Representative Publications

(See Google Scholar, ResearchGate or PubMed for expanded publiction list)

2014

Barrett, C.F., C. D. Specht, J. Leebens-Mack, D. W. Stevenson, W. B. Zomlefer, and J. I. Davis.  2014.  Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales Griseb.)? Annals of Botany. 113 (1): 119-133 doi: 10.1093/aob/mct264.

Cannon, S.  M. R. McKain, A. Harkess, M. Deyholos, M. Chase, C. N. Stewart, Y. Peng, B. Joyce, P. Soltis, D. Soltis, M. N. Nelson, N. Miles, T. Kutchan,  X. Tan, C. Chen,  E. Carpenter, Y. Zhang, G. Ka-Shu Wong, J. J. Doyle and J. H. Leebens-Mack. Independent genome duplication events and the evolution of nodulation in the legumes.  Molecular Biology and Evolution, Advanced Access. doi: 10.1093/molbev/msu296

Eserman L.A., G. P. Tiley, R. L. Jarret, J. H. Leebens-Mack, R. E. Miller.  2014.  Phylogenetics and diversification of morning glories based on whole plastome sequences.  American Journal of Botany 101:92-103 doi: 10.3732/ajb.1300207

Rentsch, J.D., and J. Leebens-Mack. 2014.  Yucca aloifolia (Agavoidea, Asparabaceae) opts out of an obligate pollination mutualism? Evidence for diurnal, non-moth pollination of a Yucca species. American Journal of Botany. Advanced Access doi:10.3732/ajb.1400351

Wickett, N.J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam, M. Barker, G. J. Burleigh, M. A. Gitzendanner, B. Ruhfel, E. Wafula, J.P. Der, S. W. Graham, S. Mathews, M. Melkonian, D. E. Soltis, P. S. Soltis, C. Rothfels, L. Pokorny, J. Shaw, L. DeGironimo, D. Stevenson, B. Surek, J.C. Villarreal, B. Roure, H. Philippe, C. W. dePamphilis, T. Chen, M. Deyholos, J. Wang, Y. Zhang, Z. Tian, Z. Yan, X. Wu, X. Sun, G. K-S. Wong, and J. Leebens-Mack.  2014.  A phylotranscriptomic analysis of the origin and early diversification of land plants.  Proceedings of the National Academy of Sciences, U.S.A. 111 (45):E4859–E4868. doi: 10.1073/pnas.1323926111

2013

Amborella Genome Project.  2013.  The Amborella Genome and the Evolution of Flowering Plants.   Science 342: DOI: 10.1126/science.1241089

Chamala, S.  A. S. Chanderbali, J. P. Der, T. Lan, B. Walts, V. A. Albert, C. W. dePamphilis, J. Leebens-Mack, S. Rounsley, S. C. Schuster, R. A. Wing, N. Xiao, R. Moore, P. S. Soltis, D. E. Soltis, and W. B. Barbazuk. 2013.  Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella.  Science 342:1516-1517 DOI: 10.1126/science.1241130

Vitte, C., M. Estep, J. Leebens-Mack and J. L. Bennetzen. Young, intact and nested retrotransposons in the onion and asparagus genomes.  Annals of Botany Advance Access 10.1093/aob/mct155

Panahiazar M, A Ranabahu, R.Vos, A Stoltzfus, AP Sheth, and J. Leebens-Mack. 2013. Advancing the Reusability of Resources in Phyloinformatics with an Ontology-Driven Semantic Web Approach. BMC Medical Genomics 6(Suppl 3):S5  doi:10.1186/1755-8794-6-S3-S5

Mercati, F., P. Riccardi, J. Leebens-Mack, M. R. Abenavoli, A. Falavigna, F. Sunseri. 2013. Single nucleotide polymorphism isolated from a novel EST dataset in garden asparagus (Asparagus officinalis L.). Plant Science 203-204:115–123.

2012

Rentsch JD, Leebens-Mack J. 2012. Homoploid hybrid origin of Yucca gloriosa: intersectional hybrid speciation in Yucca (Agavoideae, Asparagaceae). Ecol Evol. 2(9):2213-22.

Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, Depamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, et al. 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 7(11):e50226.

D’Hont, A., F. Denoeud, J-M. Aury, F-C. Baurens, F. Carreel, O. Garsmeur, B. Noel, S. Bocs, G. Droc, M. Rouard, C. Da Silva, K. Jabbari,, C. Cardi, J. Poulain, M. Souquet, K. Labadie, C. Jourda, J. Lengelle, M. Rodier-Goud, A. Alberti, M. Bernard, M. Correa, S. Ayyampalayam, M. R. Mckain, J. Leebens-Mack et al. 2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213-217.

