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Evolutionary history of the angiosperm flora of China.

Lu LM, Mao LF, Yang T, Ye JF, Liu B, Li HL, Sun M, Miller JT, Mathews S, Hu HH, Niu YT, Peng DX, Chen YH, Smith SA, Chen M, Xiang KL, Le CT, Dang VC, Lu AM, Soltis PS, Soltis DE, Li JH, Chen ZD.

Nature. 2018 Feb 8;554(7691):234-238. doi: 10.1038/nature25485. Epub 2018 Jan 31.


Cytogeography of Callisia section Cuthbertia (Commelinaceae).

Molgo IE, Soltis DE, Soltis PS.

Comp Cytogenet. 2017 Sep 1;11(4):553-577. doi: 10.3897/CompCytogen.v11i4.11984. eCollection 2017.


Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family.

Yu XQ, Gao LM, Soltis DE, Soltis PS, Yang JB, Fang L, Yang SX, Li DZ.

New Phytol. 2017 Aug;215(3):1235-1248. doi: 10.1111/nph.14683.


Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae).

Landis JB, Soltis DE, Soltis PS.

BMC Genomics. 2017 Jun 23;18(1):475. doi: 10.1186/s12864-017-3868-2.


Old Plants, New Tricks: Phenological Research Using Herbarium Specimens.

Willis CG, Ellwood ER, Primack RB, Davis CC, Pearson KD, Gallinat AS, Yost JM, Nelson G, Mazer SJ, Rossington NL, Sparks TH, Soltis PS.

Trends Ecol Evol. 2017 Jul;32(7):531-546. doi: 10.1016/j.tree.2017.03.015. Epub 2017 Apr 29. Review.


Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae).

García N, Folk RA, Meerow AW, Chamala S, Gitzendanner MA, Oliveira RS, Soltis DE, Soltis PS.

Mol Phylogenet Evol. 2017 Jun;111:231-247. doi: 10.1016/j.ympev.2017.04.003. Epub 2017 Apr 6.


Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome.

Liu X, Mei W, Soltis PS, Soltis DE, Barbazuk WB.

Mol Ecol Resour. 2017 Nov;17(6):1243-1256. doi: 10.1111/1755-0998.12670. Epub 2017 Jun 5.


Is homoploid hybrid speciation that rare? An empiricist's view.

Nieto Feliner G, Álvarez I, Fuertes-Aguilar J, Heuertz M, Marques I, Moharrek F, Piñeiro R, Riina R, Rosselló JA, Soltis PS, Villa-Machío I.

Heredity (Edinb). 2017 Jun;118(6):513-516. doi: 10.1038/hdy.2017.7. Epub 2017 Mar 15. No abstract available.


Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci.

Kates HR, Soltis PS, Soltis DE.

Mol Phylogenet Evol. 2017 Jun;111:98-109. doi: 10.1016/j.ympev.2017.03.002. Epub 2017 Mar 10.


Evolutionary Conservation of ABA Signaling for Stomatal Closure.

Cai S, Chen G, Wang Y, Huang Y, Marchant DB, Wang Y, Yang Q, Dai F, Hills A, Franks PJ, Nevo E, Soltis DE, Soltis PS, Sessa E, Wolf PG, Xue D, Zhang G, Pogson BJ, Blatt MR, Chen ZH.

Plant Physiol. 2017 Jun;174(2):732-747. doi: 10.1104/pp.16.01848. Epub 2017 Feb 23.


Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences.

Yu Y, Xiang Q, Manos PS, Soltis DE, Soltis PS, Song BH, Cheng S, Liu X, Wong G.

PLoS One. 2017 Feb 22;12(2):e0171361. doi: 10.1371/journal.pone.0171361. eCollection 2017.


Evolution of floral diversity: genomics, genes and gamma.

Chanderbali AS, Berger BA, Howarth DG, Soltis DE, Soltis PS.

Philos Trans R Soc Lond B Biol Sci. 2017 Feb 5;372(1713). pii: 20150509. Review.


