Reference
Agrawal, A. A., Conner J. K., & Rasmann S. (2010). Trade-offs and adaptive negative correlations in evolutionary ecology. Pages 243–268in M. Bell, W. Eanes, D. Futuyma, & J. Levinton, editors.Evolution after Darwin: the first 150 years . Sinauer Associates, Sunderland, Massachusetts, USA.
Agrawal, A. A. (2020). A scale‐dependent framework for trade‐offs, syndromes, and specialization in organismal biology. Ecology ,101 , e02924.
Armbruster, W. S., Pélabon, C., Bolstad, G. H., Hansen TF. 2014. Integrated phenotypes: understanding trait covariation in plants and animals. Philosophical Transactions of Royal Society London Biological Science, 369, 20130245.
Bae, J. M., Kwak, M. S., Noh, S. A., Oh, M. J., Kim, Y. S., & Shin, J. S. (2014). Overexpression of sweet potato expansin cDNA (IbEXP1) increases seed yield in Arabidopsis. Transgenic Research, 23,657– 667.
Badr, A., Rabey, H.E., Effgen, S., Ibrahim, H.H., Pozzi, C., Rohde, W., & Salamini, F. (2000). On the origin and domestication history of barley (Hordeum vulgare ). Molecular Biology and Evolution17, 499-510.
Blows, M. W., & Hoffmann, A. A. (2005). A reassessment of genetic limits to evolutionary change. Ecology, 86, 1371–1384.
Blum, J. J. (1977). On the geometry of four-dimensions and the relationship between metabolism and body mass. Journal of Theoretical Biology, 64, 599–601.
Bolmgren, K., & Cowan, P. D. (2008). Time-size trade-offs: A phylogenetic comparative study of flowering time, plant height and seed mass in a north-temperate flora. Oikos, 117, 424-429.
Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., & Buckler, E. S. (2007). TASSEL: software for association mapping of complex traits in diverse samples.Bioinformatics, 23, 2633-2635.
Brown, J. H., & West, G. B. (2000). Scaling in Biology. Oxford University Press, New York.
Chang, C. C., Chow, C. C., Tellier, L. C. A. M., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets, Gigascience , 4,7.
Charnov, E.L. (1993). Life History Invariants. Some Explorations of Symmetry in Evolutionary Biology . Oxford University Press, Oxford.
Chen, F., Dahal, P., & Bradford, K. J. (2001). Two tomato expansin genes show divergent expression and localization in embryos during seed development and germination. Plant Physiology, 127 , 928–936
Darveau, C. A., Suarez, R. K., Andrews, R. D., & Hochachka, P. W. (2002). Allometric cascade as a unifying principle of body mass effects on metabolism. Nature, 417, 166–170.
Delker, C., & Quint, M. (2011). Expression level polymorphisms: heritable traits shaping natural variation. Trends in Plant Science, 16, 481-8.
Falster, D. S., Moles, A. T., & Westoby, M. (2008). A general model for the scaling of offspring size and adult size. The American Naturalist , 172 , 299-317.
Freschet, G. T. Swart E. M., & Cornelissen J. H. (2015). Integrated plant phenotypic responses to contrasting above‐and below‐ground resources: key roles of specific leaf area and root mass fraction.New Phytologist, 206, 1247-1260.
Garnier, E. & Navas, M. L. (2012). A trait-based approach to comparative functional plant ecology: concepts, methods and applications for agroecology. A review. Agronomy for Sustainable Development ,32 , 365-399.
Gianola, D., de los Campos, G., Toro, M. A., Naya, H., Schön, C. C., & Sorensen, D. (2015) Do molecular markers inform about pleiotropy?Genetics, 201, 23–29.
Gonzalez, M. Y., Weise, S., Zhao, Y., Philipp, N., Arend, D., Börner A, … Schulthess, A. W. (2018). Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection. Scientific Data, 5, 1.
Gross. L.J.& Beckage, B. (2012) Toward a metabolic scaling theory of crop systems. Proceedings of the National Academy of Sciences, 109, 15535-6.
Grotzinger, A. D., Rhemtulla, M., de Vlaming, R., Ritchie, S. J., Mallard, T. T., Hill, W. D., … Koellinger, P. D. (2019). Genomic structural equation modelling provides insights into the multivariate genetic architecture of complex traits. Nature Human Behaviour, 3 , 513.
Grubb, P. J., Metcalfe, D. J. & Coomes, D. (2005). Comment on ‘a brief history of seed size’. Science, 310, 783A–783A.
Gupta, M., Abu‐Ghannam, N. & Gallaghar, E., 2010. Barley for brewing: Characteristic changes during malting, brewing and applications of its by‐products. Comprehensive Reviews in Food Science and Food Safety , 9 , 318-328.
