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M. Yoon Chung, Nason, J. D., and Chung, M. Gi, Patterns of hybridization and population genetic structure in the terrestrial orchids Liparis kumokiri and Liparis makinoana (Orchidaceae) in sympatric populations, Molecular Ecology, vol. 14, no. 14, pp. 4389-4402, 2005.
A. L. Toth, Sumner, S., and Jeanne, R. L., Patterns of longevity across a sociality gradient in vespid wasps, Current Opinion in Insect Science, 2016.
W. H Polley, Derner, J. D., and Wilsey, B. J., Patterns of plant species diversity in remnant and restored tallgrass prairies, Restoration Ecology, vol. 13, no. 3, pp. 480-487, 2005.
R. Cronn, Cedroni, M., Haselkorn, T., Grover, C., and Wendel, J. F., PCR-mediated recombination in amplification products derived from polyploid cotton, Theoretical and Applied Genetics, vol. 104, no. 2-3, pp. 482-489, 2002.
G. R. Almany, De Arruda, M. P., Arthofer, W., Atallah, Z. K., Beissinger, S. R., Berumen, M. L., Bogdanowicz, S. M., Brown, S. D., Bruford, M. W., and Burdine, C., Permanent genetic resources added to molecular ecology resources database 1 May 2009–31 July 2009, Molecular Ecology Resources, vol. 9, no. 6, pp. 1460-1466, 2009.
D. C. Adams and Collyer, M. L., Permutation tests for phylogenetic comparative analyses of high‐dimensional shape data: What you shuffle matters, Evolution, vol. 69, no. 3, pp. 823-829, 2015.
S. Renny-Byfield, Gong, L., Gallagher, J. P., and Wendel, J. F., Persistence of Subgenomes in Paleopolyploid Cotton after 60 My of Evolution, Molecular biology and evolution, vol. 32, no. 4, pp. 1063-1071, 2015.
C. A. Phillips, Uzzell, T., Spolsky, C. M., Serb, J. M., Szafoni, R. E., and Pollowy, T. R., Persistent high levels of tetraploidy in salamanders of the Ambystoma jeffersonianum complex, Journal of Herpetology, pp. 530-535, 1997.
R. Gabor, Hall, S., Eiriksson, D., Jameel, Y., Millington, M., Stout, T., Barnes, M., Gelderloos, A., Tennant, H., and Bowen, G., Persistent urban impacts on surface waterPersistent urban impacts on surface water quality via impacted groundwater in Red Butte Creek, 2017.
R. S. Gabor, Hall, S. J., Eiriksson, D., Jameel, Y., Millington, M., Stout, T., Barnes, M. L., Gelderloos, A., Tennant, H., and Bowen, G. J., Persistent urban influence on surface water quality via impacted groundwater, Environmental Science & Technology, 2017.
D. S. Senchina, Flagel, L. E., Wendel, J. F., and Kohut, M. L., Phenetic comparison of sevenEchinacea species based on immunomodulatory characteristics, Economic botany, vol. 60, no. 3, pp. 205-211, 2006.
M. L. Collyer, Stockwell, C. A., Adams, D. C., and M Reiser, H., Phenotypic plasticity and contemporary evolution in introduced populations: evidence from translocated populations of white sands pupfish (Cyrpinodon tularosa), Ecological Research, vol. 22, no. 6, pp. 902-910, 2007.
J. Hollander, Collyer, M. L., Adams, D. C., and Johannesson, K., Phenotypic plasticity in two marine snails: constraints superseding life history, Journal of evolutionary biology, vol. 19, no. 6, pp. 1861-1872, 2006.
Y. Jin Chun, Collyer, M. L., Moloney, K. A., and Nason, J. D., Phenotypic plasticity of native vs. invasive purple loosestrife: a two-state multivariate approach, Ecology, vol. 88, no. 6, pp. 1499-1512, 2007.
C. Edge, Rollinson, N., Brooks, R., Congdon, J., Iverson, J., Janzen, F., and Litzgus, J., Phenotypic plasticity of nest timing in a post-glacial landscape: how do reptiles adapt to seasonal time constraints?, Ecology, 2016.
