%% This BibTeX bibliography file was created using BibDesk. %% http://bibdesk.sourceforge.net/ %% Created for Nick Beaton at 2019-05-24 23:12:01 +1000 %% Saved with string encoding Unicode (UTF-8) @article{ale, Author = {Alessandrini, D.}, Journal = {arXiv:math.AG/0505269}, Title = {Amoebas, tropical varieties, and compactification of Teichm\"{u}ller spaces}, Year = {2016}} @incollection{forcey-book, Author = {Forcey, S. and Hamerlinck, G. and Sands, W.}, Booktitle = {Algebraic and Combinatorial Computational Biology}, Editor = {Robeva, R. and Macauley, M.}, Publisher = {Academic Press}, Title = {Optimization problems in phylogenetics: Polytopes, programming and interpretation.}, Year = {2018}} @article{baez, Author = {Baez, John C. and Otter, Nina}, Journal = {Theory and Applications of Categories}, Pages = {1397--1453}, Title = {Operads and phylogenetic trees}, Volume = {32}, Year = {2017}} @article{bm, Author = {Bryant, D. and Moulton, V.}, Date-Modified = {2019-05-24 23:01:28 +1000}, Doi = {10.1093/molbev/msh018 }, Journal = {Molecular Biology and Evolution}, Pages = {255--265}, Title = {Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks}, Volume = {21}, Year = {2004}} @article{hs, Author = {Huson, D. and Scornavacca, C.}, Date-Modified = {2019-05-24 23:12:01 +1000}, Doi = {10.1093/gbe/evq077 }, Journal = {Genome Biology and Evolution}, Pages = {23--35}, Title = {A survey of combinatorial methods for phylogenetic networks}, Volume = {3}, Year = {2011}} @article{Gambette2017, Author = {Gambette, P. and Huber, K. T. and Scholz, G. E.}, Date-Modified = {2019-05-24 23:09:34 +1000}, Day = {01}, Doi = {10.1007/s11538-017-0318-x}, Issn = {1522-9602}, Journal = {Bull. Math. Biol.}, Month = {Sep}, Number = {9}, Pages = {2022--2048}, Title = {Uprooted phylogenetic networks}, Volume = {79}, Year = {2017}, Bdsk-Url-1 = {https://doi.org/10.1007/s11538-017-0318-x}} @book{hrs, Author = {Huson, D. and Rupp, R. and Scornavacca, C.}, Date-Modified = {2019-05-24 23:10:51 +1000}, Publisher = {Cambridge University Press, New York}, Title = {Phylogenetic Networks}, Year = {2010}} @article{split, Author = {Huson, D.}, Journal = {Bioinformatics. [Software avail. www.splitstree.org]}, Pages = {68--73}, Title = {SplitsTree: analyzing and visualizing evolutionary data}, Volume = {14}, Year = {1998}} @book{stan, Author = {Stanley, R.}, Publisher = {Cambridge University Press}, Title = {Enumerative Combinatorics, Volume 2}, Year = {1999}} @book{git, Author = {Mumford, D. and Fogarty, J. and Kirwan, F.}, Publisher = {Springer-Verlag, New York}, Title = {Geometric Invariant Theory}, Year = {1994}} @article{lsty, Author = {Lin, B. and Sturmfels, B. and Tang, X. and Yoshida, R.}, Journal = {SIAM Journal on Discrete Mathematics}, Pages = {2015---2038}, Title = {Convexity in tree spaces}, Volume = {31}, Year = {2017}} @article{dev-petti, Author = {Devadoss, S. and Petti, S.}, Date-Modified = {2019-05-24 23:05:53 +1000}, Doi = {10.1137/16m1103129}, Journal = {SIAM J. Appl. Algebra Geom.}, Number = {1}, Pages = {683--705}, Title = {A space of phylogenetic networks}, Volume = {1}, Year = {2017}} @article{aos, Author = {Ardila, F. and Owen, M. and Sullivant, S.}, Doi = {10.1016/j.aam.2011.06.004}, Fjournal = {Advances in Applied Mathematics}, Issn = {0196-8858}, Journal = {Adv. in Appl. Math.}, Mrclass = {05C85 (05C12 06A07 52B70 68R05 68U05)}, Mrnumber = {2845512}, Mrreviewer = {Nadia Benakli}, Number = {1}, Pages = {142--163}, Title = {Geodesics in {$\rm CAT(0)$} cubical complexes}, Url = {http://dx.doi.org/10.1016/j.aam.2011.06.004}, Volume = {48}, Year = {2012}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.aam.2011.06.004}} @article{arw, Author = {Ardila, F. and Reiner, V. and Williams, L.}, Fjournal = {S\'eminaire Lotharingien de Combinatoire}, Issn = {1286-4889}, Journal = {S\'em. Lothar. Combin.}, Mrclass = {05E25 (05B35 52B05 52C35)}, Mrnumber = {2317682}, Pages = {Art. B54Aj, 25 pp. (electronic)}, Title = {Bergman complexes, {C}oxeter arrangements, and graph associahedra}, Volume = {54A}, Year = {2005/07}} @article{Ar6, Author = {Armstrong, Suzanne M. and Carr, Michael and Devadoss, Satyan L. and Engler, Eric and Leininger, Ananda and Manapat, Michael}, Fjournal = {Journal of Homotopy and Related Structures}, Journal = {J. Homotopy Relat. Struct.}, Mrclass = {18D50 (14H10 52B11)}, Mrnumber = {2520988}, Number = {1}, Pages = {83--109}, Title = {Particle configurations and {C}oxeter operads}, Volume = {4}, Year = {2009}} @article{bhv, Author = {Billera, L. and Holmes, S. and Vogtmann, K.}, Date-Modified = {2019-05-24 22:59:54 +1000}, Doi = {10.1006/aama.2001.0759}, Fjournal = {Advances in Applied Mathematics}, Issn = {0196-8858}, Journal = {Adv. in Appl. Math.}, Mrclass = {05C90 (92B10)}, Mrnumber = {1867931}, Mrreviewer = {Charles A. Semple}, Number = {4}, Pages = {733--767}, Title = {Geometry of the space of phylogenetic trees}, Volume = {27}, Year = {2001}, Bdsk-Url-1 = {http://dx.doi.org/10.1006/aama.2001.0759}} @article{blo, Author = {Bloom, Jonathan M.}, Coden = {ADMTA4}, Doi = {10.1016/j.aim.2010.10.014}, Fjournal = {Advances in Mathematics}, Issn = {0001-8708}, Journal = {Adv. Math.}, Mrclass = {57R58 (18G40 57M27)}, Mrnumber = {2764887}, Mrreviewer = {Brendan E. Owens}, Number = {4}, Pages = {3216--3281}, Title = {A link surgery spectral sequence in monopole {F}loer homology}, Url = {http://dx.doi.org/10.1016/j.aim.2010.10.014}, Volume = {226}, Year = {2011}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.aim.2010.10.014}} @book{bv, Author = {Boardman, J. M. and Vogt, R. M.}, Mrclass = {55D35}, Mrnumber = {0420609}, Mrreviewer = {J. Stasheff}, Pages = {x+257}, Publisher = {Springer-Verlag, Berlin-New York}, Series = {Lecture Notes in Mathematics, Vol. 347}, Title = {Homotopy invariant algebraic structures on topological spaces}, Year = {1973}} @article{cd, Author = {Carr, M. and Devadoss, S.}, Coden = {TIAPD9}, Doi = {10.1016/j.topol.2005.08.010}, Fjournal = {Topology and its Applications}, Issn = {0166-8641}, Journal = {Topology Appl.}, Mrclass = {52B11 (05B45 14H10 14P25)}, Mrnumber = {2239078}, Mrreviewer = {Seth Sullivant}, Number = {12}, Pages = {2155--2168}, Title = {Coxeter complexes and graph-associahedra}, Url = {http://dx.doi.org/10.1016/j.topol.2005.08.010}, Volume = {153}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.topol.2005.08.010}} @article{cdf, Author = {Carr, Michael and Devadoss, Satyan L. and Forcey, Stefan}, Coden = {JCBTA7}, Doi = {10.1016/j.jcta.2011.04.004}, Fjournal = {Journal of Combinatorial Theory. Series A}, Issn = {0097-3165}, Journal = {J. Combin. Theory Ser. A}, Mrclass = {05E30 (05C75)}, Mrnumber = {2802185}, Mrreviewer = {Benjamin Braun}, Number = {7}, Pages = {2035--2055}, Title = {Pseudograph associahedra}, Url = {http://dx.doi.org/10.1016/j.jcta.2011.04.004}, Volume = {118}, Year = {2011}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.jcta.2011.04.004}} @article{cdl, Author = {Cheng, Howard and Devadoss, Satyan L. and Li, Brian and Risteski, Andrej}, Doi = {10.1016/j.dam.2014.01.013}, Fjournal = {Discrete Applied Mathematics. The Journal of Combinatorial Algorithms, Informatics and Computational Sciences}, Issn = {0166-218X}, Journal = {Discrete Appl. Math.}, Mrclass = {52C25 (05C05)}, Mrnumber = {3176703}, Pages = {46--54}, Title = {Skeletal configurations of ribbon trees}, Url = {http://dx.doi.org/10.1016/j.dam.2014.01.013}, Volume = {170}, Year = {2014}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.dam.2014.01.013}} @book{ch1, Author = {Ching, Michael}, Doi = {10.2140/gt.2005.9.833}, Fjournal = {Geometry and Topology}, Issn = {1465-3060}, Journal = {Geom. Topol.}, Mrclass = {55P48 (18D50 55P43)}, Mrnumber = {2140994}, Mrreviewer = {Beno\^ {\i}t Fresse}, Pages = {833--933 (electronic)}, Title = {Bar constructions for topological operads and the {G}oodwillie derivatives of the identity}, Url = {http://dx.doi.org/10.2140/gt.2005.9.833}, Volume = {9}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.2140/gt.2005.9.833}} @article{ch2, Author = {Ching, Michael}, Doi = {10.1112/jtopol/jtr027}, Fjournal = {Journal of Topology}, Issn = {1753-8416}, Journal = {J. Topol.}, Mrclass = {55P48 (18D50 55P42)}, Mrnumber = {2897049}, Mrreviewer = {Beno\^ {\i}t Fresse}, Number = {1}, Pages = {39--80}, Title = {Bar-cobar duality for operads in stable homotopy theory}, Url = {http://dx.doi.org/10.1112/jtopol/jtr027}, Volume = {5}, Year = {2012}, Bdsk-Url-1 = {http://dx.doi.org/10.1112/jtopol/jtr027}} @article{cos, Author = {Costello, K.}, Journal = {arXiv:math/0402015}, Title = {The $A_\infty$ operad and the moduli space of curves}, Year = {2015}} @article{djs, Author = {Davis, M. and Januszkiewicz, T. and Scott, R.}, Coden = {SMATF6}, Doi = {10.1007/s000290050039}, Fjournal = {Selecta Mathematica. New Series}, Issn = {1022-1824}, Journal = {Selecta Math. (N.S.)}, Mrclass = {53C23 (52C35 57M07)}, Mrnumber = {1668119}, Mrreviewer = {A. Papadopoulos}, Number = {4}, Pages = {491--547}, Title = {Nonpositive curvature of blow-ups}, Url = {http://dx.doi.org/10.1007/s000290050039}, Volume = {4}, Year = {1998}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s000290050039}} @article{djs2, Author = {Davis, M. and Januszkiewicz, T. and Scott, R.}, Coden = {ADMTA4}, Doi = {10.1016/S0001-8708(03)00075-6}, Fjournal = {Advances in Mathematics}, Issn = {0001-8708}, Journal = {Adv. Math.}, Mrclass = {57M60 (53C22 57M50 57N16)}, Mrnumber = {1985196}, Mrreviewer = {Athanase Papadopoulos}, Number = {1}, Pages = {115--179}, Title = {Fundamental groups of blow-ups}, Url = {http://dx.doi.org/10.1016/S0001-8708(03)00075-6}, Volume = {177}, Year = {2003}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0001-8708(03)00075-6}} @article{dp, Author = {De Concini, C. and Procesi, C.