McKain, M.R., N. Wickett, Y. Zhang, S. Ayyampalayam, W. R. McCombie, M. W. Chase, J. C.Pires, C. W. dePamphilis and J. Leebens-Mack 2012. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany 99:397-406, doi:10.3732/ajb.1100537.

Steele, P. R., K. L. Hertweck, D. Mayfield, M. R. McKain, J. Leebens-Mack, and J. C. Pires. 2012. Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae. American Journal of Botany 99:330-348, doi:10.3732/ajb.1100491.

Jiao, Y., J. Leebens-Mack, S, Ayyampalayam, J. E. Bowers, M. R McKain, J. McNeal, M. Rolf, D. R Ruzicka, E. Wafula, N. J Wickett, X. Wu, Y. Zhang, J. Wang, Y. Zhang, E. Carpenter, M. K Deyholos, T. M Kutchan, A. S. Chanderbali, P. S. Soltis, D. W. Stevenson, R. McCombie, J. C. Pires, G. Ka-Shu Wong, D. E. Soltis and C. W. dePamphilis. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13(1):R3. doi:10.1186/gb-2012-13-1-r3.

Althoff D.M., K.A. Segraves, C.I. Smith, J. Leebens-Mack, O. Pellmyr. 2012. Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification. Mol Phylogenet Evol. 62(3):898-906.

2011

Zuccolo, A. J.E. Bowers, J. C. Estill, Z. Xiong, M. Luo,, A. Sebastian, J. L. Goicoechea, K.Collura, Y. Yu, Y. Jiao, J. Duarte, H. Tang, S. Ayyampalayam, S. Rounsley, D. Kudrna, A. H. Paterson,, J. C. Pires, D. E. Soltis, S. Chamala, B. Barbazuk, P.S. Soltis, V. A. Albert, H. Ma, D. Mandoli, J. Banks, J. E. Carlson, J. Tomkins, C. W. dePamphilis, R. A. Wing. J. Leebens-Mack. 2011. A Physical Map for the Amborella Genome Sheds Light on the Evolution of Angiosperm Genome Structure. Genome Biology12:R48

Jiao, Y., N. J. Wickett, S. Ayyampalayam, A.S. Chanderbali, L. Landherr, P. E. Ralph, L. P. Tomsho, Y. Hu, H. Liang, P. S. Soltis, D. E. Soltis, S. W. Clifton, S. E. Schlarbaum, S. C. Schuster, H. Ma, J. Leebens-Mack, C.W. dePamphilis. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473:97–100

Liang, H., S. Ayyampalayam, N. Wickett, A. Barakat,Y. Xu, L. Landherr, P. E. Ralph, Y. Jiao, Tao Xu, S. E. Schlarbaum, H. Ma, J. H. Leebens-Mack, C.W. dePamphilis. 2011. Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L. Tree Genetics & Genomes 7(5):941-954

2010

Givnish, T.J., M.A. Sevillano, J.R. McNeal, M. R. McKain, P.R. Steele, C.W. dePamphilis, S. W. Graham, J. C. Pires, D. W. Stevenson, W. B. Zomlefer, B. G. Briggs, M. R. Duvall, M. J. Moore, D. E. Soltis, P. S. Soltis, K. Thiele, and J. H. Leebens-Mack. 2010. Assembling the tree of the monocotyledons: Plastome sequence phylogeny and evolution of Poales. Annals of the Missouri Botanical Gardens 97(4):584-616.

Yellina, Y.L., S. Lange, S. Orashakova, J.H. Leebens-Mack, and A. Becker. 2010. Functional analysis of floral homeotic C function genes in the basal eudicot California poppy. Evodevo 1:13

Zahn, L.M., X. Ma, N. S. Altman, Q. Zhang, P K. Wall, D. Tian, C. J Gibas, R. Gharaibeh, J. H Leebens-Mack, C. W dePamphilis, H. Ma. 2010. Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies.  Genome Biology 11:R101

Duarte. J.M., P. K. Wall, P. P. Edger, L.L. Landherr, H. Ma, J.C. Pires, J. Leebens-Mack and C.W. dePamphilis. 2010. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology 10:61

