TY - JOUR AU - Jennings, W. B. AU - Edwards, S. V. PY - 2005 DA - 2005// TI - Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees JO - Evolution VL - 59 ID - Jennings2005 ER - TY - JOUR AU - Pollard, D. A. AU - Iyer, V. N. AU - Moses, A. M. AU - Eisen, M. B. PY - 2006 DA - 2006// TI - Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting JO - Plos Genet VL - 2 ID - Pollard2006 ER - TY - JOUR AU - Brumfield, R. T. AU - Jernigan, R. W. AU - McDonald, D. B. AU - Braun, M. J. PY - 2001 DA - 2001// TI - Evolutionary implications of divergent clines in an avian (Manacus: Aves) hybrid zone JO - Evolution VL - 55 UR - https://doi.org/10.1111/j.0014-3820.2001.tb01322.x DO - 10.1111/j.0014-3820.2001.tb01322.x ID - Brumfield2001 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Bull, J. J. AU - Cunningham, C. W. PY - 1996 DA - 1996// TI - Combining data in phylogenetic analysis JO - Trends Ecol Evol VL - 11 UR - https://doi.org/10.1016/0169-5347(96)10006-9 DO - 10.1016/0169-5347(96)10006-9 ID - Huelsenbeck1996 ER - TY - JOUR AU - de Queiroz, A. AU - Gatesy, J. PY - 2007 DA - 2007// TI - The supermatrix approach to systematics JO - Trends Ecol Evol VL - 22 UR - https://doi.org/10.1016/j.tree.2006.10.002 DO - 10.1016/j.tree.2006.10.002 ID - de Queiroz2007 ER - TY - JOUR AU - Mossel, E. AU - Roch, S. PY - 2007 DA - 2007// TI - Incomplete lineage sorting: consistent phylogeny estimation from multiple Loci JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics VL - 7 UR - https://doi.org/10.1109/TCBB.2008.66 DO - 10.1109/TCBB.2008.66 ID - Mossel2007 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 - Maddison, W. P. AU - Knowles, L. L. PY - 2006 DA - 2006// TI - Inferring phylogeny despite incomplete lineage sorting JO - Syst Biol VL - 55 UR - https://doi.org/10.1080/10635150500354928 DO - 10.1080/10635150500354928 ID - Maddison2006 ER - TY - JOUR AU - Liu, L. PY - 2008 DA - 2008// TI - BEST: Bayesian estimation of species trees under the coalescent model JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn484 DO - 10.1093/bioinformatics/btn484 ID - Liu2008 ER - TY - JOUR AU - Liu, L. AU - Pearl, D. K. PY - 2007 DA - 2007// TI - Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701429982 DO - 10.1080/10635150701429982 ID - Liu2007 ER - TY - JOUR AU - Liu, L. AU - Yu, L. AU - Pearl, D. K. AU - Edwards, S. V. PY - 2009 DA - 2009// TI - Estimating species phylogenies using coalescence times among sequences JO - Syst Biol VL - 58 UR - https://doi.org/10.1093/sysbio/syp031 DO - 10.1093/sysbio/syp031 ID - Liu2009 ER - TY - JOUR AU - Ewing, G. B. AU - Ebersberger, I. AU - Schmidt, H. A. AU - von Haeseler, A. PY - 2008 DA - 2008// TI - Rooted triple consensus and anomalous gene trees JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-118 DO - 10.1186/1471-2148-8-118 ID - Ewing2008 ER - TY - JOUR AU - Bryant, D. AU - Berry, V. PY - 2001 DA - 2001// TI - A structured family of clustering and tree construction methods JO - Adv Appl Math VL - 27 UR - https://doi.org/10.1006/aama.2001.0758 DO - 10.1006/aama.2001.0758 ID - Bryant2001 ER - TY - JOUR AU - Margush, T. AU - McMorris, F. R. PY - 1981 DA - 1981// TI - Consensus n-trees JO - B Math Biol VL - 43 ID - Margush1981 ER - TY - BOOK AU - Bryant, D. PY - 2003 DA - 2003// TI - A classification of consensus