Idiosyncratic responses of evergreen broad-leaved forest constituents in China to the late Quaternary climate changes.

Fan D, Hu W, Li B, Morris AB, Zheng M, Soltis DE, Soltis PS, Zhang Z.

Sci Rep. 2016 Aug 18;6:31044. doi: 10.1038/srep31044.


Niche divergence between diploid and autotetraploid Tolmiea.

Visger CJ, Germain-Aubrey CC, Patel M, Sessa EB, Soltis PS, Soltis DE.

Am J Bot. 2016 Aug;103(8):1396-406. doi: 10.3732/ajb.1600130. Epub 2016 Aug 9.


Patterns of abiotic niche shifts in allopolyploids relative to their progenitors.

Blaine Marchant D, Soltis DE, Soltis PS.

New Phytol. 2016 Nov;212(3):708-718. doi: 10.1111/nph.14069. Epub 2016 Jul 11.


The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century.

Hodel RG, Segovia-Salcedo MC, Landis JB, Crowl AA, Sun M, Liu X, Gitzendanner MA, Douglas NA, Germain-Aubrey CC, Chen S, Soltis DE, Soltis PS.

Appl Plant Sci. 2016 Jun 16;4(6). pii: apps.1600025. doi: 10.3732/apps.1600025. eCollection 2016 Jun.


A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes.

Hodel RG, Gitzendanner MA, Germain-Aubrey CC, Liu X, Crowl AA, Sun M, Landis JB, Segovia-Salcedo MC, Douglas NA, Chen S, Soltis DE, Soltis PS.

Appl Plant Sci. 2016 Jun 16;4(6). pii: apps.1600024. doi: 10.3732/apps.1600024. eCollection 2016 Jun.


Polyploidy: Pitfalls and paths to a paradigm.

Soltis DE, Visger CJ, Marchant DB, Soltis PS.

Am J Bot. 2016 Jul;103(7):1146-66. doi: 10.3732/ajb.1500501. Epub 2016 May 27.


Ancient WGD events as drivers of key innovations in angiosperms.

Soltis PS, Soltis DE.

Curr Opin Plant Biol. 2016 Apr;30:159-65. doi: 10.1016/j.pbi.2016.03.015. Epub 2016 Apr 8. Review.


Comparative phylogeography of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle) in Florida: Testing the maritime discontinuity in coastal plants.

Hodel RG, Cortez MB, Soltis PS, Soltis DE.

Am J Bot. 2016 Apr;103(4):730-9. doi: 10.3732/ajb.1500260. Epub 2016 Apr 7.


Evolving Ideas on the Origin and Evolution of Flowers: New Perspectives in the Genomic Era.

Chanderbali AS, Berger BA, Howarth DG, Soltis PS, Soltis DE.

Genetics. 2016 Apr;202(4):1255-65. doi: 10.1534/genetics.115.182964. Review.


Polyploidy and the proteome.

Soltis DE, Misra BB, Shan S, Chen S, Soltis PS.

Biochim Biophys Acta. 2016 Aug;1864(8):896-907. doi: 10.1016/j.bbapap.2016.03.010. Epub 2016 Mar 16. Review.


Are microsatellite fragment lengths useful for population-level studies? The case of Polygala lewtonii (Polygalaceae).

Germain-Aubrey CC, Nelson C, Soltis DE, Soltis PS, Gitzendanner MA.

Appl Plant Sci. 2016 Feb 15;4(2). pii: apps.1500115. doi: 10.3732/apps.1500115. eCollection 2016 Feb.


The Phenotypic and Genetic Underpinnings of Flower Size in Polemoniaceae.

Landis JB, O'Toole RD, Ventura KL, Gitzendanner MA, Oppenheimer DG, Soltis DE, Soltis PS.

Front Plant Sci. 2016 Jan 5;6:1144. doi: 10.3389/fpls.2015.01144. eCollection 2015.


Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution.