Chanderbali A.S., M.J. Yoo, L.M. Zahn, S.F. Brockington, P.K. Wall, M.A. Gitzendanner, V.A. Albert, J. H. Leebens-Mack, A.S. Altman, H. Ma, C.W. dePamphilis, D.E. Soltis, P.S. Soltis. 2010. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proc Natl Acad Sci U S A 107:22570-22575

2009

McNeal, J.R., J.H. Leebens-Mack, J.V. Kuehl, J.L. Boore, and C.W. dePamphilis. 2009. Parallel loss of plastid introns and their maturase in the genus Cuscuta. PLoS ONE4(6):e5982

Shan, H., L. Zahn, S. Guindon, P. K. Wall, H. Kong, H. Ma, C.W. dePamphilis and J. H. Leebens-Mack. 2009. Evolution of plant MADS box transcription factors: evidence for relaxed selection in association with early angiosperm diversification.  Molecular Biology and Evolution 26(10):2229-2244

Wall, P.K., J. Leebens-Mack, A. Chanderbali, A. Barakat, H. Liang, L. Landherr, L. P. Tomsho, Y. Hu, H. Ma, J.E. Carlson, S. Schuster, D. E. Soltis, P.S. Soltis, N. Altman, and C.W. dePamphilis. 2009. Comparison of next generation sequencing technologies for de novo transcriptome characterization. BMC Genomics. 10:347.

Chanderbali, A.S., V.A. Albert, J. Leebens-Mack, N. S. Altman, D.E. Soltis, and P. S. Soltis. 2009. Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae). Proceedings of the National Academy of Sciences. 106(22):8929-34

Soltis, D.E., V.A. Albert, J.H. Leebens-Mack, C.D. Bell, A. Paterson, C. Zheng, D. Sankoff, and P.S. Soltis. 2009. Polyploidy and angiosperm diversification. Amer. J. Bot. 96:336-348.

2008

Baucom, R.S., J.C. Estill, J.H. Leebens-Mack, J.L. Bennetzen. 2009. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Research 19(2):243-254.

Lescot M., P. Piffanelli, A. Y. Ciampi, M. Ruiz, G. Blanc, J. H. Leebens-Mack, F. R da Silva, C.M.R Santos, A. D'Hont, O. Garsmeur, A. D Vilarinhos, H. Kanamori, T. Matsumoto, C. M Ronning, F. Cheung, B. J Haas, R. Althoff, T. Arbogast, E. Hine, G. J Pappas, T. Sasaki, M. T. Souza, R. N. G. Miller, J.-C. Glaszmann and C. D Town. 2008. Insights into the Musa  genome: syntenic relationships to rice and between Musa species.  BMC Genomics 9(1):58.

Smith, C.I., O. Pellmyr, D.M. Althoff, M. Balcazar-Lara, J.H. Leebens-Mack, and K.A. Segraves. 2008. Pattern and timing of diversification in Yucca (Agavaceae): specialized pollination does not escalate rates of diversification. Proc Biol Sci. 275: 249-58.

Soltis, D.E., V.A. Albert, J.H. Leebens-Mack, J.D. Palmer, R.A. Wing, C.W. dePamphilis, H. Ma, J.E. Carlson, N. Altman , S. Kim, P.K. Wall, A. Zuccolo, and P.S. Soltis. 2008. The Amborella genome: an evolutionary reference for plant biology.  Genome Biol. 9(3):402

Chapman MA, J.H. Leebens-Mack, and J.M. Burke. 2008. Positive selection and expression divergence following gene duplication in the sunflower CYCLOIDEA gene family. Mol Biol Evol. 25(7):1260-1273.

2007

Jansen, R.K., Z. Cai, L. A. Raubeson, H. Daniell, C. W. dePamphilis, J. H. Leebens-Mack, K. F. Muller, M. Guisinger-Bellian, R. C. Haberle, A. K. Hansen, T. W. Chumley, S.-B. Lee, R. Peery, J. McNeal, J. V. Kuehl, and J. L. Boore. 2007. Analysis of 81 genes from 64 chloroplast genomes resolves relationships inangiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences. 104(49):19369-74

Wall, P.K., J.H. Leebens-Mack, K.F Muller, D. Field, N.S. Altman, and C.W. dePamphilis. 2007. PlantTribes: a gene and gene family resource for comparative genomics in plants Nucleic Acids Res. 36(Database issue):D970-976.

