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Publications

2019

Eric LoPresti, Jake Goidell, John Mola, Maureen Page, Clara Stuligross, Chelsea D. Specht, Marjorie G Weber, Neal Williams, and Richard Karban. A lever action hypothesis for pendulous hummingbird flowers; experimental evidence from a columbine. Annals of Botany. mcz134. doi.org/10.1093/aob/mcz134

Joyce G. Chery*, Pedro Acevedo-Rodriguez, Carl J. Rothfels and Chelsea D. Specht. Phylogeny of Paullinia L. (Paullinieae: Sapindaceae), a diverse genus of lianas with rapid fruit evolution. Molecular Phylogenetics and Evolution. 106577. doi.org/10.1101/673988.

 

2018

Givnish et al. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. 2018. American Journal of Botany. DOI:10.1002/ajb2.1178.

Eduardo M.B. Prata, Chodon Sass, Doriane P. Rodrigues, Fabricius M.C.B. Domingos, Chelsea D. Specht, Gabriel Damasco, Camila C. Ribas, Paul Fine and Alberto Vicentini. 2018. Towards integrative taxonomy in Neotropical Botany: disentangling the the Pagamea guianensis species complex (Rubiaceae). Botanical Journal of the Linnean Society, 188:213-231.

Ana M.R. Almeida*, Alma Pineyro-Nelson#, Roxana Yockteng, and Chelsea D. Specht. 2018. Comparative analysis of whole flower transcriptomes in the Zingiberales. PeerJ.

Dorsey, Brian L.#, Timothy J. Gregory, Chodon Sass#, and Chelsea D. Specht. 2018. Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae). American Journal of Botany 105(9): 1-19. doi: 10.1002/ajb2.1149.

Selena Y. Smith, William J.D. Iles#, John Benedict#, and Chelsea D. Specht. 2018. Building the monocot Tree of Death: progress and challenges emerging from the macrofossil-rich Zingiberales. American Journal of Botany, 105(8). doi: 10.1002/ajb2.1123

Braun I, Balhoff J, Berardini TZ, Cooper L, Gkoutos G, Harper L, Huala E, Jaiswal P, Kazic T, Lapp H, Macklin JA, Specht CD, Vision T, Walls RL, Lawrence-Dill CJ. 2018. ‘Computable’ phenotypes enable comparative and predictive phenomics among plant species across domains of life. In: Thessen, AE (Ed.) Application of Semantic Technologies in Biodiversity Science. Studies on the Semantic Web, IOS Press/AKA Verlag.

 

2017

Joyce Chery, Chodon Sass and C.D. Specht. A transcriptome approach to developing generalized markers for phylogenetics. Applications in Plant Biology.

Ana M.R. Almeida, Roxana Yockteng, and C.D. Specht. Comparative analysis of whole flower transcriptomes in the Zingiberales. PeerJ. in press.

Chelsea D. Specht & Ana M.R. Almeida. A process-based approach to the study of morphological variation. Evolutionary Developmental Biology – A reference guide. Springer. in press.

William J. D. Iles, Chodon Sass, Laura Lagomarsino, Gracie Benson-Martin, Heather E. Driscoll, & C.D. Specht. The phylogeny of Heliconia (Heliconiaceae) and the evolution of floral presentation. Molecular phylogenetics and evolution, http://dx.doi.org/10.1016/j.ympev.2016.12.001

Alma Pineyro-Nelson, Ana M.R. Almeida, Chodon Sass, William J.D. Iles and C.D. Specht. Change of fate and staminodial laminarity as agents of diversification in the Zingiberales. Journal of Experimental Zoology: Molecular and Developmental Evolution. DOI: 10.1002/jez.b.22724

 

2016

Paul J.M. Maas, Hiltje Maas van de Kamer, Jan Wiernega, and C.D. Specht. Monograph of African Costaceae. Blumea: Biodiversity, Evolution and Biogeography of Plants, 61(3): 280-318.