M. Lloyd Collyer and Adams, D. C., Phenotypic trajectory analysis: comparison of shape change patterns in evolution and ecology, Hystrix, the Italian Journal of Mammalogy, vol. 24, no. 1, pp. 75-83, 2013.
C. E. Grover, Yu, Y., Wing, R. A., Paterson, A. H., and Wendel, J. F., A phylogenetic analysis of indel dynamics in the cotton genus, Molecular Biology and Evolution, vol. 25, no. 7, pp. 1415-1428, 2008.
D. C. Adams and Jackson, J. F., A phylogenetic analysis of the southern pines (Pinus subsect. Australes Loudon): biogeographical and ecological implications, PROCEEDINGS-BIOLOGICAL SOCIETY OF WASHINGTON, vol. 110, pp. 681-692, 1997.
D. C. Adams and Collyer, M. L., Phylogenetic anova: group‐clade aggregation, biological challenges, and a refined permutation procedure, Evolution, 2018.
D. C. Adams and Nason, J. D., A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species, Evolution, 2017.
J. M. Serb, Sherratt, E., Alejandrino, A., and Adams, D. C., Phylogenetic convergence and multiple shell shape optima for gliding scallops (Bivalvia: Pectinidae), Journal of Evolutionary Biology, 2017.
T. Bureau, Hawkins, J. S., Hu, G., Rapp, R. A., Grafenberg, J. L., and Wendel, J. F., Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium, Genome, vol. 51, no. 1, pp. 11-18, 2007.
L. Attigala, Wysocki, W. P., Duvall, M. R., and Clark, L. G., Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis, Molecular Phylogenetics and Evolution, 2016.
J. F. Wendel and Doyle, J. J., Phylogenetic incongruence: window into genome history and molecular evolution, in Molecular systematics of plants II, Springer US, 1998, pp. 265-296.
C. Grover, Hawkins, J., and Wendel, J. F., Phylogenetic insights into the pace and pattern of plant genome size evolution, 2008.
D. C. Adams, Phylogenetic meta‐analysis, Evolution, vol. 62, no. 3, pp. 567-572, 2008.
L. E. Flagel, Rapp, R. A., Grover, C. E., Widrlechner, M. P., Hawkins, J., Grafenberg, J. L., Álvarez, I., Chung, G. Young, and Wendel, J. F., Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea, American journal of botany, vol. 95, no. 6, pp. 756-765, 2008.
S. Hartmann, Nason, J. D., and Bhattacharya, D., Phylogenetic origins of Lophocereus (Cactaceae) and the senita cactus–senita moth pollination mutualism, American Journal of Botany, vol. 89, no. 7, pp. 1085-1092, 2002.
C. P. Ceballos, Adams, D. C., Iverson, J. B., and Valenzuela, N., Phylogenetic patterns of sexual size dimorphism in turtles and their implications for Rensch’s rule, Evolutionary Biology, vol. 40, no. 2, pp. 194-208, 2013.
A. Schnabel, McDonel, P. E., and Wendel, J. F., Phylogenetic relationships in Gleditsia (Leguminosae) based on ITS sequences, American journal of botany, vol. 90, no. 2, pp. 310-320, 2003.
J. M. Serb and Puslednik, L., Phylogenetic relationships of the pectinidae and the evolution of sexual reproductive modes: How important is dispersal life history?, JOURNAL OF SHELLFISH RESEARCH, vol. 26, no. 4. NATL SHELLFISHERIES ASSOC C/O DR. SANDRA E. SHUMWAY, UNIV CONNECTICUT, 1080 SHENNECOSSETT RD, GROTON, CT 06340 USA, pp. 1344-1345, 2007.
L. Betancur, Singh, B., Rapp, R. A., Wendel, J. F., M Marks, D., Roberts, A. W., and Haigler, C. H., Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber, Journal of integrative plant biology, vol. 52, no. 2, pp. 205-220, 2010.
J. F. Wendel and Albert, V. A., Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications, Systematic Botany, pp. 115-143, 1992.