}, Coden = {SMATF6}, Doi = {10.1007/BF01589496}, Fjournal = {Selecta Mathematica. New Series}, Issn = {1022-1824}, Journal = {Selecta Math. (N.S.)}, Mrclass = {14D99 (32G13 52B30)}, Mrnumber = {1366622}, Mrreviewer = {V. Leksin}, Number = {3}, Pages = {459--494}, Title = {Wonderful models of subspace arrangements}, Url = {http://dx.doi.org/10.1007/BF01589496}, Volume = {1}, Year = {1995}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF01589496}} @article{dev4, Author = {Devadoss, Satyan L.}, Coden = {DSMHA4}, Doi = {10.1016/j.disc.2007.12.092}, Fjournal = {Discrete Mathematics}, Issn = {0012-365X}, Journal = {Discrete Math.}, Mrclass = {05E99 (52C07)}, Mrnumber = {2479448}, Number = {1}, Pages = {271--276}, Title = {A realization of graph associahedra}, Url = {http://dx.doi.org/10.1016/j.disc.2007.12.092}, Volume = {309}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.disc.2007.12.092}} @article{dev3, Author = {Devadoss, Satyan L.}, Coden = {AMNOAN}, Fjournal = {Notices of the American Mathematical Society}, Issn = {0002-9920}, Journal = {Notices Amer. Math. Soc.}, Mrclass = {14H10 (57M50)}, Mrnumber = {2064149}, Number = {6}, Pages = {620--628}, Title = {Combinatorial equivalence of real moduli spaces}, Volume = {51}, Year = {2004}} @article{dev2, Author = {Devadoss, Satyan L.}, Coden = {DCGEER}, Doi = {10.1007/s00454-002-2810-8}, Fjournal = {Discrete \& Computational Geometry. An International Journal of Mathematics and Computer Science}, Issn = {0179-5376}, Journal = {Discrete Comput. Geom.}, Mrclass = {57M50 (55R80 57M27)}, Mrnumber = {1946794}, Mrreviewer = {Igor Rivin}, Number = {1}, Pages = {61--75}, Title = {A space of cyclohedra}, Url = {http://dx.doi.org/10.1007/s00454-002-2810-8}, Volume = {29}, Year = {2003}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00454-002-2810-8}} @incollection{dev1, Author = {Devadoss, S.}, Booktitle = {Homotopy Invariant Algebraic Structures ({B}altimore, {MD}, 1998)}, Date-Modified = {2019-05-24 23:02:44 +1000}, Doi = {10.1090/conm/239/03599}, Mrclass = {18D50 (52B15 52B70 55P48 57M50)}, Mrnumber = {1718078}, Mrreviewer = {P. S. Green}, Number = {239}, Pages = {91--114}, Publisher = {Amer. Math. Soc., Providence, RI}, Series = {Contemp. Math.}, Title = {Tessellations of moduli spaces and the mosaic operad}, Year = {1999}, Bdsk-Url-1 = {http://dx.doi.org/10.1090/conm/239/03599}} @incollection{dfe, Author = {Devadoss, Satyan L. and Fehrman, Benjamin and Heath, Timothy and Vashist, Aditi}, Booktitle = {Associahedra, {T}amari lattices and related structures}, Doi = {10.1007/978-3-0348-0405-9_6}, Mrclass = {14H10 (18D50 51M10 52B11 53D55)}, Mrnumber = {3221536}, Mrreviewer = {Dawei Chen}, Pages = {99--117}, Publisher = {Birkh\"auser/Springer, Basel}, Series = {Prog. Math. Phys.}, Title = {Moduli spaces of punctured {P}oincar\'e disks}, Url = {http://dx.doi.org/10.1007/978-3-0348-0405-9_6}, Volume = {299}, Year = {2012}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-0348-0405-9_6}} @article{df, Author = {Devadoss, Satyan and Forcey, Stefan}, Doi = {10.2140/agt.2008.8.2081}, Fjournal = {Algebraic \& Geometric Topology}, Issn = {1472-2747}, Journal = {Algebr. Geom. Topol.}, Mrclass = {52B11 (18D50 55P48)}, Mrnumber = {2460880}, Number = {4}, Pages = {2081--2108}, Title = {Marked tubes and the graph multiplihedron}, Url = {http://dx.doi.org/10.2140/agt.2008.8.2081}, Volume = {8}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.2140/agt.2008.8.2081}} @article{poset, Author = {Devadoss, Satyan L. and Forcey, Stefan and Reisdorf, Stephen and Showers, Patrick}, Doi = {10.1016/j.ejc.2014.08.018}, Fjournal = {European Journal of Combinatorics}, Issn = {0195-6698}, Journal = {European J. Combin.}, Mrclass = {06A07 (05E15 52B12)}, Mrnumber = {3266295}, Mrreviewer = {Joseph Kung}, Pages = {229--248}, Title = {Convex polytopes from nested posets}, Url = {http://dx.doi.org/10.1016/j.ejc.2014.08.018}, Volume = {43}, Year = {2015}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.ejc.2014.08.018}} @article{dhv, Author = {Devadoss, Satyan L. and Heath, Timothy and Vipismakul, Wasin}, Coden = {AMNOAN}, Fjournal = {Notices of the American Mathematical Society}, Issn = {0002-9920}, Journal = {Notices Amer. Math. Soc.}, Mrclass = {57N05 (18D50 52B05 52B11 53D45)}, Mrnumber = {2807519}, Mrreviewer = {Athanase Papadopoulos}, Number = {4}, Pages = {530--541}, Title = {Deformations of bordered surfaces and convex polytopes}, Volume = {58}, Year = {2011}} @article{dm, Author = {Devadoss, Satyan L. and Morava, Jack}, Doi = {10.1016/j.aam.2015.03.006}, Fjournal = {Advances in Applied Mathematics}, Issn = {0196-8858}, Journal = {Adv. in Appl. Math.}, Mrclass = {14H10 (52B11 92D10)}, Mrnumber = {3339033}, Pages = {75--95}, Title = {Navigation in tree spaces}, Url = {http://dx.doi.org/10.1016/j.aam.2015.03.006}, Volume = {67}, Year = {2015}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.aam.2015.03.006}} @article{dm2, Author = {Devadoss, Satyan L. and Morava, Jack}, Journal = {arXiv:1209.5465}, Title = {Diagonalizing the genome II: toward possible applications}, Year = {2015}} @article{ehkr, Author = {Etingof, Pavel and Henriques, Andr{\'e} and Kamnitzer, Joel and Rains, Eric M.}, Coden = {ANMAAH}, Doi = {10.4007/annals.2010.171.731}, Fjournal = {Annals of Mathematics. Second Series}, Issn = {0003-486X}, Journal = {Ann. of Math. (2)}, Mrclass = {14H10 (14F99 18D50)}, Mrnumber = {2630055}, Mrreviewer = {Orsola Tommasi}, Number = {2}, Pages = {731--777}, Title = {The cohomology ring of the real locus of the moduli space of stable curves of genus 0 with marked points}, Url = {http://dx.doi.org/10.4007/annals.2010.171.731}, Volume = {171}, Year = {2010}, Bdsk-Url-1 = {http://dx.doi.org/10.4007/annals.2010.171.731}} @article{fst, Author = {Fomin, Sergey and Shapiro, Michael and Thurston, Dylan}, Coden = {ACMAA8}, Doi = {10.1007/s11511-008-0030-7}, Fjournal = {Acta Mathematica}, Issn = {0001-5962}, Journal = {Acta Math.}, Mrclass = {57Q15 (13F60 32G15 52B70)}, Mrnumber = {2448067}, Mrreviewer = {Christof Gei{\ss}}, Number = {1}, Pages = {83--146}, Title = {Cluster algebras and triangulated surfaces. {I}. {C}luster complexes}, Url = {http://dx.doi.org/10.1007/s11511-008-0030-7}, Volume = {201}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s11511-008-0030-7}} @incollection{fre, Author = {Fresse, Benoit}, Booktitle = {Homotopy theory: relations with algebraic geometry, group cohomology, and algebraic {$K$}-theory}, Doi = {10.1090/conm/346/06287}, Mrclass = {18D50 (05E25 06A07 18C15 55P48)}, Mrnumber = {2066499}, Mrreviewer = {Andrey Yu. Lazarev}, Pages = {115--215}, Publisher = {Amer. Math. Soc., Providence, RI}, Series = {Contemp. Math.}, Title = {Koszul duality of operads and homology of partition posets}, Url = {http://dx.doi.org/10.1090/conm/346/06287}, Volume = {346}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1090/conm/346/06287}} @book{fuk, Author = {Fukaya, Kenji and Oh, Yong-Geun and Ohta, Hiroshi and Ono, Kaoru}, Isbn = {978-0-8218-4836-4}, Mrclass = {53D40 (53D12 53D37)}, Mrnumber = {2553465}, Mrreviewer = {Michael J. Usher}, Pages = {xii+396}, Publisher = {American Mathematical Society, Providence, RI; International Press, Somerville, MA}, Series = {AMS/IP Studies in Advanced Mathematics}, Title = {Lagrangian intersection {F}loer theory: anomaly and obstruction. {P}art {I}}, Volume = {46}, Year = {2009}} @article{Gauthier2007, Author = {Gauthier, O. and Lapointe, F. and Baker, A.}, Date-Modified = {2019-05-24 23:09:59 +1000}, Doi = {10.1080/10635150701286549}, Journal = {Systematic Biol.}, Number = {2}, Pages = {345-355}, Title = {Seeing the Trees for the Network: Consensus, Information Content, and Superphylogenies}, Volume = {56}, Year = {2007}, Bdsk-Url-1 = {+%20http://dx.doi.org/10.1080/10635150701286549}, Bdsk-Url-2 = {https://doi.org/10.1080/10635150701286549}} @incollection{gne, Author = {Gnedbaye, Allahtan Victor}, Booktitle = {Operads: {P}roceedings of {R}enaissance {C}onferences ({H}artford, {CT}/{L}uminy, 1995)}, Doi = {10.1090/conm/202/02596}, Mrclass = {17A42 (17A30 18D10 18G60)}, Mrnumber = {1436918}, Mrreviewer = {Kathryn P. Hess}, Pages = {83--113}, Publisher = {Amer. Math. Soc., Providence, RI}, Series = {Contemp. Math.}, Title = {Op\'erades des alg\`ebres {$(k+1)$}-aires}, Url = {http://dx.doi.org/10.1090/conm/202/02596}, Volume = {202}, Year = {1997}, Bdsk-Url-1 = {http://dx.doi.org/10.1090/conm/202/02596}} @article{gm, Author = {Goncharov, A. B. and Manin, Yu. I.}, Doi = {10.1112/S0010437X03000125}, Fjournal = {Compositio Mathematica}, Issn = {0010-437X}, Journal = {Compos. Math.}, Mrclass = {11G55 (11M41 14H10)}, Mrnumber = {2004120}, Mrreviewer = {Gilberto Bini}, Number = {1}, Pages = {1--14}, Title = {Multiple {$\zeta$}-motives and moduli spaces {$\overline{\mathcal M}\sb {0,n}$}}, Url = {http://dx.doi.org/10.1112/S0010437X03000125}, Volume = {140}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1112/S0010437X03000125}} @article{hkt, Author = {Hacking, Paul and Keel, Sean and Tevelev, Jenia}, Coden = {INVMBH}, Doi = {10.1007/s00222-009-0199-1}, Fjournal = {Inventiones Mathematicae}, Issn = {0020-9910}, Journal = {Invent. Math.