reticulate evolution in plants JO - Am J Bot VL - 91 UR - https://doi.org/10.3732/ajb.91.10.1700 DO - 10.3732/ajb.91.10.1700 ID - Linder2004 ER - TY - JOUR AU - Holland, B. R. AU - Benthin, S. AU - Lockhart, P. J. AU - Moulton, V. AU - Huber, K. T. PY - 2008 DA - 2008// TI - Using supernetworks to distinguish hybridization from lineage-sorting JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-202 DO - 10.1186/1471-2148-8-202 ID - Holland2008 ER - TY - STD TI - Brysting AK, Mathiesen C. Challenges in polyploid phylogenetic reconstruction: a case story from the arctic-alpine Cerastium alpinum complex. Taxon. 2011;60:333–47. ID - ref35 ER - TY - STD TI - Vergilino R, Markova S, Ventura M, Manca M, Dufresne F. Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers. Mol Ecol. 2011;20:1191–207. ID - ref36 ER - TY - JOUR AU - Morrison, D. A. PY - 2014 DA - 2014// TI - Phylogenetic networks: a new form of multivariate data summary for data mining and exploratory data analysis JO - Wiley Interdiscip Rev Data Min Knowl Discov VL - 4 UR - https://doi.org/10.1002/widm.1130 DO - 10.1002/widm.1130 ID - Morrison2014 ER - TY - STD TI - Popp M, Erixon P, Eggens F, Oxelman B. Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae) inferred from low copy nuclear RNA polymerase introns, rDNA, and chloroplast DNA. Syst Bot. 2005;30:302–13. ID - ref38 ER - TY - JOUR AU - Mort, M. E. AU - Crawford, D. J. PY - 2004 DA - 2004// TI - The continuing search: low-copy nuclear sequences for lower-level plant molecular phylogenetic studies JO - Taxon VL - 53 UR - https://doi.org/10.2307/4135604 DO - 10.2307/4135604 ID - Mort2004 ER - TY - STD TI - Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, et al. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol Biol. 2010;10:61. ID - ref40 ER - TY - STD TI - Marcussen T, Jakobsen KS, Danihelka J, Ballard HE, Blaxland K, Brysting AK, et al. Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae). Syst Biol. 2012;61:107–26. ID - ref41 ER - TY - JOUR AU - McCormack, J. E. AU - Hird, S. M. AU - Zellmer, A. J. AU - Carstens, B. C. AU - Brumfield, R. T. PY - 2013 DA - 2013// TI - Applications of next-generation sequencing to phylogeography and phylogenetics JO - Mol Phylogenet Evol VL - 66 UR - https://doi.org/10.1016/j.ympev.2011.12.007 DO - 10.1016/j.ympev.2011.12.007 ID - McCormack2013 ER - TY - JOUR AU - Mandel, J. R. AU - Dikow, R. B. AU - Funk, V. A. PY - 2015 DA - 2015// TI - Using phylogenomics to resolve mega-families: an example from Compositae JO - J Syst Evol VL - 53 UR - https://doi.org/10.1111/jse.12167 DO - 10.1111/jse.12167 ID - Mandel2015 ER - TY - STD TI - Nicholls JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, et al. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Front Plant Sci. 2015;6:710. ID - ref44 ER - TY - JOUR AU - Griffin, P. C. AU - Robin, C. AU - Hoffmann, A. A. PY - 2011 DA - 2011// TI - A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses JO - BMC Biol VL - 9 UR - https://doi.org/10.1186/1741-7007-9-19 DO - 10.1186/1741-7007-9-19 ID - Griffin2011 ER - TY - JOUR AU - Browning, S. R. AU - Browning, B. L. PY - 2011 DA - 2011// TI - Haplotype phasing: existing methods and new developments JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg3054 DO - 10.1038/nrg3054 ID - Browning2011 ER - TY - STD TI - Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27:2987–93. ID - ref47 ER - TY - STD TI - Sasaki E, Sugino RP, Innan H. The linkage method: a novel approach for SNP detection and haplotype reconstruction from a single diploid individual using next-generation sequence data. Mol Biol Evol. 2013;30:2187-96. ID - ref48 ER - TY - JOUR AU - Zhang, Y. PY - 2013 DA - 2013// TI - A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next-generation sequencing JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt065 DO - 10.1093/bioinformatics/btt065 ID - Zhang2013 ER - TY - JOUR AU - Hedderson, T. A. AU - Chapman, R. L. AU - Rootes, W. L. PY - 1996 DA - 1996// TI - Phylogenetic relationships of bryophytes inferred from nuclear-encoded rRNA gene sequences JO - Plant Syst Evol VL - 200 UR - https://doi.org/10.1007/BF00984936 DO - 10.1007/BF00984936 ID - Hedderson1996 ER - TY - JOUR AU - Shimizu-Inatsugi, R. AU - Lihová, J. AU - Iwanaga, H. AU - Kudoh, H. AU - Marhold, K. AU - Savolainen, O. PY - 2009 DA - 2009// TI - The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri JO - Mol Ecol VL - 18 UR - https://doi.org/10.1111/j.1365-294X.2009.04329.x DO - 10.1111/j.1365-294X.2009.04329.x ID - Shimizu-Inatsugi2009 ER - TY - STD TI - Okuyama Y, Tanabe AS, Kato M. Entangling ancient allotetraploidization in Asian Mitella: an integrated approach for multilocus combinations. Mol Biol Evol. 2012;29:429–39. ID - ref52 ER - TY - STD TI - Petri A, Oxelman B. Phylogenetic relationships within Silene (Caryophyllaceae) section Physolychnis. Taxon. 2011;60:953–68. ID - ref53 ER - TY - STD TI - Fan X, Sha L-N, Zeng J, Kang H-Y, Zhang H-Q, Wang X-L, et al. Evolutionary dynamics of the Pgk1 gene in the polyploid genus Kengyilia (Triticeae: Poaceae) and its diploid relatives. PLoS One. 2012;7:e31122. ID - ref54 ER - TY - JOUR AU - Scheen, A. -. C. AU - Pfeil, B. E. AU - Petri, A. AU - Heidari, N. AU - Nylinder, S. AU - Oxelman, B. PY - 2012 DA - 2012// TI - Use of allele-specific sequencing primers is an efficient alternative to PCR subcloning of low-copy nuclear genes JO - Mol Ecol Resour VL - 12 UR - https://doi.org/10.1111/j.1755-0998.2011.03070.x DO - 10.1111/j.1755-0998.2011.03070.x ID - Scheen2012 ER - TY - STD TI - Straub SCK, Doyle JJ. Molecular phylogenetics of Amorpha (Fabaceae): an evaluation of monophyly, species relationships, and polyploid origins. Mol Phylogenet Evol. 2014;76:49–66. ID - ref56 ER - TY - STD TI - Triplett JK, Wang Y, Zhong J, Kellogg EA. Five nuclear loci resolve the polyploid history of switchgrass (Panicum virgatum L.) and relatives. PLoS One. 2012;7:e38702. ID - ref57 ER - TY - JOUR AU - Kraytsberg, Y. AU - Khrapko, K. PY - 2005 DA - 2005// TI - Single-molecule PCR: an artifact-free PCR approach for the analysis of somatic mutations JO - Expert Rev Mol Diagn VL - 5 UR - https://doi.org/10.1586/14737159.5.5.809 DO - 10.1586/14737159.5.5.809 ID - Kraytsberg2005 ER - TY - STD TI - Hori K, Tono A, Fujimoto K, Kato J, Ebihara A, Watano Y, et al. Reticulate evolution in the apogamous Dryopteris varia complex (Dryopteridaceae, subg. Erythrovariae, sec. Variae) complex and its related sexual species in Japan. J Plant Res. 2014;127:661–84. ID - ref59 ER - TY - JOUR AU - Cronn, R. AU - Knaus, B. J. AU - Liston, A. AU - Maughan, P. J. AU - Parks, M. AU - Syring, J. V. PY - 2012 DA - 2012// TI - Targeted enrichment strategies for next-generation plant biology JO - Am J Bot VL - 99 UR - https://doi.org/10.3732/ajb.1100356 DO - 10.3732/ajb.1100356 ID - Cronn2012 