methods for phylogenies ID - Bryant2003 ER - TY - JOUR AU - Day, W. H. E. AU - McMorris, F. R. AU - Wilkinson, M. PY - 2008 DA - 2008// TI - Explosions and hot spots in supertree methods JO - J Theor Biol VL - 253 UR - https://doi.org/10.1016/j.jtbi.2008.03.024 DO - 10.1016/j.jtbi.2008.03.024 ID - Day2008 ER - TY - JOUR AU - Bininda-Emonds, O. R. P. AU - Bryant, H. N. PY - 1998 DA - 1998// TI - Properties of matrix representation with parsimony analyses JO - Syst Biol VL - 47 ID - Bininda-Emonds1998 ER - TY - JOUR AU - Cotton, J. A. AU - Wilkinson, M. PY - 2007 DA - 2007// TI - Majority-rule supertrees JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701416682 DO - 10.1080/10635150701416682 ID - Cotton2007 ER - TY - JOUR AU - Page, R. D. M. PY - 2000 DA - 2000// TI - Extracting species trees from complex gene trees: Reconciled trees and vertebrate phylogeny JO - Mol Phylogenet Evol VL - 14 UR - https://doi.org/10.1006/mpev.1999.0676 DO - 10.1006/mpev.1999.0676 ID - Page2000 ER - TY - BOOK AU - Bonizzoni, P. AU - Della Vedova, G. AU - Dondi, R. PY - 2003 DA - 2003// TI - Reconciling gene trees to a species tree PB - Springer CY - Berlin UR - https://doi.org/10.1007/3-540-44849-7_18 DO - 10.1007/3-540-44849-7_18 ID - Bonizzoni2003 ER - TY - JOUR AU - Page, R. D. M. AU - Charleston, M. A. PY - 1997 DA - 1997// TI - From gene to organismal phylogeny: Reconciled trees and the gene tree species tree problem JO - Mol Phylogenet Evol VL - 7 UR - https://doi.org/10.1006/mpev.1996.0390 DO - 10.1006/mpev.1996.0390 ID - Page1997 ER - TY - JOUR AU - Slowinski, J. B. AU - Knight, A. AU - Rooney, A. P. PY - 1997 DA - 1997// TI - Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (Serpentes) based on the amino acid sequences of venom proteins JO - Mol Phylogenet Evol VL - 8 UR - https://doi.org/10.1006/mpev.1997.0434 DO - 10.1006/mpev.1997.0434 ID - Slowinski1997 ER - TY - JOUR AU - Steel, M. AU - Rodrigo, A. PY - 2008 DA - 2008// TI - Maximum likelihood supertrees JO - Syst Biol VL - 57 UR - https://doi.org/10.1080/10635150802033014 DO - 10.1080/10635150802033014 ID - Steel2008 ER - TY - JOUR AU - Ane, C. AU - Larget, B. AU - Baum, D. A. AU - Smith, S. D. AU - Rokas, A. PY - 2007 DA - 2007// TI - Bayesian estimation of concordance among gene trees JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msl170 DO - 10.1093/molbev/msl170 ID - Ane2007 ER - TY - JOUR AU - Rannala, B. AU - Yang, Z. H. PY - 2003 DA - 2003// TI - Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci JO - Genetics VL - 164 ID - Rannala2003 ER - TY - JOUR AU - Nielsen, R. PY - 1998 DA - 1998// TI - Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model JO - Theor Popul Biol VL - 53 UR - https://doi.org/10.1006/tpbi.1997.1348 DO - 10.1006/tpbi.1997.1348 ID - Nielsen1998 ER - TY - JOUR AU - Degnan, J. H. AU - Salter, L. A. PY - 2005 DA - 2005// TI - Gene tree distributions under the coalescent process JO - Evolution VL - 59 UR - https://doi.org/10.1111/j.0014-3820.2005.tb00891.x DO - 10.1111/j.0014-3820.2005.tb00891.x ID - Degnan2005 ER - TY - JOUR AU - Takahata, N. PY - 1989 DA - 1989// TI - Gene genealogy in three related populations: consistency probability between gene and population trees JO - Genetics VL - 122 ID - Takahata1989 ER - TY - JOUR AU - Degnan, J. H. AU - Rosenberg, N. A. PY - 2009 DA - 2009// TI - Gene tree discordance, phylogenetic inference, and the multispecies coalescent JO - Trends Ecol Evol VL - 24 UR - https://doi.org/10.1016/j.tree.2009.01.009 DO - 10.1016/j.tree.2009.01.009 ID - Degnan2009 ER - TY - CHAP AU - Efromovich, S. AU - Kubatko, L. S. PY - 2008 DA - 2008// TI - Coalescent time distributions in trees of arbitrary size BT - Stat Appl Genet Mol Biol ID - Efromovich2008 ER - TY - JOUR AU - Carstens, B. C. AU - Knowles, L. L. PY - 2007 DA - 2007// TI - Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701405560 DO - 10.1080/10635150701405560 ID - Carstens2007 ER - TY - JOUR AU - Liu, L. AU - Yu, L. AU - Pearl, D. K. PY - 2010 DA - 2010// TI - Maximum Tree: a consistent estimator of the species tree JO - J Math Biol VL - 60 UR - https://doi.org/10.1007/s00285-009-0260-0 DO - 10.1007/s00285-009-0260-0 ID - Liu2010 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 - BOOK AU - Wakeley, J. PY - 2008 DA - 2008// TI - Coalescent Theory: An Introduction ID - Wakeley2008 ER - TY - JOUR AU - Edwards, S. V. PY - 2009 DA - 2009// TI - Is a new and general theory of molecular systematics emerging? JO - Evolution VL - 63 UR - https://doi.org/10.1111/j.1558-5646.2008.00549.x DO - 10.1111/j.1558-5646.2008.00549.x ID - Edwards2009 ER - TY - JOUR AU - Liu, L. AU - Pearl, D. K. AU - Brumfield, R. T. AU - Edwards, S. V. PY - 2008 DA - 2008// TI - Estimating species trees using multiple-allele DNA sequence data JO - Evolution VL - 62 UR - https://doi.org/10.1111/j.1558-5646.2008.00414.x DO - 10.1111/j.1558-5646.2008.00414.x ID - Liu2008 ER - TY - JOUR AU - Degnan, J. H. AU - Rosenberg, N. A. PY - 2006 DA - 2006// TI - Discordance of species trees with their most likely gene trees JO - Plos Genetics VL - 2 UR - https://doi.org/10.1371/journal.pgen.0020068 DO - 10.1371/journal.pgen.0020068 ID - Degnan2006 ER - TY - JOUR AU - Steel, M. PY - 1992 DA - 1992// TI - The Complexity of Reconstructing Trees from Qualitative Characters and Subtrees JO - Journal of Classification VL - 9 UR - https://doi.org/10.1007/BF02618470 DO - 10.1007/BF02618470 ID - Steel1992 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 - Rokas, A. AU - Williams, B. L. AU - King, N. AU - Carroll, S. B. PY - 2003 DA - 2003// TI - Genome-scale approaches to resolving incongruence in molecular phylogenies JO - Nature VL - 425 UR - https://doi.org/10.1038/nature02053 DO - 10.1038/nature02053 ID - Rokas2003 ER - TY - JOUR AU - Pamilo, P. AU - Nei, M. PY - 1988 DA - 1988// TI - Relationships between Gene Trees and Species Trees JO - Mol Biol Evol VL - 5 ID - Pamilo1988 ER - TY - JOUR AU - Wang, J. PY - 2001 DA - 2001// TI - A pseudo-likelihood method for estimating effective population size from temporally spaced samples JO - Genet Res VL - 78 UR - https://doi.org/10.1017/S0016672301005286 DO - 10.1017/S0016672301005286 ID - Wang2001 ER - TY - JOUR AU - Besag, J. PY - 1975 DA - 1975// TI - Statistical analysis of non-lattice data JO - The Statistician VL - 24 UR - https://doi.org/10.2307/2987782 DO - 10.2307/2987782 ID - Besag1975 ER - TY - CHAP AU - Feller, W. PY - 1968 DA - 1968// TI - An Introduction to Probability Theory and Its Applications BT - New York: Wiley ID - Feller1968 ER - TY - BOOK AU - Felsenstein, J. PY - 2004 DA - 2004// TI - Inferring