}, Mrclass = {14J10 (14J26)}, Mrnumber = {2534095}, Mrreviewer = {Michael A. van Opstall}, Number = {1}, Pages = {173--227}, Title = {Stable pair, tropical, and log canonical compactifications of moduli spaces of del {P}ezzo surfaces}, Url = {http://dx.doi.org/10.1007/s00222-009-0199-1}, Volume = {178}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00222-009-0199-1}} @article{hw, Author = {Hanlon, Phil and Wachs, Michelle}, Coden = {ADMTA4}, Doi = {10.1006/aima.1995.1038}, Fjournal = {Advances in Mathematics}, Issn = {0001-8708}, Journal = {Adv. Math.}, Mrclass = {17B05 (05E25 17B01 20C30)}, Mrnumber = {1337108}, Mrreviewer = {Hartmut Laue}, Number = {2}, Pages = {206--236}, Title = {On {L}ie {$k$}-algebras}, Url = {http://dx.doi.org/10.1006/aima.1995.1038}, Volume = {113}, Year = {1995}, Bdsk-Url-1 = {http://dx.doi.org/10.1006/aima.1995.1038}} @article{has, Author = {Hassett, Brendan}, Doi = {10.1016/S0001-8708(02)00058-0}, Fjournal = {Advances in Mathematics}, Issn = {0001-8708}, Journal = {Adv. Math.}, Mrclass = {14H10 (14D22 14E30)}, Mrnumber = {1957831}, Mrreviewer = {Ivan S. Kausz}, Number = {2}, Pages = {316--352}, Title = {Moduli spaces of weighted pointed stable curves}, Url = {http://dx.doi.org/10.1016/S0001-8708(02)00058-0}, Volume = {173}, Year = {2003}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0001-8708(02)00058-0}} @article{hot, Author = {Hotz, Thomas and Huckemann, Stephan and Le, Huiling and Marron, J. S. and Mattingly, Jonathan C. and Miller, Ezra and Nolen, James and Owen, Megan and Patrangenaru, Vic and Skwerer, Sean}, Doi = {10.1214/12-AAP899}, Fjournal = {The Annals of Applied Probability}, Issn = {1050-5164}, Journal = {Ann. Appl. Probab.}, Mrclass = {60B05 (60B99 60F05)}, Mrnumber = {3127934}, Mrreviewer = {Rabi Bhattacharya}, Number = {6}, Pages = {2238--2258}, Title = {Sticky central limit theorems on open books}, Url = {http://dx.doi.org/10.1214/12-AAP899}, Volume = {23}, Year = {2013}, Bdsk-Url-1 = {http://dx.doi.org/10.1214/12-AAP899}} @article{hb, Abstract = {The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.}, Author = {Huson, Daniel H. and Bryant, David}, Doi = {10.1093/molbev/msj030}, Eprint = {http://mbe.oxfordjournals.org/content/23/2/254.full.pdf+html}, Journal = {Molecular Biology and Evolution}, Number = {2}, Pages = {254-267}, Title = {Application of Phylogenetic Networks in Evolutionary Studies}, Url = {http://mbe.oxfordjournals.org/content/23/2/254.abstract}, Volume = {23}, Year = {2006}, Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/23/2/254.abstract}, Bdsk-Url-2 = {https://doi.org/10.1093/molbev/msj030}} @article{hu, Author = {Hu, Yi}, Coden = {CMPMAF}, Doi = {10.1023/A:1001055409867}, Fjournal = {Compositio Mathematica}, Issn = {0010-437X}, Journal = {Compositio Math.}, Mrclass = {14D20 (14L24 53D30)}, Mrnumber = {1713309}, Mrreviewer = {Philip A. Foth}, Number = {2}, Pages = {159--187}, Title = {Moduli spaces of stable polygons and symplectic structures on {$\overline{\scr M}{}\sb {0,n}$}}, Url = {http://dx.doi.org/10.1023/A:1001055409867}, Volume = {118}, Year = {1999}, Bdsk-Url-1 = {http://dx.doi.org/10.1023/A:1001055409867}} @article{km, Author = {Kapovich, Michael and Millson, John J.}, Coden = {JDGEAS}, Fjournal = {Journal of Differential Geometry}, Issn = {0022-040X}, Journal = {J. Differential Geom.}, Mrclass = {58D29 (58F05)}, Mrnumber = {1431002}, Mrreviewer = {Athanase Papadopoulos}, Number = {3}, Pages = {479--513}, Title = {The symplectic geometry of polygons in {E}uclidean space}, Url = {http://projecteuclid.org/euclid.jdg/1214459218}, Volume = {44}, Year = {1996}, Bdsk-Url-1 = {http://projecteuclid.org/euclid.jdg/1214459218}} @article{kap1, Author = {Kapranov, Mikhail M.}, Coden = {JPAAA2}, Doi = {10.1016/0022-4049(93)90049-Y}, Fjournal = {Journal of Pure and Applied Algebra}, Issn = {0022-4049}, Journal = {J. Pure Appl. Algebra}, Mrclass = {52B12 (16B50 16W30 18D10 52B11 52B20 57T99)}, Mrnumber = {1207505}, Mrreviewer = {J. Stasheff}, Number = {2}, Pages = {119--142}, Title = {The permutoassociahedron, {M}ac {L}ane's coherence theorem and asymptotic zones for the {KZ} equation}, Url = {http://dx.doi.org/10.1016/0022-4049(93)90049-Y}, Volume = {85}, Year = {1993}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/0022-4049(93)90049-Y}} @incollection{kap2, Author = {Kapranov, M. M.}, Booktitle = {I. {M}. {G}elfand {S}eminar}, Mrclass = {14L30 (14M15 52B20 52B40)}, Mrnumber = {1237834}, Mrreviewer = {Michel Brion}, Pages = {29--110}, Publisher = {Amer. Math. Soc., Providence, RI}, Series = {Adv. Soviet Math.}, Title = {Chow quotients of {G}rassmannians. {I}}, Volume = {16}, Year = {1993}} @article{km, Author = {Kontsevich, M. and Manin, Yu.}, Coden = {CMPHAY}, Fjournal = {Communications in Mathematical Physics}, Issn = {0010-3616}, Journal = {Comm. Math. Phys.}, Mrclass = {14N10 (53C15 58D10 58F05)}, Mrnumber = {1291244}, Mrreviewer = {Dietmar A. Salamon}, Number = {3}, Pages = {525--562}, Title = {Gromov-{W}itten classes, quantum cohomology, and enumerative geometry}, Url = {http://projecteuclid.org/euclid.cmp/1104270948}, Volume = {164}, Year = {1994}, Bdsk-Url-1 = {http://projecteuclid.org/euclid.cmp/1104270948}} @article{lp, Author = {Levy, Dan and Pachter, Lior}, Doi = {10.1016/j.aam.2010.09.002}, Fjournal = {Advances in Applied Mathematics}, Issn = {0196-8858}, Journal = {Adv. in Appl. Math.}, Mrclass = {92B10 (05C85 05C90 68R05 90C27 92D15)}, Mrnumber = {2803801}, Number = {2}, Pages = {240--258}, Title = {The neighbor-net algorithm}, Url = {http://dx.doi.org/10.1016/j.aam.2010.09.002}, Volume = {47}, Year = {2011}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.aam.2010.09.002}} @article{lod, Author = {Loday, Jean-Louis}, Coden = {ACVMAL}, Doi = {10.1007/s00013-004-1026-y}, Fjournal = {Archiv der Mathematik}, Issn = {0003-889X}, Journal = {Arch. Math. (Basel)}, Mrclass = {52B11 (55P47 55P48)}, Mrnumber = {2108555}, Mrreviewer = {Richard John Steiner}, Number = {3}, Pages = {267--278}, Title = {Realization of the {S}tasheff polytope}, Url = {http://dx.doi.org/10.1007/s00013-004-1026-y}, Volume = {83}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00013-004-1026-y}} @book{mss, Author = {Markl, Martin and Shnider, Steve and Stasheff, Jim}, Isbn = {0-8218-2134-2}, Mrclass = {18D50 (55P48 55R80)}, Mrnumber = {1898414}, Mrreviewer = {Alexander A. Voronov}, Pages = {x+349}, Publisher = {American Mathematical Society, Providence, RI}, Series = {Mathematical Surveys and Monographs}, Title = {Operads in algebra, topology and physics}, Volume = {96}, Year = {2002}} @inproceedings{mik, Author = {Mikhalkin, Grigory}, Booktitle = {Proceedings of {G}\"okova {G}eometry-{T}opology {C}onference 2006}, Mrclass = {14D20 (14H10 14P99)}, Mrnumber = {2404949}, Mrreviewer = {Luis Felipe Tabera}, Pages = {39--51}, Publisher = {G\"okova Geometry/Topology Conference (GGT), G\"okova}, Title = {Moduli spaces of rational tropical curves}, Year = {2007}} @article{mor, Author = {Morava, Jack}, Journal = {arXiv:math.AT/0109086}, Title = {Braids, trees, and operads}} @article{mo4, Author = {Morton, Jason and Shiu, Anne and Pachter, Lior and Sturmfels, Bernd}, Doi = {10.2202/1544-6115.1286}, Fjournal = {Statistical Applications in Genetics and Molecular Biology}, Issn = {1544-6115}, Journal = {Stat. Appl. Genet. Mol. Biol.}, Mrclass = {Database Expansion Item}, Mrnumber = {2349914}, Pages = {Art. 21, 25 pp. (electronic)}, Title = {The cyclohedron test for finding periodic genes in time course expression studies}, Url = {http://dx.doi.org/10.2202/1544-6115.1286}, Volume = {6}, Year = {2007}, Bdsk-Url-1 = {http://dx.doi.org/10.2202/1544-6115.1286}} @article{mo5, Author = {Morton, Jason and Pachter, Lior and Shiu, Anne and Sturmfels, Bernd and Wienand, Oliver}, Doi = {10.1137/080715822}, Fjournal = {SIAM Journal on Discrete Mathematics}, Issn = {0895-4801}, Journal = {SIAM J. Discrete Math.}, Mrclass = {62G10 (52B05)}, Mrnumber = {2538642}, Mrreviewer = {Ruriko Yoshida}, Number = {3}, Pages = {1117--1134}, Title = {Convex rank tests and semigraphoids}, Url = {http://dx.doi.org/10.1137/080715822}, Volume = {23}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1137/080715822}} @article{owe, Author = {Owen, Megan}, Coden = {SJDMEC}, Doi = {10.1137/090751396}, Fjournal = {SIAM Journal on Discrete Mathematics}, Issn = {0895-4801}, Journal = {SIAM J. Discrete Math.}, Mrclass = {05C85 (05C05 05C12 68U05 92B10 92D15)}, Mrnumber = {2873201}, Mrreviewer = {Jesper Jansson}, Number = {4}, Pages = {1506--1529}, Title = {Computing geodesic distances in tree space}, Url = {http://dx.doi.org/10.1137/090751396}, Volume = {25}, Year = {2011}, Bdsk-Url-1 = {http://dx.doi.org/10.1137/090751396}} @article{pos, Author = {Postnikov, Alexander}, Doi = {10.1093/imrn/rnn153}, Fjournal = {International Mathematics Research Notices. IMRN}, Issn = {1073-7928}, Journal = {Int. Math. Res. Not. IMRN}, Mrclass = {05E30}, Mrnumber = {2487491}, Number = {6}, Pages = {1026--1106}, Title = {Permutohedra, associahedra, and beyond}, Url = {http://dx.doi.org/10.1093/imrn/rnn153}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1093/imrn/rnn153}} @article{rai, Author = {Rains, Eric M.}, Doi = {10.1112/jtopol/jtq027}, Fjournal = {Journal of Topology}, Issn = {1753-8416}, Journal = {J. Topol.