Soltis D.E., H. Ma, M.W. Frohlich, P.S. Soltis, V.A. Albert, D.G. Oppenheimer, N.S. Altman, C.W. dePamphilis and J.H. Leebens-Mack. 2007. The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends in Plant Science 12(8):358-367.

Kong, H., L. Landherr, M. Frohlich, J.H. Leebens-Mack, H. Ma, and C.W. dePamphilis. 2007. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. The Plant Journal  50:873-885.

Pellmyr, O., K. A. Segraves, D. M. Althoff, Balcàzar-Lara and J. H. Leebens-Mack 2007. The phylogeny of yuccas.  Molecular Phylogenetics and Evolution  43:493-501.

Gilbert M.T., J. Binladen, W. Miller, C. Wiuf, E. Willerslev, H. Poinar, J.E. Carlson, J.H. Leebens-Mack, and S.C. Schuster. 2007. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research  35:1-10.

2006

Soltis, D. E., J.H. Leebens-Mack and P.S. Soltis (eds.). 2006. Developmental Genetics of the Flower. Advances in Botanical Research  series. Elsevier Limited, London.

Tuskan, G.A., S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, et al. 2006. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596-604.

Leebens-Mack, J.H., T. Vision, E. Brenner, J.E. Bowers, S. Cannon, M.J. Clement, C.W. Cunningham, C. dePamphilis, R. Desalle, J.J. Doyle, J.A. Eisen, X. Gu, J. Harshman, R.K. Jansen, E.A. Kellogg, E.V. Koonin, B.D. Mishler, H. Philippe, J.C. Pires, Y-L. Qiu, S.Y. Rhee, K. Sjolander, D.E. Soltis, P.S. Soltis, D.W. Stevenson, K. Wall, T. Warnow, C. Zmasek. 2006. Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA). OMICS 10(2):231-237.

Althoff, D.M., K.A. Segraves. J.H. Leebens-Mack, and O. Pellmyr. 2006. Patterns of Speciation in the Yucca Moths: Parallel Species Radiations within the  Tegeticula yuccasella  Species Complex. Systematic Biology  55(3):398-410.

Cui, L., Wall K., B.G. Lindsay, J.H. Leebens-Mack, J.J. Doyle, D.E. Soltis, P.S. Soltis, J. Carlson, H. Ma, and C.W. dePamphilis, 2006. Widespread genome duplications in flowering plants. Genome Research 16(6):738-49

Cui, L., J.H. Leebens-Mack, L-S. Wang, J. Tang, L. Rymarquis, L., D. B. Stern, and C.W. dePamphilis, 2006. Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach.  BMC Evolutionary Biology 6:13

Duarte, J. M., L. Cui, P.K. Wall, Q. Zhang, X. Zhang, J.H. Leebens-Mack, H. Ma, N. Altman, and C.W. dePamphilis. 2006. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Molecular Biology and Evolution 23(2):469-78

Pellmyr, O., K.A. Segraves, D.M. Althoff, M. Balcàzar-Lara, and J.H. Leebens-Mack. 2006. Phylogeny and life history evolution of Prodoxus yucca moths (Lepidoptera: Prodoxidae). Systematic Entomology 31:1-20.

Zahn, L.M., J.H. Leebens-Mack, J.M. Arrington, Y. Hu, L. Landherr, C.W. dePamphilis,, A. Becker, G, Theissen, and H. Ma. 2006. Conservation and divergence in the AGAMOUS Subfamily of MADS-Box Genes: Evidence of Independent Sub- and Neofunctionalization Events. Evolution and Development  8:30-45.

2005

Leebens-Mack, J.H., L. A. Raubeson, L. Cui, J.V. Kuehl, M.H. Fourcade, T.W. Chumley, J.L. Boore, R.K. Jansen, and C.W. dePamphilis. 2005. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution 22(10):1948-1963

Kuhl, J.C., M.J. Havey, W.J. Martin, F. Cheung, Q. Yuan, L. Landherr, Y. Hu, J.H. Leebens-Mack, C.D. Town and K. Sink. 2005. Comparative genomic analyses of Asparagus officinalis L. Genome 48:1052-1060.

Albert, V.A., D. E. Soltis, J. E. Carlson, W.G. Farmerie, P. K. Wall, D. C. Ilut, L. A. Mueller, L. L. Landherr, Y. Hu, M. Buzgo, S. Kim, M-J. Yoo, M. W. Frohlich, R. Perl-Treves, S. Schlarbaum, B. Bliss, S. Tanksley, D. G. Oppenheimer, P. S. Soltis, H. Ma, C. W. dePamphilis and J. H. Leebens-Mack. 2005. Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biology  5(1):5

Zahn, L.M., J.H. Leebens-Mack, C.W. dePamphilis, H. Ma, and G. Theissen. 2005. To B or not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. Journal of Heredity 96(3):225-240.

