Software Packages

Baken, E.K., M.L. Collyer, A. Kaliontzopoulou, and D.C. Adams. 2021. geomorph v4.0 and gmShiny: enhanced analytics and a new graphical interface for a comprehensive morphometric experience. Methods in Ecology and Evolution. 12:2355–2363.

Collyer, M.L, and D.C. Adams. 2018. RRPP: An R package for fitting linear models to high-dimensional data using residual randomization. Methods in Ecology and Evolution. 9:1772-1779.

General Overview of Geometric Morphometrics

Adams, D.C., F. J. Rohlf, and D.E. Slice. 2013. A field comes of age: Geometric morphometrics in the 21st century. Hystrix. 24:7-14.

General Analytical Theory of Methods

Adams, D.C. and M.L. Collyer. 2022. Consilience of methods for phylogenetic analysis of variance. Evolution. 76:1406–1419.

Conaway, M.A., and D.C. Adams. 2022. An effect size for comparing the strength of morphological integration across studies. Evolution. 76: 2244-2259.

Collyer, M.L., and D.C. Adams. 2021. Phylogenetically aligned component analysis. Methods in Ecology and Evolution. 12:359-372.

Collyer, M.L., M.A. Davis, and D.C. Adams. 2020. Making heads or tails of combined landmark configurations in geometric morphometric data. Evolutionary Biology. 47:193-205.

Adams, D.C., and M.L. Collyer. 2019. Comparing the strength of modular signal, and evaluating alternative modular hypotheses, using covariance ratio effect sizes with morphometric data. Evolution. 73:2352-2367.

Adams, D.C., and M.L. Collyer. 2019. Phylogenetic comparative methods and the evolution of multivariate phenotypes. Annual Review of Ecology, Evolution, and Systematics. 50:405-425.

Adams, D.C. , and M.L. Collyer. 2018. Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure. Evolution. 72:1204-1215.

Adams, D.C., and M.L. Collyer. 2018. Multivariate phylogenetic comparative methods: Evaluations, comparisons, and recommendations. Systematic Biology. 67:14-31.

Adams, D.C. and M.L. Collyer. 2016. On the comparison of the strength of morphological integration across morphometric datasets. Evolution. 70:2623-2631.

Adams, D.C.. 2016. Evaluating modularity in morphometric data: Challenges with the RV coefficient and a new test measure. Methods in Ecology and Evolution. 7:565-572.

Davis, M.A., M.R. Douglas, M.L. Collyer, and M.E. Douglas. 2016. Deconstructing a species-complex: geometric morphometric and molecular analyses define species in the Western Rattlesnake (Crotalus viridis). PloS One. 11(1):e0146166.

Collyer, M.L., D.J. Sekora, and D.C. Adams. 2015. A method for analysis of phenotypic change for phenotypes described by high-dimensional data. Heredity. 115: 357-365.

Denton, J.S.S., and D.C. Adams. 2015. A new phylogenetic test for comparing multiple high-dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae). Evolution. 69:2425-2440.

Adams, D.C., and M.L. Collyer. 2015. Permutation tests for phylogenetic comparative analyses of high-dimensional shape data: what you shuffle matters. Evolution. 69:823-829.

Adams, D.C. 2014. A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data. Evolution. 68:2675-2688.

Adams, D.C. 2014. A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data. Systematic Biology. 63:685-697.

Adams, D.C. and R. Felice. 2014. Assessing phylogenetic morphological integration and trait covariation in morphometric data using evolutionary covariance matrices. PLoS One. 9(4):e94335.

Adams, D.C. 2014. Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data. Systematic Biology. 63:166-177.

Collyer, M. L., and D.C. Adams. 2013. Phenotypic trajectory analysis: Comparison of shape change patterns in evolution and ecology. Hystrix. 24:75-83.

Adams, D.C., and M.L. Collyer. 2009. A general framework for the analysis of phenotypic trajectories in evolutionary studies. Evolution. 63:1143-1154.

Adams, D. C., and M.L. Collyer. 2007. Analysis of character divergence along environmental gradients and other covariates. Evolution. 61:510-515.

Collyer, M. L., and D. C. Adams. 2007. Analysis of two-state multivariate phenotypic change in ecological studies. Ecology. 88:683-692.

Adams, D. C. 1999. Methods for shape analysis of landmark data from articulated structures. Evolutionary Ecology Research. 1:959-970.

Further Statistical Theory Reading

Commenges, D. 2003. Transformations which preserve exchangeability and application to permutation tests. Journal of Nonparametric Statistics. 15:171-185.

Anderson, M. J. (2001a). A new method for non-parametric multivariate analysis of variance. Austral Ecology. 26, 32–46.

Anderson, M. J. (2001b). Permutation tests for univariate or multivariate analysis of variance and regression. Canadian Journal of Fisheries and Aquatic Sciences, 58. 626–639.

Gower J.C. 1966. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika. 53:325–338.