}, Mrclass = {14N20 (14F25 14M27)}, Mrnumber = {2746338}, Mrreviewer = {Daniel Matei}, Number = {4}, Pages = {786--818}, Title = {The homology of real subspace arrangements}, Url = {http://dx.doi.org/10.1112/jtopol/jtq027}, Volume = {3}, Year = {2010}, Bdsk-Url-1 = {http://dx.doi.org/10.1112/jtopol/jtq027}} @article{spl, Abstract = {A thorough outlook on the origin of life needs to delineate a chemically rigorous, self-consistent path from highly heterogeneous, random ensembles of relatively simple organic molecules, to an entity that has rudimentary life-like characteristics. Such entity should be endowed with a capacity to express variation, undergo mutation-like changes and manifest a simple evolutionary process. For simulating such system we developed the Graded Autocatalysis Replication Domain (GARD) model for explicit kinetic analysis of mutual catalysis in sets of random oligomers derived from energized precursor monomers. The kinetic properties of the GARD model are based on vesicle enclosure and expansion. With the additional assumption of spontaneous vesicle splitting, a GARD evolution scenario is envisaged as a consequence of pure chemical kinetics. Here we show how the GARD model can serve as a platform for investigating the dynamics of self-organization mechanisms in molecular evolutionary processes.}, Author = {Segr鬠D. and Pilpel, Y. and Lancet, D.}, Doi = {10.1016/S0378-4371(97)005}, Journal = {Physica A: Statistical Mechanics and its Applications}, Keywords = {Origins of life; Primordial self-replication; Self-organized criticality}, Number = {1}, Pages = {558-564}, Title = {{Mutual catalysis in sets of prebiotic organic molecules: Evolution through computer simulated chemical kinetics}}, Url = {https://ideas.repec.org/a/eee/phsmap/v249y1998i1p558-564.html}, Volume = {249}, Year = 1998, Bdsk-Url-1 = {https://ideas.repec.org/a/eee/phsmap/v249y1998i1p558-564.html}, Bdsk-Url-2 = {https://doi.org/10.1016/S0378-4371(97)005}} @article{sy, Author = {Sekiguchi, Jiro and Yoshida, Masaaki}, Doi = {10.2206/kyushujm.51.297}, Fjournal = {Kyushu Journal of Mathematics}, Issn = {1340-6116}, Journal = {Kyushu J. Math.}, Mrclass = {14J35 (14P25 52B30)}, Mrnumber = {1470158}, Mrreviewer = {Bruce Hunt}, Number = {2}, Pages = {297--354}, Title = {{$W(E\sb 6)$}-action on the configuration space of six lines on the real projective plane}, Url = {http://dx.doi.org/10.2206/kyushujm.51.297}, Volume = {51}, Year = {1997}, Bdsk-Url-1 = {http://dx.doi.org/10.2206/kyushujm.51.297}} @article{ss, Author = {Speyer, David and Sturmfels, Bernd}, Coden = {AGDEA3}, Doi = {10.1515/advg.2004.023}, Fjournal = {Advances in Geometry}, Issn = {1615-715X}, Journal = {Adv. Geom.}, Mrclass = {14P99 (13J30 14M25)}, Mrnumber = {2071813}, Mrreviewer = {Meirav Amram-Blei}, Number = {3}, Pages = {389--411}, Title = {The tropical {G}rassmannian}, Url = {http://dx.doi.org/10.1515/advg.2004.023}, Volume = {4}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1515/advg.2004.023}} @article{Sta, Author = {Stasheff, James Dillon}, Fjournal = {Transactions of the American Mathematical Society}, Issn = {0002-9947}, Journal = {Trans. Amer. Math. Soc. 108 (1963), 275-292; ibid.}, Mrclass = {55.40}, Mrnumber = {0158400}, Mrreviewer = {A. H. Clark}, Pages = {293--312}, Title = {Homotopy associativity of {$H$}-spaces. {I}, {II}}, Volume = {108}, Year = {1963}} @article{wes, Author = {Westerland, Craig}, Coden = {MAANA}, Doi = {10.1007/s00208-007-0140-0}, Fjournal = {Mathematische Annalen}, Issn = {0025-5831}, Journal = {Math. Ann.}, Mrclass = {55N91 (18D50 55P43 55P48)}, Mrnumber = {2349769}, Mrreviewer = {Andrey Yu. Lazarev}, Number = {1}, Pages = {97--142}, Title = {Equivariant operads, string topology, and {T}ate cohomology}, Url = {http://dx.doi.org/10.1007/s00208-007-0140-0}, Volume = {340}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00208-007-0140-0}} @article{Pachter2, Author = {Levy, D. and Pachter, Lior}, Journal = {Advances in Applied Mathematics}, Pages = {240--258}, Title = {The Neighbor-Net Algorithm}, Volume = {47}, Year = {2011}} @article{pilaud, Author = {Pilaud, V. and Santos F.}, Fjournal = {European Journal of Combinatorics}, Journal = {European J. Combin.}, Title = {The brick polytope of a sorting network.}, Volume = {to appear}, Year = {2012}} @article{pournin, Author = {Pournin, Lionel}, Doi = {10.1016/j.aim.2014.02.035}, Fjournal = {Advances in Mathematics}, Issn = {0001-8708}, Journal = {Adv. Math.}, Mrclass = {52B11 (51M10 51M20)}, Mrnumber = {3197650}, Mrreviewer = {Satyan L. Devadoss}, Pages = {13--42}, Title = {The diameter of associahedra}, Url = {http://dx.doi.org/10.1016/j.aim.2014.02.035}, Volume = {259}, Year = {2014}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.aim.2014.02.035}} @article{splito, Author = {Forcey, S. and Keefe, L. and Sands, W.}, Date-Modified = {2019-05-24 23:08:59 +1000}, Doi = {10.1007/s11538-017-0264-7}, Journal = {Bull. Math. Biol.}, Month = {May}, Number = {5}, Pages = {975--994}, Title = {Split-facets for balanced minimal evolution polytopes and the permutoassociahedron}, Volume = {79}, Year = {2017}, Bdsk-Url-1 = {https://doi.org/10.1007/s11538-017-0264-7}} @article{forcey-ams, Author = {Clemons, C. and Cossey, J. and Ferrara, M. and Forcey, S. and Norfolk, T. and Obeng, G. and Ricciardi, D. and Young, G.}, Journal = {Notices of the A.M.S}, Number = {9}, Pages = {1223--1234}, Title = {When does compromise prevent more pollution?}, Volume = {59}, Year = {2012}} @article{dev-carr, Author = {Carr, Michael P. and Devadoss, Satyan L.}, Coden = {TIAPD9}, Fjournal = {Topology and its Applications}, Issn = {0166-8641}, Journal = {Topology Appl.}, Mrclass = {52B11 (05B45 14H10 14P25)}, Mrnumber = {MR2239078 (2007c:52012)}, Mrreviewer = {Seth Sullivant}, Number = {12}, Pages = {2155--2168}, Title = {Coxeter complexes and graph-associahedra}, Volume = {153}, Year = {2006}} @article{newCDF, Author = {Carr, Michael and Devadoss, Satyan and Forcey, Stefan}, Journal = {Journal of Combinatorial Theory, Series A}, Number = {7}, Pages = {2035--2055}, Title = {Pseudograph Associahedra}, Volume = {118}, Year = {2009}} @article{dev-real, Author = {Devadoss, Satyan L.}, Coden = {DSMHA4}, Fjournal = {Discrete Mathematics}, Issn = {0012-365X}, Journal = {Discrete Math.}, Mrclass = {05E99 (52C07)}, Mrnumber = {MR2479448}, Number = {1}, Pages = {271--276}, Title = {A realization of graph associahedra}, Volume = {309}, Year = {2009}} @article{dev-forc, Author = {Devadoss, Satyan and Forcey, Stefan}, Fjournal = {Algebraic \& Geometric Topology}, Journal = {Algebr. Geom. Topol.}, Mrclass = {52B11 (18D50 55P48)}, Mrnumber = {MR2460880}, Number = {4}, Pages = {2081--2108}, Title = {Marked tubes and the graph multiplihedron}, Volume = {8}, Year = {2008}} @article{barkman2011aster, Author = {Pamela J. Laureto and Todd J. Barkman}, Doi = {http://dx.doi.org/10.1600/036364411X553289}, Issn = {0363-6445}, Journal = {Systematic Botany}, Number = {1}, Pages = {209 - 226}, Title = {Nuclear and Chloroplast DNA Suggest a Complex Single Origin for the Threatened Allopolyploid Solidago houghtonii (Asteraceae) Involving Reticulate Evolution and Introgression}, Url = {http://www.bioone.org/doi/abs/10.1600/036364411X553289}, Volume = {36}, Year = {2011}, Bdsk-Url-1 = {http://www.bioone.org/doi/abs/10.1600/036364411X553289}, Bdsk-Url-2 = {http://dx.doi.org/10.1600/036364411X553289}} @article{bendiksby2010raffle, Author = {Mika Bendiksby and Trond Schumacher and Galina Gussarova and Jamili Nais and Kamarudin Mat-Salleh and Nery Sofiyanti and Domingo Madulid and Stephen A Smith and Todd Barkman}, Issn = {1055-7903}, Journal = {Molecular Phylogenetics and Evolution}, Number = {2}, Pages = {620-633}, Title = {Elucidating the evolutionary history of the Southeast Asian, holoparasitic, giant-flowered Rafflesiaceae: Pliocene vicariance, morphological convergence and character displacement}, Volume = {57}, Year = {2010}} @article{Catanzaro2015mep, Author = {Daniele Catanzaro and Roberto Aringhieri and Marco Di Summa and Raffaele Pesenti}, Doi = {http://dx.doi.org/10.1016/j.ejor.2015.02.019}, Issn = {0377-2217}, Journal = {European Journal of Operational Research}, Number = {3}, Pages = {753 - 765}, Title = {A branch-price-and-cut algorithm for the minimum evolution problem}, Url = {http://www.sciencedirect.com/science/article/pii/S0377221715001204}, Volume = {244}, Year = {2015}, Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0377221715001204}, Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.ejor.2015.02.019}} @article{zr, Author = {Maddison, D.R. and Schulz, K.S. and Maddison, W.P.}, Editor = {Zhang, Z.Q. and Shear, W.A.}, Journal = {Linnaeus Tercentenary: Progress in Invertebrate Taxonomy. Zootaxa 1668:1-766}, Pages = {19 - 40}, Title = {The Tree of Life Web Project}, Url = {http://tolweb.org/tree/}, Year = {2010}, Bdsk-Url-1 = {http://tolweb.org/tree/}} @article{eickmeyer2008on, Author = {K. Eickmeyer and P. Huggins and L. Pachter and R. Yoshida}, Journal = {Algorithms for Molecular Biology}, Number = 5, Title = {On the optimality of the neighbor-joining algorithm}, Url = {http://www.almob.org/content/3/1/5}, Volume = 3, Year = 2008, Bdsk-Url-1 = {http://www.almob.org/content/3/1/5}} @article{kapra, Author = {Kapranov, Mikhail M.}, Coden = {JPAAA2}, Doi = {10.1016/0022-4049(93)90049-Y}, Fjournal = {Journal of Pure and Applied Algebra}, Issn = {0022-4049}, Journal = {J. Pure Appl. Algebra}, Mrclass = {52B12 (16B50 16W30 18D10 52B11 52B20 57T99)}, Mrnumber = {1207505}, Mrreviewer = {J. Stasheff}, Number = {2}, Pages = {119--142}, Title = {The permutoassociahedron, {M}ac {L}ane's coherence theorem and asymptotic zones for the {KZ} equation}, Url = {http://dx.doi.org/10.1016/0022-4049(93)90049-Y}, Volume = {85}, Year = {1993}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/0022-4049(93)90049-Y}} @article{forcey2015facets, Author = {S. Forcey and Keefe, L. and Sands, W.}, Date-Modified = {2019-05-24 23:08:18 +1000}, Doi = {10.1007/s00285-015-0957-1}, Journal = {J. Math. Biol.}, Number = 2, Pages = {447--468}, Title = {Facets of the balanced minimal evolution polytope}, Volume = 73, Year = 2016} @article{gascuel1994note, Author = {Gascuel, O.