Sun Y, Moore MJ, Zhang S, Soltis PS, Soltis DE, Zhao T, Meng A, Li X, Li J, Wang H.

Mol Phylogenet Evol. 2016 Mar;96:93-101. doi: 10.1016/j.ympev.2015.12.006. Epub 2015 Dec 24.


Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus.

Matyášek R, Dobešová E, Húska D, Ježková I, Soltis PS, Soltis DE, Kovařík A.

Plant J. 2016 Feb;85(3):362-77. doi: 10.1111/tpj.13110.


Editorial overview: Genomes and evolution: "Seq-ing" answers in life's genomes.

Rokas A, Soltis PS.

Curr Opin Genet Dev. 2015 Dec;35:iv-vi. doi: 10.1016/j.gde.2015.11.005. Epub 2015 Dec 9. No abstract available.


Polyploidy and genome evolution in plants.

Soltis PS, Marchant DB, Van de Peer Y, Soltis DE.

Curr Opin Genet Dev. 2015 Dec;35:119-25. doi: 10.1016/j.gde.2015.11.003. Epub 2015 Dec 2. Review.


Cytonuclear Coordination Is Not Immediate upon Allopolyploid Formation in Tragopogon miscellus (Asteraceae) Allopolyploids.

Sehrish T, Symonds VV, Soltis DE, Soltis PS, Tate JA.

PLoS One. 2015 Dec 8;10(12):e0144339. doi: 10.1371/journal.pone.0144339. eCollection 2015.


Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set.

Stull GW, Duno de Stefano R, Soltis DE, Soltis PS.

Am J Bot. 2015 Nov;102(11):1794-813. doi: 10.3732/ajb.1500298. Epub 2015 Oct 27.


Digitization workflows for flat sheets and packets of plants, algae, and fungi.

Nelson G, Sweeney P, Wallace LE, Rabeler RK, Allard D, Brown H, Carter JR, Denslow MW, Ellwood ER, Germain-Aubrey CC, Gilbert E, Gillespie E, Goertzen LR, Legler B, Marchant DB, Marsico TD, Morris AB, Murrell Z, Nazaire M, Neefus C, Oberreiter S, Paul D, Ruhfel BR, Sasek T, Shaw J, Soltis PS, Watson K, Weeks A, Mast AR.

Appl Plant Sci. 2015 Sep 10;3(9). pii: apps.1500065. doi: 10.3732/apps.1500065. eCollection 2015 Sep.


An Exploration into Fern Genome Space.

Wolf PG, Sessa EB, Marchant DB, Li FW, Rothfels CJ, Sigel EM, Gitzendanner MA, Visger CJ, Banks JA, Soltis DE, Soltis PS, Pryer KM, Der JP.

Genome Biol Evol. 2015 Aug 26;7(9):2533-44. doi: 10.1093/gbe/evv163.


250 years of hybridization between two biennial herb species without speciation.

Matthews A, Emelianova K, Hatimy AA, Chester M, Pellicer J, Ahmad KS, Guignard MS, Rouhan G, Soltis DE, Soltis PS, Leitch IJ, Leitch AR, Mavrodiev EV, Buggs RJ.

AoB Plants. 2015 Jul 17;7. pii: plv081. doi: 10.1093/aobpla/plv081.


Population genetic variation, geographic structure, and multiple origins of autopolyploidy in Galax urceolata.

Servick S, Visger CJ, Gitzendanner MA, Soltis PS, Soltis DE.

Am J Bot. 2015 Jun;102(6):973-82. doi: 10.3732/ajb.1400554. Epub 2015 Jun 12.


Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications.

Tank DC, Eastman JM, Pennell MW, Soltis PS, Soltis DE, Hinchliff CE, Brown JW, Sessa EB, Harmon LJ.

New Phytol. 2015 Jul;207(2):454-67. doi: 10.1111/nph.13491. Epub 2015 Jun 4.


Zanne et al. reply.

Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM.

Nature. 2015 May 21;521(7552):E6-7. doi: 10.1038/nature14394. No abstract available.