Hammer, O., Harper, D. A. T., & Ryan, P.D. (2001). PAST: paleontological statistics software package for education and data analysis. Paleontologica Electronica, 4, 9.
He, T., Hill, C. B., Angessa, T. T., Zhang, X. Q., Moody, D., Telfer, P., … Li, C. (2019). Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection. Journal of Experimental Botany, 70,5603-5616.
Hine, E., McGuigan, K. & Blows, M.W. (2014) Evolutionary constraints in high-dimensional trait sets. American Naturalist, 184, 119–131.
Huxley, J. S. (1924). Constant differential growth-ratios and their significance. Nature, 114, 895.
Kaplan, R. M., Chambers, D. A., & Glasgow, R. E. (2014). Big data and large sample size: a cautionary note on the potential for bias.Clinical and translational science, 7, 342-346.
Kermack, K. A. & Haldane, J. B. S. (1950). Organic correlation and allometry. Biometrika, 37, 30–41.
Kim, T. S., Kim, W. Y., Fujiwara, S., Kim, J., Cha, J. Y., Park, J. H., … Somers, D. E. (2011). HSP90 functions in the circadian clock through stabilization of the client F-box protein ZEITLUPE.Proceedings of the National Academy of Sciences, 108,16843-16848.
Kleiber, M. (1947). Body size and metabolic rate. Physiological Review, 27, 511–541.
Kleiber, M., (1975) Metabolic turnover rate: a physiological meaning of the metabolic rate per unit body weight. Journal of Theoretical Biology, 53, 199-204.
Kluyver, T.A., Charles, M., Jones, G., Rees, M., & Osborne, C.P. (2013) Did greater burial depth increase the seed size of domesticated legumes?Journal of Experimental Botany , 64, 4101-4108.
Langridge, P. (2014). Reinventing the green revolution by harnessing crop mutant resources. Plant physiology166, 1682-1683.
Langridge, P., & Fleury, D. (2011). Making the most of ‘omics’ for crop breeding. Trends in Biotechnology , 29 , 33-40.
Lee, H., Yang, J. Goddard, M. E. Visscher, P. M. Wray, N. R. (2012). Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood. Bioinformatics, 28, 2540-2542.
Lenth, R. (2017). emmeans: Estimated marginal means, aka least-squares means. R package version 0.9.1. https://CRAN. R-project.org/package=emmeans
Lin, M., Lucas, Jr. H.C., & Shmueli, G. (2013). Research commentary—too big to fail: large samples and the p-value problem.Information Systems Research, 24, 906-917.
Listgarten. J., Lippert, C. Kadie, C. M., Davidson, R.I., Eskin E., & Heckerman, D. (2012) Improved linear mixed models for genome-wide association studies. Nature Methods, 9, 525-526.
Liu, J. H., Li, Y. C., Zhang, J., Gao, P. Z., Wang, A. B., Zhang, N., … Jin, Z.Q. (2016). Banana MaEF1A facilitates plant growth and development. Biologia plantarum, 60, 435-42.
Ma, N., Wang, Y., Qiu, S., Kang, Z., Che, S., Wang, G., Huang, J. (2013). Overexpression of OsEXPA8, a root-specific gene, improves rice growth and root system architecture by facilitating cell extension.PLoS One 8(10) , e75997.
Mcmahon TA, Bonner JT. 1983. On Size and Life. Scientific American Books, New York.
Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T.,… Stern, N. (2017). A chromosome conformation capture ordered sequence of the barley genome. Nature, 544, 427-33.
Milla, R., & Matesanz, S. (2017) Growing larger with domestication: a matter of physiology, morphology or allocation? Plant Biology ,19 , 475-483.
Milla, R., Osborne, C.P., Turcotte, M.M., & Violle, C. (2015) Plant domestication through an ecological lens. Trends in Ecology & Evolution , 30 , 463-469.
Milner, S. G., Jost, M., Taketa, S., Mazón, E. R., Himmelbach, A., Oppermann, M., … Schüler, D. (2019). Genebank genomics highlights the diversity of a global barley collection. Nature Genetics, 51,319-326.
Moles, A. T., Ackerly, D. D., Webb, C. O., Tweddle, J. C., Dickie, J. B., & Westoby, M. (2005). A brief history of seed size. Science ,307 , 576–580.
Moles, A. T., Ackerly, D. D., Webb, C. O., Tweddle, J. C., Dickie, J. B., Pitman, A. J. & Westoby, M. (2005). Factors that shape seed mass evolution. Proceedings of the National Academy of Sciences of the United States of America, 102, 10540–10544.
Moles, A. T., Falster, D. S., Leishman, M. R., & Westoby, M. (2004). Small seeded species produce more seeds per square metre of canopy per year, but not per individual per lifetime. Journal of Ecology, 92, 384–396.