}, Journal = {Molecular Biology and Evolution}, Number = 6, Pages = {961--963}, Title = {A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's Algorithms for Inferring Phylogenies from Evolutionary Distances}, Volume = {11}, Year = {1994}} @article{Steel2006, Author = {O Gascuel and M Steel}, Journal = {Molecular Biology and Evolution}, Number = 11, Pages = {1997--2000}, Title = {Neighbor-joining revealed}, Volume = 23, Year = 2006} @article{Saitou1987, Author = {N Saitou and M Nei}, Date-Modified = {2005-02-05 12:49:27 -0800}, Journal = {Molecular Biology and Evolution}, Number = {4}, Pages = {406--425}, Title = {The neighbor joining method: a new method for reconstructing phylogenetic trees}, Volume = {4}, Year = {1987}} @misc{gasquel2015stochastic, Author = {O. Gasquel and M. Steel}, Journal = {Algorithmica}, Notes = {http://arxiv.org/abs/1411.4106}, Title = {A 'stochastic safety radius' for distance-based tree reconstruction}, Year = 2015} @misc{Miller2014, Author = {E. Miller and M. Owen and J. S. Provan}, Notes = {available at arxiv:1211.7046}, Title = {Polyhedral computational geometry for averaging metric phylogenetic trees}, Year = 2014} @article{Rock2006, Author = {S. Roch}, Journal = {IEEE/ACM Trans. Comput. Biology Bioinform.}, Pages = {92--94}, Title = {A short proof that phylogenetic tree reconstruction by maximum likelihood is hard}, Volume = 3, Year = 2004} @article{Ciccarelli:2006ys, Author = {Francesca D. Ciccarelli and Tobias Doerks and Christian von Mering and Christopher J. Creevey and Berend Snel and Peer Bork}, Date-Added = {2010-07-23 13:48:51 -0400}, Date-Modified = {2010-07-23 13:51:38 -0400}, Journal = {Science}, Month = {March}, Number = {5765}, Pages = {1283 - 1287}, Title = {Toward Automatic Reconstruction of a Highly Resolved Tree of Life}, Volume = {311}, Year = {2006}} @article{haws2011optimality, Author = {D. Haws and T. Hodge and R. Yoshida}, Journal = {Bulletin of Mathematical Biology}, Number = 11, Pages = {2627--2648}, Title = {Optimality of the Neighbor Joining Algorithm and Faces of the Balanced Minimum Evolution Polytope}, Volume = 73, Year = 2011} @article{Lefort2015fastme2, Abstract = {FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of NJ. FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange (NNI). The new 2.0 version also includes Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).}, Author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier}, Doi = {10.1093/molbev/msv150}, Eprint = {http://mbe.oxfordjournals.org/content/early/2015/06/29/molbev.msv150.full.pdf+html}, Journal = {Molecular Biology and Evolution}, Title = {FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program}, Url = {http://mbe.oxfordjournals.org/content/early/2015/06/29/molbev.msv150.abstract}, Year = {2015}, Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/early/2015/06/29/molbev.msv150.abstract}, Bdsk-Url-2 = {https://doi.org/10.1093/molbev/msv150}} @article{mihaescu2009why, Author = {R. Mihaescu and D. Levy and L. Pachter}, Journal = {Algorithmica}, Number = 1, Pages = {1--24}, Title = {Why neighbor-joining works}, Volume = 54, Year = 2009} @misc{nei2003evolutionary, Author = {Zhang, J. and M. Nei}, Notes = {In: Encyclopedia of the Human Genome}, Title = {Evolutionary distance: estimation}, Year = 2003} @article{nye2008trees, Author = {Tom M. Nye}, Journal = {Systematic Biology}, Number = 5, Pages = {785--794}, Title = {Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies}, Volume = 57, Year = 2008} @book{Semple2003, Address = {Oxford}, Author = {C Semple and M Steel}, Isbn = {0-19-850942-1}, Mrclass = {92D15 (05C05 05C90 92D40)}, Mrnumber = {MR2060009}, Pages = {xiv+239}, Publisher = {Oxford University Press}, Series = {Oxford Lecture Series in Mathematics and its Applications}, Title = {Phylogenetics}, Volume = {24}, Year = {2003}} @book{Felsenstein2003, Author = {J Felsenstein}, Date-Modified = {2005-02-05 12:49:26 -0800}, Publisher = {Sinauer Associates, Inc.}, Title = {Inferring Phylogenies}, Year = {2003}} @article{roch2014likelihood, Author = {Roch, S. and Steel, M.}, Journal = {Theor. Popul. Biol.}, Pages = {56--62}, Title = {Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent}, Year = 2014} @article{weyenberg2014kdetrees, Author = {Weyenberg, G. and Huggins, P.M. and Schardl, C.L. and Howe, D.K. and Yoshida, R.}, Journal = {Bioinformatics}, Number = 16, Pages = {2280--2287}, Title = {kdetrees: non-parametric estimation of phylogenetic tree distributions}, Volume = 30, Year = 2014} @article{Gascuel1994, Author = {O~Gascuel}, Journal = {Molecular Biology and Evolution}, Number = 6, Pages = {961--963}, Title = {A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's Algorithms for Inferring Phylogenies from Evolutionary Distances}, Volume = {11}, Year = {1994}} @article{Pachter2009, Author = {R. Mihaescu and D. Levy and L. Pachter}, Journal = {Algorithmica}, Number = 1, Pages = {1--24}, Title = {Why neighbor-joining works}, Volume = 54, Year = 2009} @article{Roch2014, Author = {Roch, S. and Steel, M.}, Journal = {Theor Popul Biol.}, Pages = {56--62}, Title = {Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent}, Year = 2014} @article{KDETrees, Author = {Weyenberg, G. and Huggins, P.M. and Schardl, C.L. and Howe, D.K. and Yoshida, R.}, Journal = {Bioinformatics}, Number = 16, Pages = {2280--2287}, Title = {kdetrees: non-parametric estimation of phylogenetic tree distributions}, Volume = 30, Year = 2014} @article{nye2008, Author = {Tom M. Nye}, Journal = {Systematic Biology}, Number = 5, Pages = {785--794}, Title = {Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies}, Volume = 57, Year = 2008} @misc{nei2003, Author = {Zhang, J. and M. Nei}, Notes = {In: Encyclopedia of the Human Genome}, Title = {Evolutionary distance: estimation}, Year = 2003} @article{xi2015, Author = {Xi, Jing and Xie, Jin and Yoshida, Ruriko and Forcey, Stefan}, Journal = {http://arxiv.org/abs/1507.08734}, Title = {Stochastic safety radius on Neighbor-Joining method and Balanced Minimal Evolution on small trees}, Year = 2015} @article{williams2013, Author = {Williams, JS and Niedzwiecki, JH and Weisrock, DW}, Journal = {Molecular phylogenetics and evolution}, Number = 3, Pages = {671--82}, Title = {Species tree reconstruction of a poorly resolved clade of salamanders {({\it Ambystomatidae})} using multiple nuclear loci}, Volume = 68, Year = 2013} @article{Eickmeyer2008, Author = {K. Eickmeyer and P. Huggins and L. Pachter and R. Yoshida}, Journal = {Algorithms for Molecular Biology}, Number = 5, Title = {On the optimality of the neighbor-joining algorithm}, Url = {http://www.almob.org/content/3/1/5}, Volume = 3, Year = 2008, Bdsk-Url-1 = {http://www.almob.org/content/3/1/5}} @article{Gascuel2009, Author = {M. Bordewich and O. Gascuel and {K. T.} Huber and V. Moulton}, Journal = {IEEE/ACM Trans. Comput. Biology Bioinform.}, Number = 1, Pages = {110--117}, Title = {Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference}, Volume = 6, Year = 2009} @article{Pauplin, Author = {Pauplin, Y.}, Journal = {J. Mol. Evol.}, Pages = {41--47}, Title = {Direct calculation of a tree length using a distance matrix}, Volume = 51, Year = 2000} @article{Gascuel2003, Author = {F. Denis and O. Gascuel}, Journal = {Discrete Applied Mathematics}, Number = 1, Pages = {63--77}, Title = {On the consistency of the minimum evolution principle of phylogenetic inference}, Volume = 127, Year = 2003} @article{Bryant2005, Author = {D Bryant}, Journal = {J. Classif.}, Pages = {3--15}, Title = {On the uniqueness of the selection criterion in neighbor-joining}, Volume = {22}, Year = 2005} @article{consis, Author = {Ronald W. DeBry}, Journal = {Mol Biol Evol}, Number = 3, Pages = {537--551}, Title = {The Consistency of Several Phylogeny-Inference Methods under Varying Evolutionary Rates}, Volume = 9, Year = 1992} @article{Felsenstein1978, Author = {J. Felsenstein}, Journal = {Syst. Zool.}, Pages = {240-249}, Title = {Cases in which parsimony or compatibility methods will be positively misleading}, Volume = {22}, Year = {1978}} @misc{steel2014, Author = {O. Gasquel and M. Steel}, Notes = {http://arxiv.org/abs/1411.4106}, Title = {A 'stochastic safety radius' for distance-based tree reconstruction}, Year = 2014} @article{AguBerSot:2006, Author = {Aguiar, Marcelo and Bergeron, Nantel and Sottile, Frank}, Fjournal = {Compositio Mathematica}, Issn = {0010-437X}, Journal = {Compos. Math.}, Number = {1}, Pages = {1--30}, Title = {Combinatorial {H}opf algebras and generalized {D}ehn-{S}ommerville relations}, Volume = {142}, Year = {2006}} @article{Billera, Author = {Billera, Louis J. and Sarangarajan, A.}, Coden = {COMBDI}, Doi = {10.1007/BF01844844}, Fjournal = {Combinatorica. An International Journal on Combinatorics and the Theory of Computing}, Issn = {0209-9683}, Journal = {Combinatorica}, Mrclass = {52B12 (05C45 90C27)}, Mrnumber = {1401891 (97j:52016)}, Mrreviewer = {Alexander I. Barvinok}, Number = {2}, Pages = {175--188}, Title = {All {$0$}-{$1$} polytopes are traveling salesman polytopes}, Url = {http://dx.doi.org/10.1007/BF01844844}, Volume = {16}, Year = {1996}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF01844844}} @techreport{ReinerZiegler1993, Address = {Takustr.7, 14195 Berlin}, Author = {Victor Reiner and G{\"u}nter M. Ziegler}, Institution = {ZIB}, Language = {eng}, Number = {SC-93-11}, Title = {Coxeter-associahedra.