John C. Benedict, Selena Y. Smith, C.D. Specht, Margaret E. Collinson, Jana Leong-Skornickova, Dilworth Y. Parkinson, and Frederica Marone. Species diversity driven by morphological and ecological disparity: a case study of comparative seed morphology and anatomy across a large monocot order. AoB PLANTS 8:plw063; doi: 10.1093/aobpla/plw063.

Thiago Andre**, Shayla Salzman+, Tania Wendt, and C.D. Specht. Speciation dynamics and biogeography of Neotropical spiral gingers (Costaceae). Molecular Phylogenetics and Evolution. doi:10.1016/j.ympev.2016.07.008

Chodon Sass, Will J.D. Iles, Craig Barrett, Selena Y. Smith, and C.D. Specht. 2016. Revisiting the Zingiberales: Using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charasmatic plant lineage. PeerJ. 4-e1584.

C.D. Specht. The rise of evo-devo: the Pan American Society for Evolutionary Developmental Biology sets the stage. Am. J. Bot. 103: 1-4.

 

2015

Kelsie Morioka+, Roxana Yockteng, Ana M.R. Almeida* and C.D. Specht. 2015. Loss of YABBY2-like gene expression may underlie the evolution of the laminar style in Canna and contribute to floral morphological diversity in the Zingiberales. Frontiers in Plant Science. http://dx.doi.org/10.3389/fpls.2015.01106

John C. Benedict, Selena Y. Smith, Margaret E. Collinson, Jana Leong-Škorničková, C.D. Specht, Julie L. Fife, Federica Marone, Xianghui Xiao, and Dilworth Y. Parkinson. 2015. Seed morphoanatomy and its utility in recognizing subfamilies and tribes of the Zingiberaceae. American Journal of Botany.

Moczek, A.P. et al. 2015. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evolution & Development. 17(13): 198-219. DOI:10.111/ede.12125.

Thiago Andre, C.D. Specht, Shayla Salzman, Clarisse Palma-Silva, and Tania Wendt. 2015. Evolution of species diversity in the genus Chamaecostus (Costaceae): molecular phylogenetics and morphometric approaches. Phytotaxa 204(4): 265-276. doi: 10.11646/phytotaxa.204.4.3

Ana M.R. Almeida, Roxana Yockteng, Wagner C. Otoni, and C.D. Specht. 2015. Positive selection on the K domain of the AGAMOUS protein in Zingiberales suggests a mechanism for the evolution of androecial morphology in the order. BMC EvoDevo.

Ana M.R. Almeida, Roxana Yockteng and C.D. Specht. 2015. Evolution of petaloidy in the Zingiberales: an assessment of the relationship between untrastructure and gene expression patterns. Developmental Dynamics (special issue on Evolution & Morphological Diversity).

John C. Benedict, Selena Y. Smith, Margaret E. Collinson, Jana Leong-Škorničková, C.D. Specht, Julie L. Fife, Federica Marone, Xianghui Xiao, and Dilworth Y. Parkinson. 2015. Evolutionary significance of seed structure in Alpiniodeae (Zingiberaceae). Botanical Journal of the Linnean Society. 178 (3): 441-466. Doi: 10.111/boj.12257.

A.R. Deans et al. 2015. Finding our way through phenotypes. PloS Biology. DOI: 10.1371/journal.pbio.1002033.

Shayla Salzman+, Heather Driscoll, Tanya Renner*, Thiago Andre**, Stacy Shen*, and C.D. Specht. 2015. Spiraling into History: A molecular phylogeny and investigation of biogeographic origins of floral evolution for the genus Costus (Costaceae). Systematic Botany. 40(1): 104-115. DOI 10.1600/036364415X686404.

C.D. Specht & Dianella Howarth. 2015. Adaptation of floral form: an evodevo perspective. Tansley Review: New Phytologist. doi: 10.1111/nph.13198

 

2014

Roxana Yockteng, Ana M.R. Almeida, Alma Pineyro-Nelson and C.D. Specht. 2014. Chapter 7: Adaptation of floral form: an evo-devo approach to study adaptive evolution in floral morphology. In Mechanisms in Plant Adaptation Roosa Laitinen (ed). Wiley Press.

