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Within-species trait variation may be the result of genetic variation, environmental variation, or measurement error, for example. In phylogenetic comparative studies, failing to account for within-species variation has many adverse effects, such as increased error in testing hypotheses about evolutionary correlations, biased estimates of evolutionary rates, and inaccurate inference of the mode of evolution. These adverse effects were demonstrated in studies that considered a tree-like underlying phylogeny. Comparative methods on phylogenetic networks are still in their infancy. The impact of within-species variation on network-based methods has not been studied. Here, we introduce a phylogenetic linear model in which the phylogeny can be a network to account for within-species variation in the continuous response trait assuming equal within-species variances across species. We show how inference based on the individual values can be reduced to a problem using species-level summaries, even when the within-species variance is estimated. Our method performs well under various simulation settings and is robust when within-species variances are unequal across species. When phenotypic (within-species) correlations differ from evolutionary (between-species) correlations, estimates of evolutionary coefficients are pulled towards the phenotypic coefficients for all methods we tested. Also, evolutionary rates are either underestimated or overestimated, depending on the mismatch between phenotypic and evolutionary relationships. We applied our method to morphological and geographical data from Polemonium. We find a strong negative correlation of leaflet size with elevation, despite a positive correlation within species. Our method can explore the role of gene flow in trait evolution by comparing the fit of a network to that of a tree. We find marginal evidence for leaflet size being affected by gene flow and support for previous observations on the challenges of using individual continuous traits to infer inheritance weights at reticulations. Our method is freely available in the Julia package PhyloNetworks.
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A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree
Numerous questions in phylogenetic comparative biology revolve around the correlated evolution of two or more phenotypic traits on a phylogeny. In many cases, it may be sufficient to assume a constant value for the evolutionary correlation between characters across all the clades and branches of the tree. Under other circumstances, however, it is desirable or necessary to account for the possibility that the evolutionary correlation differs through time or in different sections of the phylogeny. Here, we present a method designed to fit a hierarchical series of models for heterogeneity in the evolutionary rates and correlation of two quantitative traits on a phylogenetic tree. We apply the method to two datasets: one for different attributes of the buccal morphology in sunfishes (Centrarchidae); and a second for overall body length and relative body depth in rock- and non-rock-dwelling South American iguanian lizards. We also examine the performance of the method for parameter estimation and model selection using a small set of numerical simulations.
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- Award ID(s):
- 1759940
- PAR ID:
- 10391207
- Date Published:
- Journal Name:
- PeerJ
- Volume:
- 10
- ISSN:
- 2167-8359
- Page Range / eLocation ID:
- e13910
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Background and Aims Wind pollination has evolved repeatedly in flowering plants, yet the identification of a wind pollination syndrome as a set of integrated floral traits can be elusive. Thalictrum (Ranunculaceae) comprises temperate perennial herbs that have transitioned repeatedly from insect to wind pollination while also exhibiting mixed pollination, providing an ideal system to test for evolutionary correlation between floral morphology and pollination mode in a biotic to abiotic continuum. Moreover, the lack of floral organ fusion across this genus additionally allows to test for specialization to pollination vectors in the absence of this feature. Methods We expanded phylogenetic sampling in the genus from a previous study using six chloroplast loci, which allowed us to test whether species cluster into distinct pollination syndromes based on floral morphology. We then used multivariate analyses on floral traits, followed by ancestral state reconstruction of the emerging flower morphotypes and determined whether these traits are evolutionarily correlated under a Bayesian framework with Brownian motion. Key Results Floral traits fell into five distinct clusters, which were reduced to three after considering phylogenetic relatedness, and were largely consistent with flower morphotypes and associated pollination vectors. Multivariate evolutionary analyses found a positive correlation between the lengths of floral reproductive structures (styles, stigmas, filaments, and anthers). Shorter reproductive structures tracked insect-pollinated species and clades in the phylogeny while longer structures tracked wind-pollinated ones, consistent with selective pressures exerted by biotic vs. abiotic pollination vectors, respectively. Conclusions While detectable suites of integrated floral traits across Thalictrum correlated with wind or insect pollination at the extremes of the morphospace distribution, a presumed intermediate, mixed pollination mode morphospace was also detected. Thus, our data broadly support the existence of detectable flower morphotypes from convergent evolution underlying pollination mode evolution in Thalictrum, presumably via different paths from an ancestral mixed pollination state.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.7717/peerj.13910