Zahn, L.M., H. Kong, J,H. Leebens-Mack, S. Kim, P.S. Soltis, L. Landherr, D.E. Soltis, C.W. dePamphilis, and H. Ma. 2005. The evolution of the SEPELLATA subfamily of MADS-box genes: A pre-angiosperm origin with multiple duplications throughout angiosperm history. Genetics 169(4):2209-2223.

Soltis, D. E., V. A. Albert, S. Kim, M.-J. Yoo, P.S. Soltis, M.W. Frohlich, J.H. Leebens-Mack, H. Kong, P.K. Wall, H. Ma, H., and C.W. dePamphilis, 2004 Evolution of the Flower. In R. Henry (ed.) Diversity and Evolution of Plants, CABI Publishers.

2004

Leebens-Mack, J.H. and O. Pellmyr. 2004. Patterns of Genetic Structure among Populations of an Oligophagous Pollinating Yucca Moth (Tegeticula yuccasella). Journal of Heredity 95:127-135.

Wang J.P., B.G. Lindsay, J.H. Leebens-Mack, L. Cui, K. Wall, W.C. Miller, and C.W. dePamphilis. 2004. EST clustering error evaluation and correction.  Bioinformatics 20:2892-2905.

Kong, H., J.H. Leebens-Mack, W. Ni, C.W. dePamphilis and H. Ma. 2004. Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: Functional and evolutionary implications.  Molecular Biology and Evolution 21:117-128.

2002

Leebens-Mack, J.H., and C.W. dePamphilis. 2002. Power analysis of tests for loss of selective constraint in cave crayfish and nonphotosynthetic plant lineages. Molecular Biology and Evolution 19:1292-1302

Hoham, R.W., T. A. Benome, C. Martin and J.H. Leebens-Mack. 2002 . A combined 18S rDNA and rbcL based phylogenetic analysis of Chloromonas and Chlamydomonas (Chlorophyceae, Volvocales) species from cold-temperature habitats. Journal of Phycology 38:1051-1064.

2000

Pellmyr, O. and J.H. Leebens-Mack. 2000. Reversal of mutualism as a mechanism for adaptive radiation in yucca moths. American Naturalist  156:S62-S76.

Marr, D., J.H. Leebens-Mack, L. Elms, and O. Pellmyr. 2000. Pollen dispersal in Yucca filamentosa (Agavaceae): the paradox of self-pollination behavior by Tegeticula yuccasella  (Prodoxidae). American Journal of Botany 87:670-677.

Earlier

Pellmyr, O. and J.H. Leebens-Mack. 1999. Forty million years of mutualism: evidence for eocene origin of the yucca-yucca moth association. Proceedings of the National Academy of Sciences 96:9178-9183.

Leebens-Mack, J.H., O. Pellmyr, and M.T. Brock. 1998. Host specificity and genetic structure of two yucca moth species in a yucca hybrid zone. Evolution  52:1376-1382.

Leebens-Mack J.H. and B.G. Milligan. 1998 Pollination biology in hybridizing Baptisia (Fabaceae) populations. American Journal of Botany  85:500-507.

Pellmyr, O., J.H. Leebens-Mack, and J.N.Thompson. 1998. Herbivores and molecular clocks as a tool in plant biogeography. Biological Journal of the Linnean Society 63:367-378.

Brown, J.M., J.H. Leebens-Mack, J.N. Thompson, O. Pellmyr, and R.G. Harrison. 1997. Phylogeography and host association in a pollinating seed parasite, Greya politella  (Lepidoptera: Prodoxidae). Molecular Ecology 6:215-224

Strand, A.E., J.H. Leebens-Mack, and B.G. Milligan. 1997. Nuclear DNA based markers for plant evolutionary biology. Molecular Ecology  6:113-118.

Pellmyr, O., J.H. Leebens-Mack, and Huth, C.J. 1996. Non-mutualistic yucca moths and their evolutionary consequences. Nature 380:155-156.

Milligan, B.G., J.H. Leebens-Mack, J.H., and A.E. Strand. 1994. Conservation genetics: beyond the maintenance of marker diversity. Molecular Ecology 3:423-435.