BBMV: an R package for the estimation of macroevolutionary landscapes

Boucher, Florian C.

doi:10.1111/ecog.04045

Cited by 8 publications

(17 citation statements)

References 24 publications

(38 reference statements)

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“…2018), which relies on inferring an evolutionary potential that biases the underlying random walk of all lineages toward different regions of morphospace. This model, as well as the previously described BBM, can be thought of as special cases of a general model (BBMV; Boucher 2019) that combines the attractive force of the evolutionary potential with maximum and minimum trait boundaries.…”

Section: Methodsmentioning

confidence: 99%

“…More recently, alternative ways to conceptualize adaptive landscapes have been introduced (Boucher et al. 2018; Boucher 2019). These approaches assume lineages are simultaneously influenced by all adaptive optima, thus deviating from the traditional interpretation that macroevolutionary adaptive landscapes are dynamic and punctuated by innovation (Simpson 1944; Uyeda et al.…”

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confidence: 99%

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Exploring adaptive landscapes across deep time: A case study using echinoid body size

Koch

2021

Evolution

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Adaptive landscapes are a common way of conceptualizing the phenotypic evolution of lineages across deep time. Although multiple approaches exist to implement this concept into operational models of trait evolution, inferring adaptive landscapes from comparative datasets remains challenging. Here, I explore the macroevolutionary dynamics of echinoid body size using data from over 5000 specimens and a phylogenetic framework incorporating a dense fossil sampling and spanning approximately 270 million years. Furthermore, I implement a novel approach of exploring alternative parameterizations of adaptive landscapes that succeeds in finding simpler, yet better‐fitting models. Echinoid body size has been constrained to evolve within a single adaptive optimum for much of the clade's history. However, most of the morphological disparity of echinoids was generated by multiple regime shifts that drove the repeated evolution of miniaturized and gigantic forms. Events of body size innovation occurred predominantly in the Late Cretaceous and were followed by a drastic slowdown following the Cretaceous‐Paleogene mass extinction. The discovery of these patterns is contingent upon directly sampling fossil taxa. The macroevolution of echinoid body size is therefore characterized by a late increase in disparity (likely linked to an expansion of ecospace), generated by active processes driving lineages toward extreme morphologies.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Exploring adaptive landscapes across deep time: A case study using echinoid body size

Koch

2021

Evolution

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“…This is achieved by inferring an evolutionary potential, which biases the underlying random walk of all lineages towards different regions of morphospace. This model, as well as the previously described BBM can be thought of as special cases of a general model (BBMV; Boucher 2019) that combines the attractive force of the evolutionary potential with maximum and minimum trait boundaries.…”

Section: Methodsmentioning

confidence: 99%

“…Model fitting relied on packages geiger (Harmon et al 2008), BBMV (Boucher 2019), pulsR (Landis and Schraiber 2017), SURFACE (Ingram and Mahler 2013) and OUwie (Beaulieu and O’Meara 2019). We compared the fit of all of the models described above through the use of AICc weights.…”

Section: Methodsmentioning

confidence: 99%

“…We compared the fit of all of the models described above through the use of AICc weights. For BBMV, the shape of the evolutionary potential was estimated using one, two and three free parameters (Boucher 2019), and only the best option was included in the final model comparison. Similarly, for the pulsed models, the fit of the JN, NIG, BMJN and BMNIG models was first compared and only the best was used for model selection (Landis and Schraiber 2017).…”

Section: Methodsmentioning

confidence: 99%

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A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Koch

Thompson

2020

Preprint

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12Several unique properties of echinoids (sea urchins) make them useful for exploring 13 macroevolutionary dynamics, including their remarkable fossil record that can be incorporated 14 into explicit phylogenetic hypotheses. However, this potential cannot be exploited without a 15 robust resolution of the echinoid tree of life. We revisit the phylogeny of crown group 16 Echinoidea using both the largest phylogenomic dataset compiled for the clade, as well as a 17 large-scale morphological matrix with a dense fossil sampling. We also gather a new 18 compendium of both tip and node age constraints, allowing us to combine phylogenomic, 19 morphological and stratigraphic data using a total-evidence dating approach. For this, we 20 develop a novel method for subsampling phylogenomic datasets that selects loci with high 21 phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our approach 22 restructure much of the higher-level phylogeny of echinoids, and demonstrates that combining 23 different data sources increases topological accuracy. We are able to resolve multiple alleged 24 conflicts between molecular and morphological datasets, such as the position of Echinothurioida 25 and Echinoneoida, as well as unravelling the relationships between sand dollars and their closest 26 relatives. We then use this topology to trace the evolutionary history of echinoid body size 27 through more than 270 million years, revealing a complex pattern of convergent evolution to 28 stable peaks in macroevolutionary adaptive landscape. Our efforts show how combining 29 phylogenomic and paleontological evidence offers new ways of exploring evolutionary forces 30 operating across deep timescales.31 32

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Stabilized Morphological Evolution of Spiders Despite Mosaic Changes in Foraging Ecology

et al. 2022

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A prominent question in animal research is how the evolution of morphology and ecology interact in the generation of phenotypic diversity. Spiders are some of the most abundant arthropod predators in terrestrial ecosystems and exhibit a diversity of foraging styles. It remains unclear how spider body size and proportions relate to foraging style, and if the use of webs as prey capture devices correlates with changes in body characteristics. Here we present the most extensive dataset to date of morphometric and ecological traits in spiders. We used this dataset to estimate the change in spider body sizes and shapes over deep time and to test if and how spider phenotypes are correlated with their behavioural ecology. We found that phylogenetic variation of most traits best fitted an Ornstein-Uhlenbeck model, which is a model of stabilizing selection. A prominent exception was body length, whose evolutionary dynamics were best explained with a Brownian Motion (free trait diffusion) model. This was most expressed in the araneoid clade (ecribellate orb-weaving spiders and allies) that showed bimodal trends towards either miniaturization or gigantism. Only few traits differed significantly between ecological guilds, most prominently leg length and thickness, and although a multivariate framework found general differences in traits among ecological guilds, it was not possible to unequivocally associate a set of morphometric traits with the relative ecological mode. Long, thin legs have often evolved with aerial webs and a hanging (suspended) locomotion style, but this trend is not general. Eye size and fang length did not differ between ecological guilds, rejecting the hypothesis that webs reduce the need for visual cue recognition and prey immobilization. For the inference of the ecology of species with unknown behaviours, we propose not to use morphometric traits, but rather consult (micro-)morphological characters, such as the presence of certain podal structures. These results suggest that, in contrast to insects, the evolution of body proportions in spiders is unusually stabilized, and ecological adaptations are dominantly realized by behavioural traits and extended phenotypes in this group of predators. This work demonstrates the power of combining recent advances in phylogenomics with trait-based approaches to better understand global functional diversity patterns through space and time.

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BBMV: an R package for the estimation of macroevolutionary landscapes

Cited by 8 publications

References 24 publications

Exploring adaptive landscapes across deep time: A case study using echinoid body size

Exploring adaptive landscapes across deep time: A case study using echinoid body size

A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Stabilized Morphological Evolution of Spiders Despite Mosaic Changes in Foraging Ecology

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