}, Urn = {urn:nbn:de:0297-zib-1075}, Year = {1993}} @article{Catan, Author = {Catanzaro, Daniele and Labb{\'e}, Martine and Pesenti, Raffaele and Salazar-Gonz{\'a}lez, Juan-Jos{\'e}}, Doi = {10.1287/ijoc.1110.0455}, Fjournal = {INFORMS Journal on Computing}, Issn = {1091-9856}, Journal = {INFORMS J. Comput.}, Mrclass = {92D15 (90C11)}, Mrnumber = {2924705}, Number = {2}, Pages = {276--294}, Title = {The balanced minimum evolution problem}, Url = {http://dx.doi.org/10.1287/ijoc.1110.0455}, Volume = {24}, Year = {2012}, Bdsk-Url-1 = {http://dx.doi.org/10.1287/ijoc.1110.0455}} @article{Cueto, Author = {Cueto, Mar{\'{\i}}a Ang{\'e}lica and Matsen, Frederick A.}, Doi = {10.1007/s11538-010-9556-x}, Fjournal = {Bulletin of Mathematical Biology}, Issn = {0092-8240}, Journal = {Bull. Math. Biol.}, Mrclass = {92B10}, Mrnumber = {2799936 (2012b:92007)}, Number = {6}, Pages = {1202--1226}, Title = {Polyhedral geometry of phylogenetic rogue taxa}, Url = {http://dx.doi.org/10.1007/s11538-010-9556-x}, Volume = {73}, Year = {2011}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s11538-010-9556-x}} @article{Day, Author = {Day, William H. E.}, Coden = {BMBTAP}, Doi = {10.1016/S0092-8240(87)80007-1}, Fjournal = {Bulletin of Mathematical Biology}, Issn = {0092-8240}, Journal = {Bull. Math. Biol.}, Mrclass = {92A10 (68Q25 92A05)}, Mrnumber = {908160 (88j:92041)}, Number = {4}, Pages = {461--467}, Title = {Computational complexity of inferring phylogenies from dissimilarity matrices}, Url = {http://dx.doi.org/10.1016/S0092-8240(87)80007-1}, Volume = {49}, Year = {1987}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0092-8240(87)80007-1}} @article{fastme, Author = {Desper, R. and Gascuel, O.}, Fjournal = {Journal of Computational Biology}, Journal = {J. Comp. Biol.}, Number = {5}, Pages = {687--705}, Title = {Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle}, Volume = {9}, Year = {2002}} @article{Despernew, Author = {Desper, R. and Gascuel, O.}, Date-Modified = {2019-05-24 23:02:13 +1000}, Doi = {10.1093/molbev/msh049}, Journal = {Molecular Biology and Evolution}, Number = {3}, Pages = {587-598}, Title = {Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting}, Volume = {21}, Year = {2004}, Bdsk-Url-1 = {https://doi.org/10.1093/molbev/msh049}} @article{Eickmeyer, Author = {Eickmeyer, K. and Huggins, P. and Pachter, L. and Yoshida, R.}, Fjournal = {Algorithms for Molecular Biology}, Journal = {Alg. Mol. Biol.}, Title = {On the optimality of the neighbor-joining algorithm}, Volume = {3}, Year = {2008}} @article{Fiorini, Author = {Fiorini, Samuel and Joret, Gwena{\"e}l}, Coden = {ORLED5}, Doi = {10.1016/j.orl.2011.10.003}, Fjournal = {Operations Research Letters}, Issn = {0167-6377}, Journal = {Oper. Res. Lett.}, Mrclass = {05C90 (05C05 90C35 90C60 92D15)}, Mrnumber = {2877448}, Mrreviewer = {Peter Lochhead Ralph}, Number = {1}, Pages = {31--35}, Title = {Approximating the balanced minimum evolution problem}, Url = {http://dx.doi.org/10.1016/j.orl.2011.10.003}, Volume = {40}, Year = {2012}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.orl.2011.10.003}} @article{freedom, Author = {Forcey, S.}, Fjournal = {Notices of the American Math Society}, Journal = {Notices of the AMS}, Number = {1}, Pages = {7}, Title = {Dear {N}{S}{A}: Long-Term Security Depends on Freedom}, Volume = {61}, Year = {2014}} @article{Gascuel, Author = {Gascuel, O. and Steel, M.}, Fjournal = {Molecular Biology and Evolution}, Journal = {Mol. Biol. and Evol.}, Pages = {1997--2000}, Title = {Neighbor-joining revealed}, Volume = {23}, Year = {2006}} @article{Huggins, Author = {Huggins, P.}, Journal = {Ph.D. Dissertation, U.C. Berkeley}, Title = {Polytopes in computational biology}, Year = {2008}} @book{RobevaHodge, Doi = {10.1016/B978-0-12-415780-4.00001-6}, Editor = {Robeva, Raina and Hodge, Terrell L.}, Isbn = {978-0-12-415780-4}, Mrclass = {92-01 (92Dxx)}, Mrnumber = {3295938}, Note = {Using modern discrete models}, Pages = {xxi+349}, Publisher = {Elsevier/Academic Press, Amsterdam}, Title = {Mathematical concepts and methods in modern biology}, Url = {http://dx.doi.org/10.1016/B978-0-12-415780-4.00001-6}, Year = {2013}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/B978-0-12-415780-4.00001-6}} @book{Robeva, Editor = {Robeva, Raina}, Publisher = {Elsevier/Academic Press}, Title = {Algebraic and Discrete Mathematical Methods for Modern Biology 1st Edition}, Year = {2015}} @article{Rudy2008, Author = {K. Eickmeyer and P. Huggins and L. Pachter and R. Yoshida}, Journal = {Algorithms for Molecular Biology}, Number = 5, Title = {On the optimality of the neighbor-joining algorithm}, Url = {http://www.almob.org/content/3/1/5}, Volume = 3, Year = 2008, Bdsk-Url-1 = {http://www.almob.org/content/3/1/5}} @article{Rudy, Author = {Haws, D. and Hodge, T. and Yoshida, R.}, Date-Modified = {2019-05-24 23:10:32 +1000}, Doi = {10.1007/s11538-011-9640-x}, Fjournal = {Bulletin of Mathematical Biology}, Issn = {0092-8240}, Journal = {Bull. Math. Biol.}, Mrclass = {92D15 (05C05 05C90 52B12)}, Mrnumber = {2855185 (2012h:92108)}, Number = {11}, Pages = {2627--2648}, Title = {Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope}, Volume = {73}, Year = {2011}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s11538-011-9640-x}} @article{pachter, Author = {Mihaescu, Radu and Levy, Dan and Pachter, Lior}, Coden = {ALGOEJ}, Doi = {10.1007/s00453-007-9116-4}, Fjournal = {Algorithmica. An International Journal in Computer Science}, Issn = {0178-4617}, Journal = {Algorithmica}, Mrclass = {05C85 (68W40 92D15)}, Mrnumber = {2496663 (2010c:05132)}, Mrreviewer = {Hua Wang}, Number = {1}, Pages = {1--24}, Title = {Why neighbor-joining works}, Url = {http://dx.doi.org/10.1007/s00453-007-9116-4}, Volume = {54}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00453-007-9116-4}} @article{Saitou, Author = {Saitou, N. and Nei, M.}, Fjournal = {Molecular Biology and Evolution}, Journal = {Mol. Biol. and Evol.}, Pages = {406--425}, Title = {The neighbor joining method: a new method for reconstructing phylogenetic trees}, Volume = {4}, Year = {1987}} @article{Steel, Author = {Semple, Charles and Steel, Mike}, Doi = {10.1016/S0196-8858(03)00098-8}, Fjournal = {Advances in Applied Mathematics}, Issn = {0196-8858}, Journal = {Adv. in Appl. Math.}, Mrclass = {05C05 (05A05 92D15)}, Mrnumber = {2053839 (2005g:05042)}, Mrreviewer = {Vincent L. Moulton}, Number = {4}, Pages = {669--680}, Title = {Cyclic permutations and evolutionary trees}, Url = {http://dx.doi.org/10.1016/S0196-8858(03)00098-8}, Volume = {32}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0196-8858(03)00098-8}} @article{Pauplin, Author = {Pauplin, Yves}, Fjournal = {Journal of Molecular Evolution}, Journal = {J. of Mol. Evol.}, Number = {1}, Pages = {41--47}, Title = {Direct calculation of a tree length using a distance matrix}, Volume = {51}, Year = {2000}} @incollection{polymake, Author = {Ewgenij Gawrilow and Michael Joswig}, Booktitle = {Polytopes --- Combinatorics and Computation}, Editor = {Gil Kalai and G\"unter M. Ziegler}, Pages = {43-74}, Publisher = {Birkh\"auser}, Title = {polymake: a Framework for Analyzing Convex Polytopes}, Year = {2000}} @article{Gomez, Abstract = {The early diversification of angiosperms in diverse ecological niches is poorly understood. Some have proposed an origin in a darkened forest habitat and others an open aquatic or near aquatic habitat. The research presented here centers on Montsechia vidalii, first recovered from lithographic limestone deposits in the Pyrenees of Spain more than 100 y ago. This fossil material has been poorly understood and misinterpreted in the past. Now, based upon the study of more than 1,000 carefully prepared specimens, a detailed analysis of Montsechia is presented. The morphology and anatomy of the plant, including aspects of its reproduction, suggest that Montsechia is sister to Ceratophyllum (whenever cladistic analyses are made with or without a backbone). Montsechia was an aquatic angiosperm living and reproducing below the surface of the water, similar to Ceratophyllum. Montsechia is Barremian in age, raising questions about the very early divergence of the Ceratophyllum clade compared with its position as sister to eudicots in many cladistic analyses. Lower Cretaceous aquatic angiosperms, such as Archaefructus and Montsechia, open the possibility that aquatic plants were locally common at a very early stage of angiosperm evolution and that aquatic habitats may have played a major role in the diversification of some early angiosperm lineages.}, Author = {Gomez, Bernard and Daviero-Gomez, V鲯nique and Coiffard, Cl魥nt and Mart�Closas, Carles and Dilcher, David L.}, Doi = {10.1073/pnas.1509241112}, Eprint = {http://www.pnas.org/content/112/35/10985.full.pdf}, Journal = {Proceedings of the National Academy of Sciences}, Number = {35}, Pages = {10985-10988}, Title = {Montsechia, an ancient aquatic angiosperm}, Url = {http://www.pnas.org/content/112/35/10985.abstract}, Volume = {112}, Year = {2015}, Bdsk-Url-1 = {http://www.pnas.org/content/112/35/10985.abstract}, Bdsk-Url-2 = {https://doi.org/10.1073/pnas.1509241112}} @article{Goremykin2015, Abstract = {Support for Amborella as the sole survivor of an evolutionary lineage that is sister to all other angiosperms comes from positions in DNA multiple-sequence alignments that have a poor fit to time-reversible substitution models. These sites exhibit significant levels of homoplasy, compositional heterogeneity, and strong heterotachy. We report phylogenetic analyses with observed, randomized, and simulated data which show there is little or no expectation that these sites provide useful information for understanding relationships among basal angiosperms. Their inclusion in phylogenetic analyses leads to a long-branch attraction artifact that favors Amborella as sister to other angiosperms in reconstructed phylogenies. Using parametric simulations, we show that sites in chloroplast sequences that exhibit less homoplasy between angiosperms and gymnosperms provide more reliable information for inferring basal angiosperm relationships. We confirm our earlier findings that the basal angiosperm Amborella is most closely related to aquatic herbs. Our current and previously reported (Goremykin et al. 2013) analyses highlight an essential aspect of the total evidence approach to phylogenetic inference. They suggest that data partitioning aimed at identifying components of the data that better fit evolutionary models is a more reliable approach to phylogeny reconstruction at deep taxonomic levels.