A. Kaliontzopoulou and Adams, D. C., Phylogenies, the Comparative Method, and the Conflation of Tempo and Mode., Systematic biology, 2015.
M. R. Duvall, Fisher, A. E., J Columbus, T., Ingram, A. L., Wysocki, W. P., Burke, S. V., Clark, L. G., Kelchner, S. A., and Edwards, E., Phylogenomics and Plastome Evolution of the Chloridoid Grasses (Chloridoideae: Poaceae), International Journal of Plant Sciences, vol. 177, no. 3, pp. 235-246, 2016.
S. Vincent Burke, Lin, C. - S., Wysocki, W. Patrick, Clark, L. G., and Duvall, M. R., Phylogenomics and plastome evolution of tropical forest grasses (Leptaspis, Streptochaeta: Poaceae), Frontiers in Plant Science, vol. 7, p. 1993, 2016.
R. L. Small and Wendel, J. F., Phylogeny, duplication, and intraspecific variation of Adh sequences in new world diploid cottons (Gossypium L., Malvaceae), Molecular Phylogenetics and Evolution, vol. 16, no. 1, pp. 73-84, 2000.
D. C. Campbell, Serb, J. M., Buhay, J. E., Roe, K. J., Minton, R. L., and Lydeard, C., Phylogeny of North American amblemines (Bivalvia, Unionoida): prodigious polyphyly proves pervasive across genera, Invertebrate Biology, vol. 124, no. 2, pp. 131-164, 2005.
L. G. Clark, Zhang, W., and Wendel, J. F., A phylogeny of the grass family (Poaceae) based on ndhF sequence data, Systematic Botany, pp. 436-460, 1995.
I. Álvarez, Cronn, R., and Wendel, J. F., Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes, Plant Systematics and Evolution, vol. 252, no. 3-4, pp. 199-214, 2005.
E. H. Crane, Farrar, D. R., and Wendel, J. F., Phylogeny of the Vittariaceae: convergent simplification leads to a polyphyletic Vittaria, American Fern Journal, pp. 283-305, 1995.
D. Badenhorst, Hillier, L. W., Literman, R., Montiel, E. E., Radhakrishnan, S., Shen, Y., Minx, P., Janes, D., Warren, W. C., and Edwards, S. V., Physical mapping and refinement of the painted turtle genome (Chrysemys picta) inform amniote genome evolution and challenges turtle-bird chromosomal conservation., Genome biology and evolution, 2015.
J. M. Jandt and Toth, A. L., Physiological and Genomic Mechanisms of Social Organization in Wasps (Family: Vespidae), Advances in Insect Physiology, 2015.
B. A Duthie and Nason, J. D., Plant connectivity underlies plant‐pollinator‐exploiter distributions in Ficus petiolaris and associated pollinating and non‐pollinating fig wasps, Oikos, 2016.
D. Craven, Isbell, F., Manning, P., Connolly, J., Bruelheide, H., Ebeling, A., Roscher, C., van Ruijven, J., Weigelt, A., and Wilsey, B., Plant diversity effects on grassland productivity are robust to both nutrient enrichment and drought, Phil. Trans. R. Soc. B, vol. 371, no. 1694, p. 20150277, 2016.
W. H Polley, Isbell, F. I., and Wilsey, B. J., Plant functional traits improve diversity‐based predictions of temporal stability of grassland productivity, Oikos, vol. 122, no. 9, pp. 1275-1282, 2013.
J. Greilhuber, Dolezel, J., Leitch, I. J., and Wendel, J. F., Plant Genome Diversity: Vol. 1: Plant Genomes, Their Residents, and Their Evolutionary Dynamics. Springer, 2012.
I. J. Leitch, Greilhuber, J., Dolezel, J., and Wendel, J. F., Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes, vol. 2. Springer Science & Business Media, 2012.
B. J. Wilsey, Plant responses to elevated atmospheric CO 2 among terrestrial biomes, Oikos, pp. 201-206, 1996.
L. H. Rieseberg and Wendel, J. F., Plant speciation–rise of the poor cousins, New Phytologist, vol. 161, no. 1, pp. 3-8, 2004.

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