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 physiology , 166, 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.