}, Author = {Goremykin, V. V. and Nikiforova, S. V. and Cavalieri, D. and Pindo, M. and Lockhart, Peter}, Doi = {10.1093/sysbio/syv028}, Eprint = {http://sysbio.oxfordjournals.org/content/64/5/879.full.pdf+html}, Journal = {Systematic Biology}, Number = {5}, Pages = {879-891}, Title = {The Root of Flowering Plants and Total Evidence}, Url = {http://sysbio.oxfordjournals.org/content/64/5/879.abstract}, Volume = {64}, Year = {2015}, Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/64/5/879.abstract}, Bdsk-Url-2 = {https://doi.org/10.1093/sysbio/syv028}} @article{Xi2014, Abstract = {The molecular era has fundamentally reshaped our knowledge of the evolution and diversification of angiosperms. One outstanding question is the phylogenetic placement of Amborella trichopoda Baill., commonly thought to represent the first lineage of extant angiosperms. Here, we leverage publicly available data and provide a broad coalescent-based species tree estimation of 45 seed plants. By incorporating 310 nuclear genes, our coalescent analyses strongly support a clade containing Amborella plus water lilies (i.e., Nymphaeales) that is sister to all other angiosperms across different nucleotide rate partitions. Our results also show that commonly applied concatenation methods produce strongly supported, but incongruent placements of Amborella: slow-evolving nucleotide sites corroborate results from coalescent analyses, whereas fast-evolving sites place Amborella alone as the first lineage of extant angiosperms. We further explored the performance of coalescent versus concatenation methods using nucleotide sequences simulated on (i) the two alternate placements of Amborella with branch lengths and substitution model parameters estimated from each of the 310 nuclear genes and (ii) three hypothetical species trees that are topologically identical except with respect to the degree of deep coalescence and branch lengths. Our results collectively suggest that the Amborella alone placement inferred using concatenation methods is likely misled by fast-evolving sites. This appears to be exacerbated by the combination of long branches in stem group angiosperms, Amborella, and Nymphaeales with the short internal branch separating Amborella and Nymphaeales. In contrast, coalescent methods appear to be more robust to elevated substitution rates.}, Author = {Xi, Zhenxiang and Liu, Liang and Rest, Joshua S. and Davis, Charles C.}, Doi = {10.1093/sysbio/syu055}, Eprint = {http://sysbio.oxfordjournals.org/content/63/6/919.full.pdf+html}, Journal = {Systematic Biology}, Number = {6}, Pages = {919-932}, Title = {Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies}, Url = {http://sysbio.oxfordjournals.org/content/63/6/919.abstract}, Volume = {63}, Year = {2014}, Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/63/6/919.abstract}, Bdsk-Url-2 = {https://doi.org/10.1093/sysbio/syu055}} @article{Drew, Abstract = {Since the advent of molecular phylogenetics more than 25 years ago, a major goal of plant systematists has been to discern the root of the angiosperms. Although most studies indicate that Amborella trichopoda is sister to all remaining extant flowering plants, support for this position has varied with respect to both the sequence data sets and analyses employed. Recently, Goremykin et al. (2013) questioned the ねborella-sister hypothesis䠵sing a 㮯ise-reduction䠡pproach and reported a topology with Amborella?+?Nymphaeales (water lilies) sister to all remaining angiosperms. Through a series of analyses of both plastid genomes and mitochondrial genes, we continue to find mostly strong support for the Amborella-sister hypothesis and offer a rebuttal of Goremykin et al. (2013). The major tenet of Goremykin et al. is that the Amborella-sister position is determined by noisy data紨at is, characters with high rates of change and lacking true phylogenetic signal. To investigate the signal in these noisy data further, we analyzed the discarded characters from their noise-reduced alignments. We recovered a tree identical to that of the currently accepted angiosperm framework, including the position of Amborella as sister to all other angiosperms, as well as all other major clades. Thus, the signal in the 㮯isy䠤ata is consistent with that of our complete data sets硲guing against the use of their noise-reduction approach. We also determined that one of the alignments presented by Goremykin et al. yields results at odds with their central claim紨eir data set actually supports Amborella as sister to all other angiosperms, as do larger plastid data sets we present here that possess more complete taxon sampling both within the monocots and for angiosperms in general. Previous unpartitioned, multilocus analyses of mitochondrial DNA (mtDNA) data have provided the strongest support for Amborella?+?Nymphaeales as sister to other angiosperms. However, our analysis of third codon positions from mtDNA sequence data also supports the Amborella-sister hypothesis. Finally, we challenge the conclusion of Goremykin et al. that the first flowering plants were aquatic and herbaceous, reasserting that even if Amborella?+?water lilies, or water lilies alone, are sister to the rest of the angiosperms, the earliest angiosperms were not necessarily aquatic and/or herbaceous. [Angiosperms; Amborella; Nymphaeales; plastid genome; water lilies.]}, Author = {Drew, Bryan T. and Ruhfel, Brad R. and Smith, Stephen A. and Moore, Michael J. and Briggs, Barbara G. and Gitzendanner, Matthew A. and Soltis, Pamela S. and Soltis, Douglas E.}, Doi = {10.1093/sysbio/syt108}, Eprint = {http://sysbio.oxfordjournals.org/content/63/3/368.full.pdf+html}, Journal = {Systematic Biology}, Number = {3}, Pages = {368-382}, Title = {Another Look at the Root of the Angiosperms Reveals a Familiar Tale}, Url = {http://sysbio.oxfordjournals.org/content/63/3/368.abstract}, Volume = {63}, Year = {2014}, Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/63/3/368.abstract}, Bdsk-Url-2 = {https://doi.org/10.1093/sysbio/syt108}} @article{Goremykin2013, Abstract = {Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse taxon sampling among basal angiosperms. Here, we provide further evidence for concern over substitution model misspecification in analyses of chloroplast DNA sequences. We show that support for Amborella as the sole representative of the most basal angiosperm lineage is founded on sequence site patterns poorly described by time-reversible substitution models. Improving the fit between sequence data and substitution model identifies Trithuria, Nymphaeaceae, and Amborella as surviving relatives of the most basal lineage of flowering plants. This finding indicates that aquatic and herbaceous species dominate the earliest extant lineage of flowering plants. [; ; ; ; ; .]}, Author = {Goremykin, Vadim V. and Nikiforova, Svetlana V. and Biggs, Patrick J. and Zhong, Bojian and Delange, Peter and Martin, William and Woetzel, Stefan and Atherton, Robin A. and Mclenachan, Patricia A. and Lockhart, Peter J.}, Doi = {10.1093/sysbio/sys070}, Eprint = {http://sysbio.oxfordjournals.org/content/62/1/50.full.pdf+html}, Journal = {Systematic Biology}, Number = {1}, Pages = {50-61}, Title = {The Evolutionary Root of Flowering Plants}, Url = {http://sysbio.oxfordjournals.org/content/62/1/50.abstract}, Volume = {62}, Year = {2013}, Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/62/1/50.abstract}, Bdsk-Url-2 = {https://doi.org/10.1093/sysbio/sys070}} @article{Leebens-Mack, Abstract = {While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea, and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca, and Typha), a water lily (Nuphar), a ranunculid (Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein data sets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on the method of analysis, with parsimony favoring Amborella as sister to all other angiosperms and maximum likelihood (ML) and neighbor-joining methods favoring an Amborella + Nymphaeales clade as sister. The ML phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single-gene phylogenies, estimated divergence dates, and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 MYA for the most recent common ancestor (MRCA) of all extant angiosperms and 145 MYA for the MRCA of monocots, magnoliids, and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.}, Author = {Leebens-Mack, Jim and Raubeson, Linda A. and Cui, Liying and Kuehl, Jennifer V. and Fourcade, Matthew H. and Chumley, Timothy W. and Boore, Jeffrey L. and Jansen, Robert K. and dePamphilis, Claude W.