Data from: On measurements of phenotypic parallel evolution
Data files
May 23, 2025 version files 19.59 KB
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Dial_2016.csv
2.64 KB
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README.md
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Sup1_R_code.rmd
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Abstract
Several metrics have been proposed to measure phenotypic parallel evolution. All of these metrics stem from a geometric definition of parallel evolution in which two evolutionary trajectories are, literally, parallel or non-parallel to each other. Two metrics fit this definition: the interaction term between population and habitat in a two-factor ANOVA and a measure of the angle between two multivariate trajectories of evolution. A third metric is derived from the general direction of multivariate trajectories; although this might fit our intuition about parallel evolution, it does not fit the geometric definition. A fourth metric is based on the amount of variation explained by the habitat variable in a one-factor ANOVA (i.e., the R2). We show here that the R2 metric does not reliably measure any aspect of parallelism and should be avoided. We also discuss the importance of establishing proper ancestor-descendent relationships in attempting to use any of the valid metrics to quantify parallel evolution. Finally, because different metrics measure different aspects of evolutionary trajectories, we recommend being explicit about what one is trying to measure (angle, direction, or length of trajectories).
https://doi.org/10.5061/dryad.ksn02v7g2
Description of the data and file structure
R code described in the publication:
Arendt, J., Travis, J., and Reznick, D. On measurements of phenotypic parallel evolution. The American Naturalist.
Contact information for Jeff Arendt
Summary
We discuss several metrics proposed for measuring parallelism in evolutionary trajectories. One of these, the R2 metric, does not actually measure parallelism as suggested by the originators. Rather, we suggest using a fully factorial ANOVA including habitat, replicate populations, and their interaction as factors. The interaction term can be used as an inverse measure of parallelism. That is, if the interaction term is not significant, then we can conclude that independent replicate populations have shown parallel adaptations to the habitat variable. To obtain a continuous metric of just how parallel these trajectories are, we suggest using the partial-Eta2 for the interaction term. The closer this metric is to zero, the more parallel the trajectories are. The files provided include R code for calculating partial-Eta2 and several examples.
The data provided for the examples are abridged from:
Dial, T. R., D. N. Reznick, and E. L. Brainerd. 2016. Effects of neonatal size on maturity and escape performance in the Trinidadian guppy. Functional Ecology 30:943-952.
Files included:
Supplement 1_R code A R markdown file for calculating partial-Eta2. The code demonstrates how to estimate and interpret partial-η² to assess the degree of parallel evolution (how similar trait changes are across environments/populations).
Dial 2016.csv A csv file of the data used in the examples.
Column heading: Description of data
- replicate Aripo or Oropuche, two rivers in Trinidad
- habitat HP for high predation, LP for low predation population within each river
- body length standard length of each fish in mm, ln-transformed
- tail_fin_length length of the caudal fin in mm, ln-transformed
- body_depth body depth of each fish in mm, ln-transformed
We used version 4.4.1 of R to run these examples.
For the analyses in the main paper and in Supplement 2, we downloaded datasets from Dryad. The following papers are the sources for these datasets:
- Brask, J. B., D. P. Croft, M. Edenbrow, R. James, B. H. Bleakley, I. W. Ramnarine, R. J. P. Heathcote et al. 2019. Evolution of non-kin cooperation: social assortment by cooperative phenotype in guppies. Royal Society Open Science 6:181493.
- Dalziel, A. C., T. H. Vines, and P. M. Schulte. 2011. Reductions in prolonged swimming capacity following freshwater colonization in multiple threespine stickleback populations. Evolution 66:1226-1239.
- de Lira, J. J. P. R., Y. Yan, S. Levasseur, C. D. Kellly, and A. P. Hendry. 2021. The complex ecology of genitalia: Gonopodium length and allometry in the Trinidadian guppy. Ecology and Evolution 11:4564-4576.
- Dial, T. R., L. P. Hernandez, and E. L. Brainerd. 2017. Morphological and functional maturity of the oral jaws covary with offspring size in Trinidadian guppies. Scientific Reports 7:1-10.
- Dial, T. R., D. N. Reznick, and E. L. Brainerd. 2016. Effects of neonatal size on maturity and escape performance in the Trinidadian guppy. Functional Ecology 30:943-952.
- Edenbrow, M., B. H. Bleakley, S. K. Darden, C. R. Tyler, I. W. Ramnarine, and D. P. Croft. 2017. The evolution of cooperation: Interacting phenotypes and social partners. The American
- Naturalist 189:630-643.
- Evans, M. L., and L. Bernatchez. 2012. Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and nonparallel physiological divergence. Journal of Evolutionary Biology 25:1823-1834.
- Evans, M. L., K. Praebel, S. Peruzzi, and L. Bernatchez. 2012. Parallelism in the oxygen transport system of the lake whitefish: the role of physiological divergence in ecological speciation. Molecular Ecology 21:4038-4050.
- Fischer, E. K., C. K. Ghalambor, and K. L. Hoke. 2016. Plasticity and evolution in correlated suites of traits. Journal of Evolutionary Biology 29:991-1002.
- Furness, A. I., M. R. Walsh, and D. N. Reznick. 2012. Convergence of life-history phenotypes in a Trinidadian killifish (Rivulus hartii). Evolution 66:1240-1254.
- Herbert-Read, J. E., E. Rosen, A. Szorkovsky, C. C. Ioannou, B. Rogell, A. Perna, I. W.
- Ramnarine et al. 2017. How predation shapes the social interaction rules of shoaling fish. Proceedings of the Royal Society of London, series B 284:20171126.
- Herbert-Read, J. E., A. S. I. Wade, I. W. Ramnarine, and C. C. Ioannou. 2019. Collective decision-making appears more egalitarian in populations where group fission costs are higher. Biology Letters 15:20190556.
- Kaeuffer, R., C. L. Peichel, D. I. Bolnick, and A. P. Hendry. 2011. Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback. Evolution 66:402-418.
- Reddon, A. R., L. Chouinard-Thuly, I. Leris, and S. M. Reader. 2018. Wild and laboratory exposure to cues of predation risk increases relative brain mass in male guppies. Functional Ecology 32:1847-1856.
- Sandkam, B., C. M. Young, and F. Breden. 2015. Beauty in the eyes of the beholders: colour vision is tuned to mate preference in the Trinidadian guppy (Poecilia reticulata). Molecular Ecology 24:596-609.
- Stephenson, J. F., C. Van Oosterhout, and J. Cable. 2015. Pace of life, predators and parasites: predator-induced life-history evolution in Trinidadian guppies predicts decrease in parasite tolerance. Biology Letters 11:20150806.
- Tobler, M., M. Palacios, L. J. Chapman, I. Mitrofanov, D. Bierbach, M. Plath, L. Arias-Rodriguez et al. 2011. Evolution in extreme environments: replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs. Evolution 65:2213-2228.
- Torres-Dowdall, J., C. A. Handelsman, D. N. Reznick, and C. K. Ghalambor. 2012. Local adaptation and the evolution of phenotypic plasticity in Trinidadian guppies (Poecilia reticulata). Evolution 66:3432-3443.
Data from the paper
Dial, T. R., D. N. Reznick, and E. L. Brainerd. 2016. Effects of neonatal size on maturity and escape performance in the Trinidadian guppy. Functional Ecology 30:943-952, were downloaded from Dryad and trimmed to the first three columns, and rows with missing data.