Models based on the Ornstein–Uhlenbeck process have become standard for the comparative study of adaptation. Cooper et al. (2016) have cast doubt on this practice by claiming statistical problems with fitting Ornstein–Uhlenbeck models to comparative data. Specifically, they claim that statistical tests of Brownian motion may have too high Type I error rates and that such error rates are exacerbated by measurement error. In this note, we argue that these results have little relevance to the estimation of adaptation with Ornstein–Uhlenbeck models for three reasons. First, we point out that Cooper et al. (2016) did not consider the detection of distinct optima (e.g. for different environments), and therefore did not evaluate the standard test for adaptation. Second, we show that consideration of parameter estimates, and not just statistical significance, will usually lead to correct inferences about evolutionary dynamics. Third, we show that bias due to measurement error can be corrected for by standard methods. We conclude that Cooper et al. (2016) have not identified any statistical problems specific to Ornstein–Uhlenbeck models, and that their cautions against their use in comparative analyses are unfounded and misleading. [adaptation, Ornstein–Uhlenbeck model, phylogenetic comparative method.]
The advent of fast computational algorithms for phylogenetic comparative methods allows for considering multiple hypotheses concerning the co-adaptation of traits and also for studying if it is possible to distinguish between such models based on contemporary species measurements. Here we demonstrate how one can perform a study with multiple competing hypotheses using mvSLOUCH by analyzing two data sets, one concerning feeding styles and oral morphology in ungulates, and the other concerning fruit evolution in Ferula (Apiaceae). We also perform simulations to determine if it is possible to distinguish between various adaptive hypotheses. We find that Akaike’s information criterion corrected for small sample size has the ability to distinguish between most pairs of considered models. However, in some cases there seems to be bias towards Brownian motion or simpler Ornstein–Uhlenbeck models. We also find that measurement error and forcing the sign of the diagonal of the drift matrix for an Ornstein–Uhlenbeck process influences identifiability capabilities. It is a cliché that some models, despite being imperfect, are more useful than others. Nonetheless, having a much larger repertoire of models will surely lead to a better understanding of the natural world, as it will allow for dissecting in what ways they are wrong. [Adaptation; AICc; model selection; multivariate Ornstein–Uhlenbeck process; multivariate phylogenetic comparative methods; mvSLOUCH.]
more » « less- Award ID(s):
- 2225683
- NSF-PAR ID:
- 10487316
- Editor(s):
- Beaulieu, Jeremy
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Systematic Biology
- Volume:
- 72
- Issue:
- 2
- ISSN:
- 1063-5157
- Page Range / eLocation ID:
- 275 to 293
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract -
ABSTRACT Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require data collection from many species, a challenge when this is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework – the Ornstein–Uhlenbeck process – that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate use of the model through studying the evolution of thermal physiology in treefrogs. Frogs of the family Hylidae have twice colonized the temperate zone from the tropics, and such colonization likely involved a fundamental change in physiology due to colder and more seasonal temperatures. However, which traits changed to allow colonization is unclear. We measured cold tolerance and characterized thermal performance curves in jumping for 12 species of treefrogs distributed from the Neotropics to temperate North America. We then conducted phylogenetic comparative analyses to examine how tolerances and performance curves evolved and to test whether that evolution was adaptive. We found that tolerance to low temperatures increased with the transition to the temperate zone. In contrast, jumping well at colder temperatures was unrelated to biogeography and thus did not adapt during dispersal. Overall, our study shows how comparative phylogenetic methods can be leveraged in biomechanics and physiology to test the evolutionary drivers of variation among species.more » « less
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Abstract How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining “microbiome traits”, we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein‐Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.
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Premise Male gametophytes of most seed plants deliver sperm to eggs via a pollen tube. Pollen tube growth rates (
PTGR s) of angiosperms are exceptionally rapid, a pattern attributed to more effective haploid selection under stronger pollen competition. Paradoxically, whole genome duplication (WGD ) has been common in angiosperms but rare in gymnosperms. Pollen tube polyploidy should initially acceleratePTGR because increased heterozygosity and gene dosage should increase metabolic rates. However, polyploidy should also independently increase tube cell size, causing more work which should decelerate growth. We asked how genome size changes have affected the evolution of seed plantPTGR s.Methods We assembled a phylogenetic tree of 451 species with known
PTGR s. We then used comparative phylogenetic methods to detect effects of neo‐polyploidy (within‐genus origins),DNA content, andWGD history onPTGR , and correlated evolution ofPTGR andDNA content.Results Gymnosperms had significantly higher
DNA content and slowerPTGR optima than angiosperms, and theirPTGR andDNA content were negatively correlated. For angiosperms, 89% of model weight favored Ornstein‐Uhlenbeck models with a fasterPTGR optimum for neo‐polyploids, whereasPTGR andDNA content were not correlated. For within‐genus and intraspecific‐cytotype pairs,PTGR s of neo‐polyploids < paleo‐polyploids.Conclusions Genome size increases should negatively affect
PTGR when genetic consequences ofWGD s are minimized, as found in intra‐specific autopolyploids (low heterosis) and gymnosperms (fewWGD s). But in angiosperms, the higherPTGR optimum of neo‐polyploids and non‐negativePTGR ‐DNA content correlation suggest that recurrentWGD s have caused substantialPTGR evolution in a non‐haploid state. -
These are the Supplementary Material, R scripts and numerical results accompanying Bartoszek, Fuentes Gonzalez, Mitov, Pienaar, Piwczyński, Puchałka, Spalik and Voje "Model Selection Performance in Phylogenetic Comparative Methods under multivariate Ornstein–Uhlenbeck Models of Trait Evolution". The four data files concern two datasets. Ungulates: measurements of muzzle width, unworn lower third molar crown height, unworn lower third molar crown width and feeding style and their phylogeny; Ferula: measurements of ratio of canals, periderm thickness, wing area, wing thickness, and fruit mass, and their phylogeny.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/sysbio/syac079
