2008

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.

Barakat, A., P.K. Wall, J.H. Leebens-Mack, Y.J. Wang, J.E. Carlson and C.W. dePamphilis 2007. Identification of microRNAs from a basal eudicot (Eschscholzia californica). The Plant Journal 51(6):991-1003.

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.

Cai Z, C. Penaflor, J.V. Kuehl, J. H. Leebens-Mack, J.E. Carlson, C.W. dePamphilis, J.L. Boore, and R.K. Jansen. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evolutionary Biology 6:77.

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

McNeal, J.R., J.H. Leebens-Mack, K. Arumuganathan, J.V. Kuehl, J.L. Boore, and C. W. dePamphilis. 2006. Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques 41(1):69-73

Cui, L., N. Veeraraghavan, P.K. Wall, R.K. Jansen, J.H. Leebens-Mack, I. Makalowska, and C. W. dePamphilis. 2006. ChloroplastDB: the chloroplast genome database. Nucleic Acids Research 34:D692-696.

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.

Jansen, R.K., L.A.,Raubeson, J.L. Boore, C.W. dePamphilis, T.W. Chumley, R.C. Haberle, S.K. Wyman, A.J. Alverson, R. Peery, S.J. Herman, H.M. Fourcade, J.V. Kuehl, J.R. McNeal, J.H. Leebens-Mack, and L. Cui. 2005. Methods for Obtaining and Analyzing Whole Chloroplast Genome Sequences. Methods in Enzymology 395:348-84.

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.