}, Doi = {10.1093/molbev/msi191}, Eprint = {http://mbe.oxfordjournals.org/content/22/10/1948.full.pdf+html}, Journal = {Molecular Biology and Evolution}, Number = {10}, Pages = {1948-1963}, Title = {Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way Out of the Felsenstein Zone}, Url = {http://mbe.oxfordjournals.org/content/22/10/1948.abstract}, Volume = {22}, Year = {2005}, Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/22/10/1948.abstract}, Bdsk-Url-2 = {https://doi.org/10.1093/molbev/msi191}} @article{Simmons, Author = {Simmons, Mark P. and Gatesy, John}, Fjournal = {Molecular Phylogenetics and Evolution}, Journal = {Mol. Phyl. and Evol.}, Pages = {98--122}, Title = {Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms}, Volume = {91}, Year = {2015}} @article{Wickett, Abstract = {Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.}, Author = {Wickett, Norman J. and Mirarab, Siavash and Nguyen, Nam and Warnow, Tandy and Carpenter, Eric and Matasci, Naim and Ayyampalayam, Saravanaraj and Barker, Michael S. and Burleigh, J. Gordon and Gitzendanner, Matthew A. and Ruhfel, Brad R. and Wafula, Eric and Der, Joshua P. and Graham, Sean W. and Mathews, Sarah and Melkonian, Michael and Soltis, Douglas E. and Soltis, Pamela S. and Miles, Nicholas W. and Rothfels, Carl J. and Pokorny, Lisa and Shaw, A. Jonathan and DeGironimo, Lisa and Stevenson, Dennis W. and Surek, Barbara and Villarreal, Juan Carlos and Roure, B顴rice and Philippe, Herv頡nd dePamphilis, Claude W. and Chen, Tao and Deyholos, Michael K. and Baucom, Regina S. and Kutchan, Toni M. and Augustin, Megan M. and Wang, Jun and Zhang, Yong and Tian, Zhijian and Yan, Zhixiang and Wu, Xiaolei and Sun, Xiao and Wong, Gane Ka-Shu and Leebens-Mack, James}, Doi = {10.1073/pnas.1323926111}, Eprint = {http://www.pnas.org/content/111/45/E4859.full.pdf}, Journal = {Proceedings of the National Academy of Sciences}, Number = {45}, Pages = {E4859-E4868}, Title = {Phylotranscriptomic analysis of the origin and early diversification of land plants}, Url = {http://www.pnas.org/content/111/45/E4859.abstract}, Volume = {111}, Year = {2014}, Bdsk-Url-1 = {http://www.pnas.org/content/111/45/E4859.abstract}, Bdsk-Url-2 = {https://doi.org/10.1073/pnas.1323926111}} @article{Morton, Author = {Morton, Cynthia M.}, Fjournal = {Annals of the Missouri Botanical Garden}, Journal = {Ann. of Missouri Botanical Garden}, Number = {1}, Pages = {63--89}, Title = {Newly Sequenced Nuclear Gene (Xdh) for Inferring Angiosperm Phylogeny}, Volume = {98}, Year = {2011}} @article{Ruhfel, Author = {Ruhfel, B.R. and Gitzendanner, M.A. and Soltis, P.S. and Soltis, D.E. and Burleigh, J.G.}, Fjournal = {BMC Evolutionary Biology}, Journal = {BMC Evol. Biol.}, Number = {23}, Pages = {online}, Title = {From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes.}, Volume = {14}, Year = {2014}} @article{Huang, Author = {Huang, Ruiqi and Hippauf, Frank and Rohrbeck, Diana and Haustein, Maria and Wenke, Katrin and Feike, Janie and Sorrelle, Noah and Piechulla, Birgit and Barkman, Todd J.}, Fjournal = {Proceedings of the National Academy of Sciences}, Journal = {Proc. Nat. Acad. Sci.}, Pages = {2966--2971}, Title = {Enzyme functional evolution through improved catalysis of ancestrally non-preferred substrates.}, Volume = {109}, Year = {2012}} @article{Barkman2000, Abstract = {Plant phylogenetic estimates are most likely to be reliable when congruent evidence is obtained independently from the mitochondrial, plastid, and nuclear genomes with all methods of analysis. Here, results are presented from separate and combined genomic analyses of new and previously published data, including six and nine genes (8,911 bp and 12,010 bp, respectively) for different subsets of taxa that suggest Amborella + Nymphaeales (water lilies) are the first-branching angiosperm lineage. Before and after tree-independent noise reduction, most individual genomic compartments and methods of analysis estimated the Amborella + Nymphaeales basal topology with high support. Previous phylogenetic estimates placing Amborella alone as the first extant angiosperm branch may have been misled because of a series of specific problems with paralogy, suboptimal outgroups, long-branch taxa, and method dependence. Ancestral character state reconstructions differ between the two topologies and affect inferences about the features of early angiosperms.}, Author = {Barkman, Todd J. and Chenery, Gordon and McNeal, Joel R. and Lyons-Weiler, James and Ellisens, Wayne J. and Moore, Gerry and Wolfe, Andrea D. and dePamphilis, Claude W.}, Doi = {10.1073/pnas.220427497}, Eprint = {http://www.pnas.org/content/97/24/13166.full.pdf}, Journal = {Proceedings of the National Academy of Sciences}, Number = {24}, Pages = {13166-13171}, Title = {Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny}, Url = {http://www.pnas.org/content/97/24/13166.abstract}, Volume = {97}, Year = {2000}, Bdsk-Url-1 = {http://www.pnas.org/content/97/24/13166.abstract}, Bdsk-Url-2 = {https://doi.org/10.1073/pnas.220427497}} @article{Skippington, Author = {Skippington, Elizabeth and Barkman, Todd J. and Rice, Danny W. and Palmer, Jeff D.}, Fjournal = {Proceedings of the National Academy of Sciences}, Journal = {Proc. Nat. Acad. Sci.}, Pages = {E3515--E3524}, Title = {The miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes.}, Volume = {112}, Year = {2015}} @article{weisrock2013, Author = {Weisrock, DW and Smith, SD and Chan, LM and Biebouw, K. and Kappeler, PM and Yoder, AD}, Journal = {Molecular biology and evolution}, Number = 6, Pages = {1615--30}, Title = {Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics}, Volume = 29, Year = 2012} @article{weisrock2012, Author = {Weisrock, DW}, Journal = {Molecular phylogenetics and evolution}, Number = 1, Pages = {194--202}, Title = {Concordance analysis in mitogenomic phylogenetics}, Volume = 65, Year = 2012} @article{kajita2013, Author = {Kajita, Y. and O'Neill, EM and Zheng, Y. and Obrycki, JJ and Weisrock, DW}, Journal = {Molecular ecology}, Number = 22, Pages = {5473--83}, Title = {A population genetic signature of human releases in an invasive ladybeetle}, Volume = 21, Year = 2012} @article{oneill2013, Author = {O'Neill, EM and Schwartz, R. and Bullock, CT and Williams, JS and Shaffer, HB and Aguilar-Miguel, X. and Parra-Olea, G. and Weisrock, DW}, Journal = {Molecular ecology}, Number = 1, Pages = {111--29}, Title = {Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander ({{\it Ambystoma tigrinum}}) species complex}, Volume = 22, Year = 2013} @incollection{hoy, Address = {Hackensack, NJ}, Author = {P. Huggins and M. Owen and R. Yoshida}, Booktitle = {the Proceedings of the Second CREST--SBM International Conference ``Harmony of Gr��r Bases and the Modern Industrial Society.''}, Pages = {99--116}, Publisher = {World Scientific Publishing Company}, Title = {First steps toward the geometry of cophylogeny}, Year = 2012} @article{svn, Author = {D. Haws and P. Huggins and E. M. O'Neill and D. W. Weisrock and R. Yoshida}, Date-Modified = {2011-10-24 21:41:02 -0400}, Journal = {BMC Bioinformatics}, Note = {doi:10.1186/1471-2105-13-210}, Number = 210, Title = {A support vector machine based test for incongruence between sets of trees in tree space}, Volume = 13, Year = 2012} @article{diffmean, Author = {E. Arnaoudova and D. Haws and P. Huggins and J. W. Jaromczyk and N. Moore and C. Schardl and R. Yoshida}, Journal = {Front. Psychiatry}, Note = {doi:10.3389/fnins.2010.0004}, Number = 47, Title = {Statistical Phylogenetic Tree Analysis Using Differences of Means}, Volume = 1, Year = 2010} @article{bayes, Author = {P. Huggins and W. Li and D. Haws and T. Friedrich and J. Liu and R. Yoshida}, Journal = {Systematic Biology}, Number = 4, Pages = {528--540}, Title = {Bayes estimators for phylogenetic reconstruction}, Volume = 60, Year = 2010} @article{weisrock2013b, Author = {D. Weisrock and JR Macey and M. Matsui and DG Malcahy and TJ Papenfuss}, Journal = {Zootaxa}, Pages = {77--93}, Title = {Molecular phylogenetic reconstruction of the endemic Asian salamander family {Hynobiidae (Amphibia, Caudata)}}, Volume = 1, Year = 2013} @article{layne2012nested, Author = {Layne, L. and Dimitrova, E. and Macauley, M.}, Journal = {Bull. Math. Biol.}, Number = {2}, Pages = {422--433}, Publisher = {Springer}, Title = {Nested canalyzing depth and network stability}, Volume = {74}, Year = {2012}} @article{Macauley:13, Author = {Macauley, M. and Mortveit, H.S.}, Journal = {Theor. Comput. Sci.}, Pages = {26--37}, Publisher = {Elsevier}, Title = {An atlas of limit set dynamics for asynchronous elementary cellular automata}, Volume = {504}, Year = {2013}} @inproceedings{macauley2014cycle, Author = {Macauley, M. and Mortveit, H.}, Booktitle = {Proceedings of the 20th International Workshop, AUTOMATA}, Location = {Himeji, Japan}, Pages = {64--76}, Title = {Cycle equivalence of finite dynamical systems containing symmetries}, Year = {2014}} @inproceedings{macauley2014analysis, Author = {Macauley, M. and Thomas, G.}, Booktitle = {Proceedings of the 20th International Workshop, AUTOMATA}, Location = {Himeji, Japan}, Pages = {170--177}, Title = {Analysis and dynamics of bi-threshold functions}, Year = {2014}} @misc{develin2015toric, Author = {Develin, M. and Macauley, M. and Reiner, V.}, Journal = {Trans. Amer. Math. Soc.}, Note = {Trans. Amer. Math. Soc. In press. arXiv:1211.4247}, Title = {Toric partial orders}, Year = {2015}} @misc{he2015stratification, Author = {He, Q. and Macauley, M.}, Journal = {Trans. Amer. Math. Soc.}, Note = {Submitted to Physica D. arXiv:1504.07591}, Title = {Stratification and enumerate of Boolean functions by canalizing depth}, Year = {2015}}