Niklas, K. J. (1994). Plant Allometry. University of Chicago Press, Chicago.
Niklas, K. J., (2004). Plant allometry: is there a grand unifying theory? Biological Reviews, 79 , 871-889.
Novack-Gottshall, P. M. (2008) Ecosystem-wide body-size trends in Cambrian–Devonian marine invertebrate lineages. Paleobiology 34,210–228.
Odunuga, O. O., Longshaw, V. M., & Blatch, G. L. (2016). Hop: more than an Hsp70/Hsp90 adaptor protein. BioEssays , 26, 1058–1068.
R Core Team (2018). R: A language and environment for statistical computing (R Foundation for Statistical Computing).
Rees, M. & Venable, D. L. (2007) Why do big plants make big seeds?Journal of Ecology 95 , 926-936.
Rollinson, N., Nilsson‐Örtman, V., & Rowe, L. (2019). Density‐dependent offspring interactions do not explain macroevolutionary scaling of adult size and offspring size. Evolution, 73, 2162-74.
Saltz, J. B., Hessel, F. C., & Kelly, M.W. (2017) Trait correlations in the genomics era. Trends in Ecology and Evolution, 32, 279–290.
Sangster, T. A.; Salathia, N.; Undurraga, S.; Milo, R.; Schellenberg, K.; Lindquist, S., & Queitsch, C. (2008). HSP90 affects the expression of genetic variation and developmental stability in quantitative traitsProceedings of the National Academy of Sciences , 105, 2963–2968.
Sangster, T. A., Salathia, N., Lee, H. N., Watanabe, E., Schellenberg, K., Morneau, K., … Lindquist, S. (2008). HSP90-buffered genetic variation is common in Arabidopsis thaliana . Proceedings of the National Academy of Sciences , 105, 2969-2974.
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30,1312-1313.
Stark, H., Rodnina, M.V., Wieden, H. J., Van Heel, M., & Wintermeyer, W. (2000). Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell ,100 , 301-309.
Turnbull, L. A., Rees, M., Crawley, M. J. (1999). Seed mass and the competition/colonization trade-off: a sowing experiment. Journal of Ecology, 87, 899-912.
Vasseur, F., Fouqueau, L., de Vienne, D., Nidelet, T., Violle, C., & Weigel, D. (2019). Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana . PLoS Biology ,17 (4), e3000214.
Venable, D. L., & Rees, M., (2009). The scaling of seed size.Journal of Ecology , 97, 27-31.
Wang, R., Zhang, Y., Kieffer, M., Yu, H., Kepinski, S., Estelle, M. (2016). HSP90 regulates temperature-dependent seedling growth inArabidopsis by stabilizing the auxin co-receptor F-box protein TIR1. Nature Communications , 7, 11677.
Wagner, G.P., & Zhang, J. (2011). The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms.Nature Reviews Genetics , 12 , 204-213.
Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24(18), 2098-2100.
Weibel, E. R. (2002). The pitfalls of power laws. Nature,417, 131-132.
West, G. B., Brown, J. H., & Enquist, B. J. (1997). A general model for the origin of allometric scaling laws in biology. Science,276,122-126.
West, G.B., & Brown, J.H. (2005). The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization. Journal of Experimental Biology, 208, 1575-1592.
Westoby, M., Leishman, M., & Lord, J. (1996) Comparative ecology of seed size and dispersal. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences , 351, 1309-1318.
Westoby, M., Moles, A. T., & Falster, D. S. (2009). Evolutionary coordination between offspring size at independence and adult size.Journal of Ecology, 97, 23-26.
Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, New York).
Xiao, Y., Liu, H., Wu, L., Warburton, M., and Yan, J. (2017). Genome-wide association studies in maize: praise and stargaze.Molecular Plant, 10, 359–374.
Yang, J., Bakshi, A., Zhu, Z., Hemani, G., Vinkhuyzen, A. A. E., Lee, S. H., … Visscher, P. M. (2015). Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index. Nature Genetics, 47, 1114-1120.
Yang, J., Lee, S. H., Goddard, M. E., Visscher, P. M. (2011). GCTA: a tool for genome-wide complex trait analysis. American Journal of Human Genetics, 88, 76-82.
Zhang, W., Yan, H., Chen, W., Liu, J., Jiang, C., Jiang, H., & Cheng, B. (2014). Genome-wide identification and characterization of maize expansin genes expressed in endosperm. Molecular Genetics and Genomics, 289, 1061–1074
Zhang, C., Dong, S. S., Xu, J. Y., He, W. M., & Yang, T. L. (2019) PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 35,1786–1788.
Zhou, S., Han, Y., Chen, Y., Kong, X., & Wang, W. (2015). The involvement of expansins in response to water stress during leaf development in wheat. Journal of Plant Physiology , 183, 64–74.