Ana M.R. Almeida*, Roxana Yockteng, James C. Schnable**, Elena R. Alvarez-Buylla, Michael Freeling & C. D. Specht. 2014. Co-option of the polarity gene network shapes filament morphology in the angiosperms. Nature: Scientific Reports, 4: 6194. doi:10.1038/srep06194.

Etelvina Gandara**, C.D. Specht and Victoria Sosa. 2014. Origin and diversification of the Milla clade (Brodiaeoideae, Asparagaceae): a neotropical group of six geophyte genera. Molecular Phylogenetics and Evolution. Doi: 10.1016/j.ympev.2014.02.014

Craig F. Barrett, C.D. Specht, Jim Leebens-Mack, Dennis Wm. Stevenson, Wendy B. Zomlefer and Jerrold I. Davis. 2014. Resolving ancient radiations: can more data help resolve deep relationships among the tropical gingers (Zingiberales Griseb.). Annals of Botany, 113: 119–133. doi:10.1093/aob/mct264

Eduardo Ruiz-Sanchez & C.D. Specht. 2014. Ecological speciation in Nolina parviflora (Asparagaceae): Lacking spatial connectivity along the Trans-Mexican Volcanic Belt. PloS ONE. 9(6):e98754. DOI:10.1371/journal.pone.0098754.

 

2013

Roxana Yockteng, Ana M.R. Almeida*, Stephen Yee*, Thiago Andre**, Colin Hill+ and C.D. Specht. 2013. A method for extraction high quality RNA for next-generation sequencing and gene expression analyses. Applications in Plant Sciences. 1(12). DOI: 10.3732/apps1300070.

Roxana Yockteng, Ana M.R. Almeida*, Kelsie Morioka+,Elena R. Alvarez-Buylla & C.D. Specht. 2013. Molecular evolution and patterns of duplication in the SEP/AGL6-like lineage of the Zingiberales: a proposed mechanism for floral diversification. Molecular Biology and Evolution 30(11):2401–2422. DOI: 10.1093/molbev/mst137.

Tanya Renner & C.D. Specht. 2013. Inside the trap: gland morphologies, digestive enzymes, and the evolution of plant carnivory in the Caryophyllales. Current Opinions in Plant Biology. DOI: 10.1016/j.pbi.2013.06.009.

Ana M.R. Almeida*, Andrew Brown+ & C.D. Specht. 2013. Tracking the development of the petaloid fertile stamen in Canna indica: Insights into the origin of androecial petaloidy in the Zingiberales. AoB PLANTS. DOI: 10.1093/aobpla/plt009.

Luke J. Harmon, Jeff Baumes, Charles Hughes, Jorge Soberon, C.D. Specht, Wesley Turner, Curtis Lisle, Robert Thacker. 2013. Arbor: comparative analysis workflows for the tree of life. PLOS Currents 5. DOI: 10.1371./currents.tol.099161de5eabdee073fd3d21a44518dc.

Eduardo Ruiz-Sanchez and C.D. Specht. 2013. Influence of the geological history of the Trans-Mexican Volcanic Belt on the diversification of Nolina parviflora (Asparagaceae: Nolinoideae). Journal of Biogeography. 40(7): 1336-1347. DOI: 10.1111/jli.12073.

Feng-Xia Xu, Dong-Qin Chen, and C.D. Specht. 2013. Comparative microsporogenesis and anther development of selected species of Magnoliaceae. Nordic Journal of Botany. DOI: 10.1111/j.1756-1051.2012.01445.x

Vincent S.F.T. Merckx, J. Kissling, H. Hentrich, S.B. Janssens, C.B. Mennes, C.D. Specht and Erik F. Smets. 2013. The phylogenetic relationships of the mycoheterotropic genus Voyria and their implications for the early biogeographic history of Gentianaceae. American Journal of Botany. DOI: 10.3732/ajb.1200330.