ER - TY - JOUR AU - Amini, S. AU - Pushkarev, D. AU - Christiansen, L. AU - Kostem, E. AU - Royce, T. AU - Turk, C. PY - 2014 DA - 2014// TI - Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing JO - Nat Genet VL - 46 UR - https://doi.org/10.1038/ng.3119 DO - 10.1038/ng.3119 ID - Amini2014 ER - TY - JOUR AU - Bansal, V. AU - Bafna, V. PY - 2008 DA - 2008// TI - HapCUT: an efficient and accurate algorithm for the haplotype assembly problem JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn298 DO - 10.1093/bioinformatics/btn298 ID - Bansal2008 ER - TY - JOUR AU - DePristo, M. A. AU - Banks, E. AU - Poplin, R. AU - Garimella, K. V. AU - Maguire, J. R. AU - Hartl, C. PY - 2011 DA - 2011// TI - A framework for variation discovery and genotyping using next-generation DNA sequencing data JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.806 DO - 10.1038/ng.806 ID - DePristo2011 ER - TY - JOUR AU - Aguiar, D. AU - Istrail, S. PY - 2013 DA - 2013// TI - Haplotype assembly in polyploid genomes and identical by descent shared tracts JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt213 DO - 10.1093/bioinformatics/btt213 ID - Aguiar2013 ER - TY - STD TI - Berger E, Yorukoglu D, Peng J, Berger B. HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data. PLoS Comput Biol. 2014;10:e1003502. ID - ref65 ER - TY - JOUR AU - Das, S. AU - Vikalo, H. PY - 2015 DA - 2015// TI - SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1408-5 DO - 10.1186/s12864-015-1408-5 ID - Das2015 ER - TY - STD TI - Weitemier K, Straub SCK, Cronn RC, Fishbein M, Schmickl R, McDonnell A, et al. Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics. Appl Plant Sci. 2014;2:1400042 ID - ref67 ER - TY - STD TI - Fortune PM, Pourtau N, Viron N, Ainouche ML. Molecular phylogeny and reticulate origins of the polyploid Bromus species from section Genea (Poaceae). Am J Bot. 2008;95:454–64. ID - ref68 ER - TY - STD TI - Sessa EB, Zimmer EA, Givnish TJ. Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae). BMC Evol Biol. 2012;12:104. ID - ref69 ER - TY - JOUR AU - Huber, K. T. AU - Oxelman, B. AU - Lott, M. AU - Moulton, V. PY - 2006 DA - 2006// TI - Reconstructing the evolutionary history of polyploids from multilabeled trees JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msl045 DO - 10.1093/molbev/msl045 ID - Huber2006 ER - TY - STD TI - Wendel JF, Doyle JJ. Phylogenetic incongruence: window into genome history and molecular evolution. In: DE Soltis, PS Soltis, JJ Doyle, eds. Molecular Systematics of Plants II. New York City: Springer; 1998. pp. 265–96. ID - ref71 ER - TY - JOUR AU - Degnan, J. H. AU - DeGiorgio, M. AU - Bryant, D. AU - Rosenberg, N. A. PY - 2009 DA - 2009// TI - Properties of consensus methods for inferring species trees from gene trees JO - Syst Biol VL - 58 UR - https://doi.org/10.1093/sysbio/syp008 DO - 10.1093/sysbio/syp008 ID - Degnan2009 ER - TY - JOUR AU - Jin, G. AU - Nakhleh, L. AU - Snir, S. AU - Tuller, T. PY - 2006 DA - 2006// TI - Maximum likelihood of phylogenetic networks JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl452 DO - 10.1093/bioinformatics/btl452 ID - Jin2006 ER - TY - JOUR AU - Kubatko, L. S. AU - Carstens, B. C. AU - Knowles, L. L. PY - 2009 DA - 2009// TI - STEM: species tree estimation using maximum likelihood for gene trees under coalescence JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp079 DO - 10.1093/bioinformatics/btp079 