Corrigendum: Three keys to the radiation of angiosperms into freezing environments.

Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM.

Nature. 2015 May 21;521(7552):380. doi: 10.1038/nature14371. No abstract available.


MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.

Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, Barbazuk WB, Soltis DE, Soltis PS.

Appl Plant Sci. 2015 Apr 6;3(4). pii: apps.1400115. doi: 10.3732/apps.1400115. eCollection 2015 Apr.


Optical sectioning and 3D reconstructions as an alternative to scanning electron microscopy for analysis of cell shape.

Landis JB, Ventura KL, Soltis DE, Soltis PS, Oppenheimer DG.

Appl Plant Sci. 2015 Apr 3;3(4). pii: apps.1400112. doi: 10.3732/apps.1400112. eCollection 2015 Apr.


Out of the Water: Origin and Diversification of the LBD Gene Family.

Chanderbali AS, He F, Soltis PS, Soltis DE.

Mol Biol Evol. 2015 Aug;32(8):1996-2000. doi: 10.1093/molbev/msv080. Epub 2015 Apr 2.


Repeated range expansions and inter-/postglacial recolonization routes of Sargentodoxa cuneata (Oliv.) Rehd. et Wils. (Lardizabalaceae) in subtropical China revealed by chloroplast phylogeography.

Tian S, Lei SQ, Hu W, Deng LL, Li B, Meng QL, Soltis DE, Soltis PS, Fan DM, Zhang ZY.

Mol Phylogenet Evol. 2015 Apr;85:238-46. doi: 10.1016/j.ympev.2015.02.016. Epub 2015 Feb 27.


Data access for the 1,000 Plants (1KP) project.

Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK.

Gigascience. 2014 Oct 27;3:17. doi: 10.1186/2047-217X-3-17. eCollection 2014. Review.


Multiple origins and chromosomal novelty in the allotetraploid Tragopogon castellanus (Asteraceae).

Mavrodiev EV, Chester M, Suárez-Santiago VN, Visger CJ, Rodriguez R, Susanna A, Baldini RM, Soltis PS, Soltis DE.

New Phytol. 2015 May;206(3):1172-83. doi: 10.1111/nph.13227. Epub 2015 Jan 3.


Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae).

Dobešová E, Malinská H, Matyášek R, Leitch AR, Soltis DE, Soltis PS, Kovařík A.

Heredity (Edinb). 2015 Mar;114(3):356-65. doi: 10.1038/hdy.2014.111. Epub 2014 Dec 24.


Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae.

Deng JB, Drew BT, Mavrodiev EV, Gitzendanner MA, Soltis PS, Soltis DE.

Mol Phylogenet Evol. 2015 Feb;83:86-98. doi: 10.1016/j.ympev.2014.11.011. Epub 2014 Dec 3.


Deep phylogenetic incongruence in the angiosperm clade Rosidae.

Sun M, Soltis DE, Soltis PS, Zhu X, Burleigh JG, Chen Z.

Mol Phylogenet Evol. 2015 Feb;83:156-66. doi: 10.1016/j.ympev.2014.11.003. Epub 2014 Nov 18.


Phylogeny of ambrosia beetle symbionts in the genus Raffaelea.

Dreaden TJ, Davis JM, de Beer ZW, Ploetz RC, Soltis PS, Wingfield MJ, Smith JA.

Fungal Biol. 2014 Dec;118(12):970-8. doi: 10.1016/j.funbio.2014.09.001. Epub 2014 Sep 22.


Nonadditive gene expression in polyploids.

Yoo MJ, Liu X, Pires JC, Soltis PS, Soltis DE.

Annu Rev Genet. 2014;48:485-517. doi: 10.1146/annurev-genet-120213-092159. Review.


Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae).

Chester M, Riley RK, Soltis PS, Soltis DE.

Heredity (Edinb). 2015 Mar;114(3):309-17. doi: 10.1038/hdy.2014.101. Epub 2014 Nov 5.


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