Vincent S.F.T. Merckx, Erik F. Smets and C.D. Specht. 2013. Biogeography and conservation of mycoheterotrophic plants. In V. Merckx [ed.], Mycoheterotrophic plants: The Biology of Plants Living on Fungi. Springer Science, New York, NY.

 

2012

C.D.Specht, Roxana Yockteng, Ana M.R. Almeida*, Bruce K. Kirchoff, W. John Kress. 2012. Homoplasy, Pollination, and emerging complexity during the evolution of floral development in the tropical gingers (Zingiberales). Botanical Review 78: 440-462.

Hiltje Maas-Van de Kamer, Paul J.M. Maas and C.D. Specht. 2012. Costus loangensis, an exciting new species from Gabon. Phytokeys 18: 11-18.

Glenys V. Cron, Cary Pirone**, Madelaine E. Bartlett*, W. John Kress and C.D. Specht. 2012. Phylogenetic relationships and evolution in the Strelitziaceae (Zingiberales). Systematic Botany 37(3): 606-619. doi: 10.1600/036364412X648562

Tanya Renner* and C.D. Specht. 2012. Molecular evolution and selection patterns of class I chitinase genes in the carnivorous plants of the Caryophyllales. Molecular Biology and Evolution. 29(10):2971-2985. doi: 10.1093/molbev/mss106

Vincent S.F.T. Merckx, S.B. Janssens, Nicole A. Hynson, C.D. Specht, Tom D. Bruns, and Erik F. Smets. 2012. Mycoheterotrophic interactions are not limited to a narrow phylogenetic range of arbuscular mycorrhizal fungi. Molecular Ecology, 21(6): 1524-1532. doi: 10.1111/j.1365-294X.2012.05472.x.

Angelova, Z. Shenghuo, Y. Lin, J. Wong+, and C.D. Specht. Development and deployment of a large-scale flower recognition mobile app. NEC technologies report, 2012.

 

2011

Tanya Renner* and C.D. Specht. 2011. Escaping the trap: Redefining carnivorous plant gland evolution in the Caryophyllales. International Journal of Plant Sciences 172(7): 889-901.

Andrew Carroll** and C.D. Specht. 2011. Understanding plant cellulose synthases through a comprehensive investigation of the cellulose synthase family sequences. Frontiers in Plant Genetics and Genomics (Front. Plant Sci.) 2:5.

Madelaine E. Bartlett* and C.D. Specht. 2011. Changes in copy number and expression pattern of the TEOSINTE BRANCHED-like genes in the Zingiberales provide a mechanism for evolutionary shifts in symmetry across the order. American Journal of Botany, 98(2):227-243.

David B. Wake, Marvalee H. Wake and C. D. Specht. 2011. Homoplasy: from detecting pattern to determining process and mechanism of evolution. Science. 331:1032-1034.

 

2010

Axel D. Poulsen and C.D. Specht. 2010. A new species of Costaceae from Borneo. Gardens Bulletin Singapore 62 (1): 143-150.

Chodon Sass* and C.D. Specht. 2010. Phylogenetic estimation of the core Bromeliads with an emphasis on the genus Aechmea (Bromeliaceae). Molecular Phylogenetics and Evolution. 55(2): 559-571.

Madelaine E. Bartlett* and C.D. Specht. 2010. Evidence for the involvement of GLOBOSA-like gene duplications and expression divergence in the evolution of floral morphology in the Zingiberales. New Phytologist, 187: 521-541.

Gene Robinson, Jody Banks, Dianna Padilla, Warren Burggren, C. Cohen, Charles Delwiche, Vicki Funk, Hopi Hoekstra, Erich Jarvis, Loretta Johnson, Mark Martindale, Carlos Martinez del Rio, Mónica Medina, David Salt, Saurabh Sinha, Chelsea Specht, Allan Spradling, Kevin Strange, Joan Strassmann, Billie Swalla, and Lars Tomanek. 2010. Empowering 21st Century Biology. BioScience. 60(11): 923-930.

