Biology subjects

Beaulieu, J. M.

Publications and source records attributed to Beaulieu, J. M..

9 recordsLinked to original sources

bioRxiv2026

A fossilized birth-death model for fossil records lacking sampled ancestors

Fossilized birth-death (FBD) models provide a powerful framework for estimating diversification from phylogenies that include fossil taxa. However, the original formulation makes a key assumption that sampled ancestors (k-type fossils) should be commonly observed. Beaulieu & OMeara (2023) showed that this assumption is often violated in empirical datasets, where fossils are represented mostly or entirely as extinct terminal taxa (m-type fossils), which can lead to biased parameter estimates. Here, we derive the fossilized birth-death of terminal fossils (FBDT) model, an extension of the FBD that accommodates incomplete fossil samples in which only terminal fossil occurrences are observed. We implement the model within the state-dependent speciation and extinction (SSE) framework and evaluate its performance using simulations spanning homogeneous and heterogeneous diversification scenarios. Across a wide range of fossil sampling rates, the FBDT model recovered diversification parameters that closely matched those obtained from complete fossil samples while avoiding the systematic biases that arise when sampled ancestors are unobserved. These results demonstrate that modifying the likelihood to reflect how fossil datasets are assembled provides a simple and effective extension of the FBD framework for many empirical applications.

evolutionary biology↗

bioRxiv2026

Fluoxetine-induced neurogenesis and chronic antidepressant effects requires the dopamine D2 receptor.

Major depressive disorder (MDD) is a common psychiatric illness with a high proportion of patients being nonresponsive to therapy. Selective serotonin reuptake inhibitors (SSRI) are widely prescribed for treating depression. Chronic SSRI administration is needed for therapeutic effects, a process implicating in part, increased neurogenesis in the hippocampus. Recent genome wide association studies (GWAS) identified the DrD2 locus, which encodes the dopamine D2 receptor (D2R) as a major risk factor in MDD. Here we demonstrate that behavioural effects associated with chronic administration of the SSRI drug fluoxetine and its accompanying neurogenic effects require D2R. Administration of fluoxetine to congenital D2R-knockout mice, or co-administration of the antidepressant with the antipsychotic D2R antagonist drug haloperidol prevented the neurogenic effects of fluoxetine. Furthermore, while acute behavioural responses to fluoxetine did not require D2R, this receptor was essential for the behavioural effects of chronic fluoxetine. The neurogenic impact of chronic fluoxetine was further associated with beta-arrestin 2-mediated signalling and the hippocampal regulation of the pro-neurogenic factor BDNF. These results support a role of D2R in regulating the therapeutically relevant chronic effects of fluoxetine on mood, BDNF signalling, and associated hippocampal neurogenesis. Furthermore, our findings suggest an unappreciated interaction between genetic risk for MDD and treatment responsiveness as well as a negative interaction between SSRIs and antipsychotic drugs in the regulation of hippocampal neurogenesis.

neuroscience↗

bioRxiv2025

Longevity in plants impacts phylogenetic and population dynamics

Many long-lived plant species exhibit notable patterns in phylogenies, such as short molecular branch lengths and high gene-tree conflict. However, it is not clear what biological properties of long-lived plant species or concomitant processes acting within these lineages generate these patterns. To explore this mystery, we implemented an agent-based model and conducted simulations to investigate how longevity affects molecular evolution and population dynamics. Through these simulations, we demonstrated that the patterns exhibited in empirical datasets for long-lived species can be explained by their lifespan and overlapping generations. We also show that somatic mutations can exacerbate these patterns, although evidence for substantive rates in empirical systems high enough to impact phylogenetic patterns is scarce. We discuss several empirical datasets containing life history shifts that exhibit diverse phylogenomic patterns. The variation produced through different parameterizations of our simulations reflects the diversity of patterns found in empirical datasets. Our results have broad implications for phylogenomic patterns and population genetics in general, as well as for specifically explaining patterns of evolution in long-lived lineages.

evolutionary biology↗

bioRxiv2024

Navigating "tip fog": Embracing uncertainty in tip measurements

Nature is full of messy variation, which serves as the raw material for evolution. However, in comparative biology this variation is smoothed into averages. Overlooking this variation not only weakens our analyses but also risks selecting inaccurate models, generating false precision in parameter estimates, and creating artificial patterns. Furthermore, the complexity of uncertainty extends beyond traditional "measurement error," encompassing various sources of intraspecific variance. To address this, we propose the term "tip fog" to describe the variance between the true species mean and what is recorded, without implying a specific mechanism. We show why accounting for tip fog remains critical by showing its impact on continuous comparative models and discrete comparative and diversification models. We rederive methods to estimate this variance and use simulations to assess its feasibility and importance in a comparative context. Our findings reveal that ignoring tip fog substantially affects the accuracy of rate estimates, with higher tip fog levels showing greater biases from the true rates, as well as affecting which models are chosen. The findings underscore the importance of model selection and the potential consequences of neglecting tip fog, providing insights for improving the accuracy of comparative methods in evolutionary biology.