ID - Kubatko2009 ER - TY - JOUR AU - Meng, C. AU - Kubatko, L. S. PY - 2009 DA - 2009// TI - Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model JO - Theor Popul Biol VL - 75 UR - https://doi.org/10.1016/j.tpb.2008.10.004 DO - 10.1016/j.tpb.2008.10.004 ID - Meng2009 ER - TY - JOUR AU - Gerard, D. AU - Gibbs, H. L. AU - Kubatko, L. PY - 2011 DA - 2011// TI - Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling JO - BMC Evol Biol VL - 11 UR - https://doi.org/10.1186/1471-2148-11-291 DO - 10.1186/1471-2148-11-291 ID - Gerard2011 ER - TY - JOUR AU - Yu, Y. AU - Barnett, R. M. AU - Nakhleh, L. PY - 2013 DA - 2013// TI - Parsimonious inference of hybridization in the presence of incomplete lineage sorting JO - Syst Biol VL - 62 UR - https://doi.org/10.1093/sysbio/syt037 DO - 10.1093/sysbio/syt037 ID - Yu2013 ER - TY - STD TI - Than C, Ruths D, Nakhleh L. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformat. 2008;9:322. ID - ref78 ER - TY - STD TI - Liston A, Cronn R, Ashman T-L. Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights. Am J Bot. 2014;101:1686–99. ID - ref79 ER - TY - STD TI - Edwards D, Batley J, Snowdon RJ. Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet. 2013;126:1–11. ID - ref80 ER - TY - JOUR AU - Njuguna, W. AU - Liston, A. AU - Cronn, R. AU - Ashman, T. -. L. AU - Bassil, N. PY - 2013 DA - 2013// TI - Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing JO - Mol Phylogenet Evol VL - 66 UR - https://doi.org/10.1016/j.ympev.2012.08.026 DO - 10.1016/j.ympev.2012.08.026 ID - Njuguna2013 ER - TY - STD TI - Staudt G. Strawberry biogeography, genetics and systematics. Acta Hortic. 2009;842:71–84. ID - ref82 ER - TY - STD TI - Potter D, Luby JJ, Harrison RE. Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Syst Bot. 2000;25:337–48. ID - ref83 ER - TY - STD TI - Rousseau-Gueutin M, Gaston A, Aïnouche A, Aïnouche ML, Olbricht K, Staudt G, et al. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Mol Phylogenet Evol. 2009;51:515–30. ID - ref84 ER - TY - STD TI - DiMeglio LM, Staudt G, Yu H, Davis TM. A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene. PLoS One. 2014;9:e102237. ID - ref85 ER - TY - STD TI - Hummer KE. A new species of Fragaria (Rosaceae) from Oregon. J Bot Res Inst Tex. 2012;6:9–15. ID - ref86 ER - TY - JOUR AU - Aguiar, D. AU - Istrail, S. PY - 2012 DA - 2012// TI - HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0084 DO - 10.1089/cmb.2012.0084 ID - Aguiar2012 ER - TY - JOUR AU - Kubatko, L. S. PY - 2009 DA - 2009// TI - Identifying hybridization events in the presence of coalescence via model selection JO - Syst Biol VL - 58 UR - https://doi.org/10.1093/sysbio/syp055 DO - 10.1093/sysbio/syp055 ID - Kubatko2009 ER - TY - STD TI - Liston A. 257 nuclear genes for Rosaceae phylogenomics. 2015. http://dx.doi.org/10.6084/m9.figshare.1060394. Accessed 29 Jul 2017. ID - ref89 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT--the BLAST-like alignment tool JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229202 DO - 10.1101/gr.229202 ID - Kent2002 ER - TY - STD TI - Kamneva OK. Assembling haplotypes from NGS data for di- and polyploids: online tutorial. 