 

2009

C.D. Specht and M.E. Bartlett*. 2009. Flower evolution: the origin and subsequent diversification of the angiosperm flower. Annual Review of Ecology Evolution and Systematics 40:217-243.

Bruce K. Kirchoff, Laura P. Lagomarsino+, Willie H. Newman, Madelaine E. Bartlett* & C.D. Specht. 2009. Early floral development in Heliconia latispatha and comparative evolution across Zingiberales. American Journal of Botany 96(3):1-15.

Tanya Renner, *, Jennifer Bragg, Heather E. Driscoll, Johana Cho**, Andrew Jackson & C.D. Specht. 2009. Viral Induced Gene Silencing as a tool for investigating floral developmental genetics in the Zingiberales. Molecular Plant 3:1-11.

Ling-Jing Chen, Zhao-Yan Diao, C.D. Specht, and Z. Renee Sung. 2009. Molecular Evolution of VEF-Domain-Containing PcG Genes in Plants. Molecular Plant 2:738-754. doi:10.1093/mp/ssp032

 

2008

Nyu Nguyen**, Heather E. Driscoll, and C.D. Specht. 2008. A molecular phylogeny of the wild onions (Allium; Alliaceae) with a focus on the western North American center of diversity. Molecular Phylogenetics and Evolution 47: 1157-1172.

Madelaine E. Bartlett,* Bruce K. Kirchoff, and C.D. Specht. 2008. Epi-illuminescence microscopy coupled to in situ hybridization and its utility in the study of evolution and development in non-model species. Development, Genes and Evolution 218(5): 273-279.

 

2007

John Kress, M. Newman, Axel Poulsen, and C. D. Specht.  2007.  An analysis of generic circumscriptions in tribe Alpinieae (Alpinioideae: Zingiberaceae).  The Gardens’ Bulletin Singapore 59: 113-128.

Chodon Sass,* Damon Little, Dennis Wm. Stevenson and C.D. Specht. 2007. DNA-Barcoding in the Cycadales: Testing the potential of proposed barcoding markers for species identification of Cycads. PloS-ONE. 11: e1154.

Vicki Funk and C.D. Specht. 2007. Meta-trees: grafting for a global perspective. Proceedings of the Biological Society of Washington. 120(2): 233-241.

C.D. Specht. 2007. A fine look at gingers of South India: Review of “Zingiberaceae and Costaceae of South India” by M. Sabu. Taxon 56(1): 276-277. (February 2007)

Kimmen Sjölander and Specht, C.D. “Functional prediction through phylogenetic inference and structural classification of proteins.” 2007. In R. Apweiler [ed.], The Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics. J. Wiley & Sons, Ltd., West Sussex, UK.

 

2006

Jerold I Davis, Gitte Petersen, Ole Seberg, Dennis Wm. Stevenson, Christopher R. Hardy, Mark P. Simmons, Fabian A. Michelangeli, D.H. Goldman, Lisa M. Campbell, C.D. Specht, and James I. Cohen.  2006.  Are mitochondrial genes useful for the analysis of monocot relationships?  Taxon 55:857-870.

C.D. Specht. “Gondwanan Vicariance or Dispersal in the Tropics? The biogeographic history of the tropical monocot family Costaceae (Zingiberales).” 2006. In J. T. Columbus, E. A. Friar, C. W. Hamilton, J. M. Porter, L. M. Prince, and M. G. Simpson, [eds.], Monocots: comparative biology and evolution. Rancho Santa Ana Botanic Garden, Claremont, California.

John Kress and Specht, C.D. “The evolutionary and biogeographic origin and diversification of the tropical monocot order Zingiberales.” 2006. In J. T. Columbus, E. A. Friar, C. W. Hamilton, J. M. Porter, L. M. Prince, and M. G. Simpson, [eds.], Monocots: comparative biology and evolution. Rancho Santa Ana Botanic Garden, Claremont, California.