evolutionary biology↗

bioRxiv2023

Historical causes for the greater proportion of polyploid plants in higher latitudes

Premise of the StudyThe proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aim to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assess whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization). MethodsWe reconstruct the ploidy states and ancestral niches of 1,032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We use ancestral niche reconstruction models alongside a customized discrete character evolution model to allow reconstruction of states at specific time slices. Patterns of latitudinal movement are reconstructed and compared in relation to inferred ploidy shifts. Key ResultsWe find that no single hypothesis applies equally well across all analyzed clades. While significant differences in median latitudinal occurrence were detected in the largest clade, Pooideae, no significant differences were detected in latitudinal movement in any clade. ConclusionsOur preliminary study is the first to attempt to connect ploidy changes to continuous latitudinal movement, but we cannot favor one hypothesis over another. Given that patterns seem to be clade-specific, a larger number of clades must be analyzed in future studies for generalities to be drawn.

plant biology↗

bioRxiv2021

Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity

The fossilized birth-death (FBD) model is a naturally appealing way of directly incorporating fossil information when estimating diversification rates. However, an important yet often overlooked property of the original FBD derivation is that it distinguishes between two types of sampled lineages. Here we first discuss and demonstrate the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants. We then explore the benefits of including fossils, generally, by implementing and then testing two-types of FBD models, including one that converts a fossil set into stratigraphic ranges, in more complex likelihood-based models that assume multiple rate classes across the tree. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperforms analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. Similarly, we found that converting the fossil set to stratigraphic ranges, which is one way to remedy the effects of undercounting the number of k-type fossils, results in turnover rates and extinction fraction estimates that are generally underestimated. While fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.

evolutionary biology↗

bioRxiv2021

Hidden-state-only speciation and extinction models provide accurate tip estimates of diversification rates

Estimates of diversification rates at the tips of a phylogeny provide a flexible approach for correlation analyses with multiple traits and to map diversification rates in space, while also avoiding the uncertainty of deep time rate reconstructions. Available methods for tip rate estimation make different assumptions, and thus their accuracy usually depends on characteristics of the underlying model generating the tree. Here we introduce MiSSE, a trait-free, state-dependent speciation and extinction approach that can be used to estimate varying speciation, extinction, net-diversification, turnover rates, and extinction fraction at the tips of the tree. We compare the accuracy of tip rates inferred by MiSSE against similar methods and demonstrate that, due to certain characteristics of the model, the error is generally low across a broad range of speciation and extinction scenarios. MiSSE can be used alongside regular phylogenetic comparative methods in trait related diversification hypotheses, and we also describe a simple correction to avoid pseudoreplication from sister tips in analyses of independent contrasts. Finally, we demonstrate the capabilities of MiSSE, with a renewed focus on classic comparative methods, to examine correlation between plant height and turnover rates in eucalypts, a species-rich lineage of flowering plants.

evolutionary biology↗

bioRxiv2019

Comparative analyses of phenotypic sequences using phylogenetic trees

Phenotypic sequences are a type of multivariate trait organized structurally, such as teeth distributed along the dental arch, or temporally, such as the stages of an ontogenetic series. However, unlike other multivariate traits, the elements of a phenotypic sequence are arranged along a vector, which allows for distinct evolutionary patterns between neighboring and distant positions. In fact, sequence traits share many characteristics with molecular sequences. We implement an approach to estimate rates of trait evolution that explicitly incorporates the sequence organization of traits. We apply models to study the temporal pattern evolution of cricket calling songs. We test whether songs show autocorrelation of rates (i.e., neighboring positions along a phenotypic sequence have correlated rates of evolution), or if they are best described by rate variation independent of sequence position. Our results show that models perform well when used with sequence phenotypes even under small sample sizes. We also show that silent regions of the songs evolve faster than chirp regions, which suggests that macroevolutionary changes are faster when associated with axes of variation less constrained by multiple sources of selection. Our approach is flexible and can be applied to any multivariate trait with units organized in a sequence-like structure.

evolutionary biology↗

bioRxiv2018

Freshwater diatoms diversify faster than marine in both planktonic and benthic habitats

Many clades that span the marine-freshwater boundary are disproportionately more diverse in the younger, shorter-lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification across the salinity divide should also account for other potentially interacting variables. In diatoms, freshwater and substrate-associated (benthic) lineages are several-fold more diverse than their marine and suspended (planktonic) counterparts. These imbalances provide an excellent system to understand whether these variables interact with diversification. Using multistate hidden-state speciation and extinction models we found that freshwater lineages diversify faster than marine lineages regardless of whether they inhabit the plankton or the benthos. Freshwater lineages also had higher turnover rates (speciation + extinction), suggesting that habitat transitions impact speciation and extinction rates jointly. The plankton-benthos contrast was also consistent with state-dependent diversification, but with modest differences in diversification and turnover rates. Asymmetric, and bidirectional transitions rejected hypotheses about the plankton and freshwaters as absorbing, inescapable habitats. Our results further suggest that the high turnover rate of freshwater diatoms is related to high turnover of freshwater systems themselves.

evolutionary biology↗