2017. http://web.stanford.edu/~okamneva/haplotype_assembly.html. Accessed 29 Jul 2017. UR - http://web.stanford.edu/~okamneva/haplotype_assembly.html ID - ref91 ER - TY - JOUR AU - Shulaev, V. AU - Sargent, D. J. AU - Crowhurst, R. N. AU - Mockler, T. C. AU - Folkerts, O. AU - Delcher, A. L. PY - 2011 DA - 2011// TI - The genome of woodland strawberry (Fragaria vesca) JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.740 DO - 10.1038/ng.740 ID - Shulaev2011 ER - TY - STD TI - Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9. ID - ref93 ER - TY - STD TI - Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20. ID - ref94 ER - TY - STD TI - Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60. ID - ref95 ER - TY - STD TI - Kamneva OK. Phylogeny reconstruction using haplotype and consensus sequences from several Fragaria species: online tutorial. 2017. http://web.stanford.edu/~okamneva/phylogeny_fragaria.html. Accessed 29 Jul 2017. UR - http://web.stanford.edu/~okamneva/phylogeny_fragaria.html ID - ref96 ER - TY - JOUR AU - Katoh, K. AU - Standley, D. M. PY - 2013 DA - 2013// TI - MAFFT multiple sequence alignment software version 7: improvements in performance and usability JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst010 DO - 10.1093/molbev/mst010 ID - Katoh2013 ER - TY - JOUR AU - Guindon, S. AU - Dufayard, J. -. F. AU - Lefort, V. AU - Anisimova, M. AU - Hordijk, W. AU - Gascuel, O. PY - 2010 DA - 2010// TI - New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 JO - Syst Biol VL - 59 UR - https://doi.org/10.1093/sysbio/syq010 DO - 10.1093/sysbio/syq010 ID - Guindon2010 ER - TY - JOUR AU - Darriba, D. AU - Taboada, G. L. AU - Doallo, R. AU - Posada, D. PY - 2012 DA - 2012// TI - jModelTest 2: more models, new heuristics and parallel computing JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.2109 DO - 10.1038/nmeth.2109 ID - Darriba2012 ER - TY - STD TI - Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol. 1999;16:1114-6. ID - ref100 ER - TY - STD TI - Shimodaira H, Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 2001;17:1246–7. ID - ref101 ER - TY - STD TI - Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics. 2014;30:i541–8. ID - ref102 ER - TY - STD TI - Kamneva OK. Finding and testing hybridization events in Fragaria species history: online tutorial. 2017. http://web.stanford.edu/~okamneva/testing_hybridizations.html. Accessed 29 Jul 2017. UR - http://web.stanford.edu/~okamneva/testing_hybridizations.html ID - ref103 ER - TY - JOUR AU - Lott, M. AU - Spillner, A. AU - Huber, K. T. AU - Moulton, V. PY - 2009 DA - 2009// TI - PADRE: a package for analyzing and displaying reticulate evolution JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp133 DO - 10.1093/bioinformatics/btp133 ID - Lott2009 ER - TY - STD TI - Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol. 2012;61:1061–7. ID - ref105 ER - TY - STD TI - Meacham CA. Theoretical and computational considerations of the compatibility of qualitative taxonomic characters. In: J Felsenstein, ed. Numerical Taxonomy. Heidelberg: Springer; 1983. pp. 304–14. ID - ref106 ER - TY - STD TI - Huson DH, Rupp R. Summarizing multiple gene trees using cluster networks. In: KA Crandall, J Lagergren, eds. Algorithms in Bioinformatics. Heidelberg: Springer; 2008. pp. 296–305. ID - ref107 ER - TY - STD TI - Hummer KE, Bassil N, Njuguna W. Fragaria. In: C Kole, ed. Wild Crop Relatives: Genomic and Breeding Resources, Temperate Fruits. New York City: Springer; 2011. pp. 17-44. ID - ref108 ER - TY - JOUR AU - Göker, M. AU - Grimm, G. W. PY - 2008 DA - 2008// TI - General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-86 DO - 10.1186/1471-2148-8-86 ID - Göker2008 ER - TY - STD TI - Joly S, Bruneau A. Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: an example from Rosa in North America. Syst Biol. 2006;55:623–36. ID - ref110 ER - TY - JOUR AU - Potts, A. J. AU - Hedderson, T. A. AU - Grimm, G. W. PY - 2014 DA - 2014// TI - Constructing phylogenies in the presence of intra-individual site polymorphisms (2ISPs) with a focus on the nuclear ribosomal cistron JO - Syst Biol VL - 63 UR - https://doi.org/10.1093/sysbio/syt052 DO - 10.1093/sysbio/syt052 ID - Potts2014 ER - TY - JOUR AU - Joly, S. AU - Bryant, D. AU - Lockhart, P. J. PY - 2015 DA - 2015// TI - Flexible methods for estimating genetic distances from single nucleotide polymorphisms JO - Methods Ecol Evol VL - 6 UR - https://doi.org/10.1111/2041-210X.12343 DO - 10.1111/2041-210X.12343 ID - Joly2015 ER - TY - STD TI - Bertrand YJK, Scheen A-C, Marcussen T, Pfeil BE, de Sousa F, Oxelman B. Assignment of homoeologs to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (Papaveraceae). Syst Biol. 2015;64:448–71. ID - ref113 ER - TY - STD TI - Yu Y, Dong J, Liu KJ, Nakhleh L. Maximum likelihood inference of reticulate evolutionary histories. Proc Natl Acad Sci U S A. 2014;111:16448–53. ID - ref114 ER - TY - JOUR AU - Roux, C. AU - Pannell, J. R. PY - 2015 DA - 2015// TI - Inferring the mode of origin of polyploid species from next-generation sequence data JO - Mol Ecol VL - 24 UR - https://doi.org/10.1111/mec.13078 DO - 10.1111/mec.13078 ID - Roux2015 ER - TY - STD TI - Kubatko L, Chifman J. An invariants-based method for efficient identification of hybrid species from large-scale genomic data. 2015; doi: https://doi.org/10.1101/034348. ID - ref116 ER - TY - STD TI - Kamneva OK, Rosenberg NA. Simulation-based evaluation of hybridization network reconstruction methods in the presence of incomplete lineage sorting. Evol Bioinf. 2017;13:1176934317691935. ID - ref117 ER - TY - JOUR AU - Grover, C. E. AU - Gallagher, J. P. AU - Jareczek, J. J. AU - Page, J. T. AU - Udall, J. A. AU - Gore, M. A. PY - 2015 DA - 2015// TI - Re-evaluating the phylogeny of allopolyploid Gossypium L JO - Mol Phylogenet Evol VL - 92 UR - https://doi.org/10.1016/j.ympev.2015.05.023 DO - 10.1016/j.ympev.2015.05.023 ID - Grover2015 ER - TY - JOUR AU - Snyder, M. W. AU - Adey, A. AU - Kitzman, J. O. AU - Shendure, J. PY - 2015 DA - 2015// TI - Haplotype-resolved genome sequencing: experimental methods and applications JO - Nat Rev Genet VL - 16 UR - https://doi.org/10.1038/nrg3903 DO - 10.1038/nrg3903 ID - Snyder2015 ER - TY - STD TI - Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, et al. WhatsHap: haplotype assembly for future-generation sequencing reads. In: R Sharan, ed. Research in Computational Molecular Biology. New York City: Springer; 2014. pp. 237–49. ID - ref120 ER - TY - STD TI - Halldórsson BV, Aguiar D, Istrail S. Haplotype phasing by multi-assembly of shared haplotypes: phase-dependent interactions between rare variants. Pac Symp Biocomput. 2011:16:88–99. ID - ref121 ER - TY - STD TI - Staudt G, Dickore W. Notes on Asiatic Fragaria species: Fragaria pentaphylla Losinsk. and Fragaria tibetica spec. nov. Bot Jahrb. 2001;123:341–54. ID - ref122 ER - TY - STD TI - Staudt G. Notes on Asiatic Fragaria species: III. Fragaria orientalis Losinsk. and Fragaria mandshurica spec. nov. Bot Jahrb. 2003;124:397–419. ID - ref123 ER -