Adaptation & the phylogenetic comparative method

In a long term collaboration with Thomas Hansen, Kzrysztof Bartozek, Jesualdo Fuentes Gonzalez, Staffan Andersson and others, we develop phylogenetic comparative methods based on processes that are compatible with trait adaptation. We also use these methods on a variety of organisms, and in the process get to learn about so many different biological systems and collaborate with a variety of specialists for organisms and traits ranging through plant genomes, fish body shapes, lizard thermobiology, trade-offs between bird tail lengths and patch sizes (see figure above), primate brain sizes and so on.

Supported by an NSF CAREER award # 2225683

relevant publications

PCM METHOD development

Bartoszek K, Fuentes-González JA, Mitov V, Pienaar J, Piwczynsky M, Puchalka R, Spalik K, Voje KL (2024) Fast mvSLOUCH: Ornstein-Uhlenbeck based models of trait evolution on large phylogenies. Methods in Ecology and Evolution 15(9),1507-1515. https://doi.org/10.1111/2041-210X.14376

Bartoszek K, Fuentes-González JA, Mitov V, Pienaar J, Piwczyński M, Puchałka R, Spalik K. and Voje K (2024). Analytical advances alleviate model misspecification in non-Brownian multivariate comparative methods. Evolution, 78(3), 389-400. https://doi.org/10.1093/evolut/qpad185

Grabowsky M, Pienaar J, Voje K, Andersson S, Fuentes-González JA, Kopperud B, Moen DS, Tsuboi M, Uyeda J & Hansen TF. (2023) A cautionary note on “a cautionary note on the use of Ornstein-Uhlenbeck models” in macroevolutionary studies. Systematic Biology 72(4), 955-963. https://doi.org/10.1093/sysbio/syad012

Bartoszek K, Clarke J, Fuentes-González JA & Pienaar J. (2023) mvSLOUCH multivariate Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses. R package V 2.7.6 10.32614/CRAN.package.mvSLOUCH

Bartoszek K, Fuentes-González JA*, Mitov V, Pienaar J, Piwczynsky M, Puchalka R, Spalik K, Voje K. (2022) Model Selection Performance in Phylogenetic Comparative Methods under multivariate Ornstein-Uhlenbeck Models of Trait Evolution. Systematic Biology 72(2): 275-293 https://doi.org/10.1093/sysbio/syac079

Kopperud BT, Pienaar J, Voje K, Orzack SH, Hansen TF & M Grabowski (2020) SLOUCH Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses. R package V 2.1.2 http://github.com/kopperud/slouch

Bartoszek, J. Pienaar, P. Mostad, S. Andersson, and T. F. Hansen. (2012) A phylogenetic comparative method for studying multivariate adaptation. In: Journal of Theoretical Biology 314: 204–215.http://dx.doi.org/10.1016/j.jtbi.2012.08.005

Hansen TF, Pienaar J. & Orzack SH (2008) A comparative method for studying adaptation to a randomly evolving environment. Evolution 62: 1965-1977. https://doi.org/10.1111/j.1558-5646.2008.00412.x

Pienaar J, Orzack SH & Hansen TF (2008) SLOUCH Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses. R code & Manual V 1.0. https://freshpond.org/software/SLOUCH/

PCM analyses

Adams PE, Milwood JD, Sutton JM, Pienaar J & Fierst JL. (2023). Genome size changes by duplication, insertion and divergence in Caenorhabditis worms. Molecular Biology and Evolution 40(3) msad039 https://doi.org/10.1093/molbev/msad039

Sasha E. Greenspan, Peloso P, Fuentes-González JA, Bletz M, Lyra ML, Machado IF, Martins RA, Medina D, Moura-Campos D, Neely WJ, Preuss J, Sturaro MJ, Vaz RI, Navas CA, Toledo LF, Tozetti AM, Vences M, Woodhams DC, Haddad CFB, Pienaar J & Becker GC. (2022) Low microbiome diversity in threatened amphibians from two biodiversity hotspots.   Animal Microbiome 4(1), 1-9 https://doi.org/10.1186/s42523-022-00220-w

García-Cabello KN, Fuentes-González JA, Saleh-Subaie N, Pienaar J & Zúñiga-Vega JJ (2022). Increased superfetation precedes the evolution of advanced degrees of placentotrophy in viviparous fishes of the family Poeciliidae. Biology Letters, 18(10), 20220173 https://doi.org/10.1098/rsbl.2022.0173

Styga JM, Pienaar J, Scott PA & Earley RL (2019). Does body shape in Fundulus adapt to variation in habitat salinity? Frontiers in Physiology (Aquatic Physiology) 10: 1400.

Turberville CM, Fuentes-González JA, Rogers S, & Pienaar J. (2021). Moss phyllid morphology varies systematically with substrate slope. Plant Ecology and Evolution, 154(3), 419-431. https://doi.org/10.5091/plecevo.2021.1839

Pienaar, J., Ilany, A., Geffen E., & Yom-Tov, Y. (2013) Macroevolution of life history traits in passerine birds: adaptation and phylogenetic inertia. Ecology Letters 16: 571-576.

Davis, R. B., Javois, J., Pienaar, J., Ounap, E. & Tammaru, T. (2012) Disentangling determinants of egg size using an advanced phylogenetic comparative method: Maternal body size is the primary factor in geometrid moths. Journal of Evolutionary Biology 25: 210-219.

Uyeda, J. C., Hansen, T. F., Arnold, S. J. & Pienaar, J. (2011) The million year wait for macroevolutionary bursts. Proceedings of the National Academy of Sciences 108: 15908-15913.

Labra, A., Pienaar, J. & Hansen, T. F. (2009) Evolution of thermal physiology in liolaemus lizards: adaptation, phylogenetic inertia and niche tracking. The American Naturalist 174: 204-220.

Butler, M; O’Meara, B.C. & Pienaar, J. Comparative methods and data analysis in R (2008) University of Hawaii, online publication