Phylogenies PB - Sinauer Associates CY - Sunderland, Massachusetts ID - Felsenstein2004 ER - TY - JOUR AU - Felsenstein, J. PY - 1981 DA - 1981// TI - Evolutionary trees from DNA sequences: a maximum likelihood approach JO - J Mol Evol VL - 17 UR - https://doi.org/10.1007/BF01734359 DO - 10.1007/BF01734359 ID - Felsenstein1981 ER - TY - JOUR AU - Efron, B. PY - 1981 DA - 1981// TI - Nonparametric estimates of standard error - the Jackknife, the Bootstrap and other methods JO - Biometrika VL - 68 UR - https://doi.org/10.1093/biomet/68.3.589 DO - 10.1093/biomet/68.3.589 ID - Efron1981 ER - TY - JOUR AU - Seo, T. -. K. PY - 2008 DA - 2008// TI - Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn043 DO - 10.1093/molbev/msn043 ID - Seo2008 ER - TY - JOUR AU - Soltis, P. S. AU - Soltis, D. E. PY - 2003 DA - 2003// TI - Applying the bootstrap in phylogeny reconstruction JO - Stat Sci VL - 18 UR - https://doi.org/10.1214/ss/1063994980 DO - 10.1214/ss/1063994980 ID - Soltis2003 ER - TY - CHAP AU - Maddison, W. P. AU - Maddison, D. R. PY - 2009 DA - 2009// BT - Mesquite: a modular system for evolutionary analysis ID - Maddison2009 ER - TY - CHAP AU - Liu, L. AU - Yu, L. PY - 2010 DA - 2010// TI - Phybase: an R package for species tree analysis BT - Bioinformatics ID - Liu2010 ER - TY - BOOK AU - Casella, G. AU - Berger, R. L. PY - 2002 DA - 2002// TI - Statistical Inference ID - Casella2002 ER - TY - JOUR AU - Robinson, D. R. AU - Foulds, L. R. PY - 1981 DA - 1981// TI - Comparison of phylogenetic trees JO - Mathematical Biosciences VL - 53 UR - https://doi.org/10.1016/0025-5564(81)90043-2 DO - 10.1016/0025-5564(81)90043-2 ID - Robinson1981 ER - TY - JOUR AU - Guindon, S. AU - Gascuel, O. PY - 2003 DA - 2003// TI - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood JO - Syst Biol VL - 52 UR - https://doi.org/10.1080/10635150390235520 DO - 10.1080/10635150390235520 ID - Guindon2003 ER - TY - JOUR AU - Driskell, A. C. AU - Ane, C. AU - Burleigh, J. G. AU - McMahon, M. M. AU - O'Meara, B. C. AU - Sanderson, M. J. PY - 2004 DA - 2004// TI - Prospects for building the tree of life from large sequence databases JO - Science VL - 306 UR - https://doi.org/10.1126/science.1102036 DO - 10.1126/science.1102036 ID - Driskell2004 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Ronquist, F. PY - 2001 DA - 2001// TI - MRBAYES: Bayesian inference of phylogenetic trees JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.8.754 DO - 10.1093/bioinformatics/17.8.754 ID - Huelsenbeck2001 ER - TY - JOUR AU - Springer, M. S. AU - Burk-Herrick, A. AU - Meredith, R. AU - Eizirik, E. AU - Teeling, E. AU - O'Brien, S. J. AU - Murphy, W. J. PY - 2007 DA - 2007// TI - The adequacy of morphology for reconstructing the early history of placental mammals JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701491149 DO - 10.1080/10635150701491149 ID - Springer2007 ER - TY - BOOK AU - Felsenstein, J. PY - 2005 DA - 2005// TI - PHYLIP PB - Department of Genome Science, University of Washington CY - Seattle ID - Felsenstein2005 ER - TY - CHAP AU - Sanderson, M. J. AU - Shaffer, H. B. PY - 2002 DA - 2002// TI - Troubleshooting phylogenies BT - Annu Rev Ecol Syst ID - Sanderson2002 ER - TY - JOUR AU - Cummings, M. P. AU - Handley, S. A. AU - Myers, D. S. AU - Reed, D. L. AU - Rokas, A. AU - Winka, K. PY - 2003 DA - 2003// TI - Comparing bootstrap and posterior probability values in the four-taxon case JO - Syst Biol VL - 52 UR - https://doi.org/10.1080/10635150390218213 DO - 10.1080/10635150390218213 ID - Cummings2003 ER - TY - JOUR AU - Douady, C. J. AU - Delsuc, F. AU - Boucher, Y. AU - Doolittle, W. F. AU - Douzery, E. J. PY - 2003 DA - 2003// TI - Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg042 DO - 10.1093/molbev/msg042 ID - Douady2003 ER - TY - JOUR AU - Hallstrom, B. M. AU - Kullberg, M. AU - Nilsson, M. A. AU - Janke, A. PY - 2007 DA - 2007// TI - Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm136 DO - 10.1093/molbev/msm136 ID - Hallstrom2007 ER - TY - JOUR AU - Shoshani, J. AU - McKenna, M. C. PY - 1998 DA - 1998// TI - Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data JO - Mol Phylogenet Evol VL - 9 UR - https://doi.org/10.1006/mpev.1998.0520 DO - 10.1006/mpev.1998.0520 ID - Shoshani1998 ER - TY - JOUR AU - Kriegs, J. O. AU - Churakov, G. AU - Kiefmann, M. AU - Jordan, U. AU - Brosius, J. AU - Schmitz, J. PY - 2006 DA - 2006// TI - Retroposed elements as archives for the evolutionary history of placental mammals JO - PLoS Biol VL - 4 UR - https://doi.org/10.1371/journal.pbio.0040091 DO - 10.1371/journal.pbio.0040091 ID - Kriegs2006 ER - TY - JOUR AU - Kjer, K. M. AU - Honeycutt, R. L. PY - 2007 DA - 2007// TI - Site specific rates of mitochondrial genomes and the phylogeny of eutheria JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-8 DO - 10.1186/1471-2148-7-8 ID - Kjer2007 ER - TY - JOUR AU - Nikolaev, S. AU - Montoya-Burgos, J. I. AU - Margulies, E. H. AU - Rougemont, J. AU - Nyffeler, B. AU - Antonarakis, S. E. PY - 2007 DA - 2007// TI - Early history of mammals is elucidated with the ENCODE multiple species sequencing data JO - PLoS Genet VL - 3 UR - https://doi.org/10.1371/journal.pgen.0030002 DO - 10.1371/journal.pgen.0030002 ID - Nikolaev2007 ER - TY - JOUR AU - Churakov, G. AU - Kriegs, J. O. AU - Baertsch, R. AU - Zemann, A. AU - Brosius, J. AU - Schmitz, J. PY - 2009 DA - 2009// TI - Mosaic retroposon insertion patterns in placental mammals JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.090647.108 DO - 10.1101/gr.090647.108 ID - Churakov2009 ER - TY - JOUR AU - Hallstrom, B. M. AU - Janke, A. PY - 2008 DA - 2008// TI - Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-162 DO - 10.1186/1471-2148-8-162 ID - Hallstrom2008 ER - TY - JOUR AU - Nishihara, H. AU - Maruyama, S. AU - Okada, N. PY - 2009 DA - 2009// TI - Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals JO - Proc Natl Acad Sci USA VL - 106 UR - https://doi.org/10.1073/pnas.0809297106 DO - 10.1073/pnas.0809297106 ID - Nishihara2009 ER - TY - JOUR AU - Eckert, A. J. AU - Carstens, B. C. PY - 2008 DA - 2008// TI - Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow JO - Mol Phylogenet Evol VL - 49 UR - https://doi.org/10.1016/j.ympev.2008.09.008 DO - 10.1016/j.ympev.2008.09.008 ID - Eckert2008 ER - TY - JOUR AU - Liu, L. AU - Yu, L. AU - Kubatko, L. S. AU - Pearl, D. K. AU - Edwards, S. V. PY - 2009 DA - 2009// TI - Coalescent methods for estimating multilocus phylogenetic trees JO - Mol Phylogenet Evol VL - 53 UR - https://doi.org/10.1016/j.ympev.2009.05.033 DO - 10.1016/j.ympev.2009.05.033 ID - Liu2009 ER -