Petersen, G., O. Seberg, J.I. Davis, D.H. Goldman, D.W. Stevenson, L.M. Campbell, F.A. Michelangeli, C.D. Specht, M.W. Chase, M.F. Fay, J.C. Pires, J.V. Freudenstein, C. R. Hardy and M.P. Simmons. “Mitochondrial DNA and Monocot Phylogeny.” 2006. In J. T. Columbus, E. A. Friar, C. W. Hamilton, J. M. Porter, L. M. Prince, and M. G. Simpson, [eds.], Monocots: comparative biology and evolution. Rancho Santa Ana Botanic Garden, Claremont, California.

C.D. Specht. and Stevenson, D.W. 2006. “A revised taxonomy for Costaceae (Zingiberales).” Taxon 55(1): 153-163.

C.D. Specht. 2006. “Systematics and Evolution of the tropical monocot family Costaceae (Zingiberales): a multiple dataset approach.” Systematic Botany 31(1):88-108.

 

2001 – 2005

C.D. Specht. 2005. “Phylogenetics, Floral Evolution, and Rapid Radiation in the Tropical Monocot Family Costaceae (Zingiberales).” Pp. 29-60 in Plant Genome: Biodiversity and Evolution. A.K Sharma and A. Sharma (Eds.) Science Publishers, Inc. Enfield, NH. USA.

Kress, W. J. and C. D. Specht. 2005. “Between Cancer and Capricorn: phylogeny, evolution, and ecology of the tropical Zingiberales.“ In I. Friis and H. Balslev, eds. Proceedings of a symposium on plant diversity and complexity patterns – local, regional and global dimensions. Biologiske Skrifter, The Royal Danish Academy of Sciences and Letters, Copenhagen.

Davis, J.I., D.W. Stevenson, G. Petersen, O. Seberg, L.M. Campbell, J.V. Freudenstein, D.H. Goldman, C.R. Hardy, F.A. Michelangeli, M.P. Simmons, C.D. Specht, F. Vergara-Silva, and M.A. Gandolfo. 2004. “A phylogeny of the monocots, as inferred from rbcL and atpA sequence variation, and a comparison of methods for calculating jackknife and bootstrap values.” Systematic Botany 29(3):467-510.

C.D. Specht and Dennis Wm. Stevenson. 2003. “Easy Trees? – Review of “Phylogenetic trees made easy: a how-to manual for molecular biologists” by Barry Hall.” Molecular Phylogenetics and Evolution. 27:168-171.

C.D. Specht, W. John Kress, Dennis Wm. Stevenson, and Rob DeSalle. 2001. “A Molecular Phylogeny of Costaceae (Zingiberales).” Molecular Phylogenetics and Evolution 21(3):333-345.

 

1997-2000

Stevenson, D.W., Davis, J.D., Freudenstein, J.V., Hardy, C.R., Simmons, M.P., and Specht, C.D. 2000. “A Phylogenetic analysis of the Monocotyledons based on Morphological and Molecular character sets, with comments on the placement of Acoris and Hydetellaceae.” Monocots: Systematics and Evolution. Eds K.L. Wilson and D.A. Morrison. CSIRO:Melbourne.

Lim, J., Heliarutta, Y., Specht, C.D., Jung, J., Sims, L., Bruce, W.B., Diehn, S., and Benfey, P.N. 2000. “Molecular Analysis of the SCARECROW Gene in Maize Reveals a Common Basis for Radial Patterning in Diverse Meristems.” The Plant Cell 12:1307-1318.

C.D. Specht and Patricia Caffrey. 1999. “Manejo Sostenible de Recursos y Conservación de la Biodiversidad.” BOLFOR 17: 1-3.

Paul Z. Goldstein and C.D. Specht. 1997. “Pitfalls in phylogenetic analysis of Large Molecular Data.” In Molecular Ecology and Evolution, in B. Schierwater et al. (eds.) Berlin: Birkhauser Verlag.

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