Joint Species And Niche Evolution

Project Information

INSANE

Grant agreement ID: 897225

DOI

10.3030/897225

Project closed

EC signature date 17 March 2020

Start date 1 June 2020

End date 31 May 2022

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 184 707,84

EU contribution

€ 184 707,84

Coordinated by

ECOLE NORMALE SUPERIEURE
France

Periodic Reporting for period 1 - INSANE (Joint Species And Niche Evolution)

Reporting period: 2020-06-01 to 2022-05-31

Summary of the context and overall objectives of the project

The great diversity of species, each with their specific ecologies, was brought about by speciation and extinction events (diversification), concomitant with the evolution of their species-specific niches. Why some groups accumulate higher numbers of species and/or include more dissimilar species is a central yet still a hotly debated question in evolutionary biology. Biological theory suggests that environmental and species characteristics might explain such variation in the evolution of niches and the accumulation of species in different taxonomic groups. However, hitherto, available models to study diversification and niche evolution remain simplistic and do not allow a direct test of how diversification is associated with niche evolution.

The aim of this project is to study how diversification is related to niche evolution and environmental factors and, to achieve this, develop new models that are sufficiently flexible to enable a direct link between these two evolutionary processes. Main objectives: i) To develop flexible niche evolution models that allow for rates of evolutionary change to vary across lineages using dimensional species' niches. ii) To develop flexible diversification models that allow speciation and extinction rates to fluctuate through time and across species and can incorporate fossil information. iii) To develop a joint model of niche evolution and species diversification where we can test if a given niche and its rate of change has an effect on diversification. iv) Apply these models to empirical datasets.

The fellow developed the mathematical, computational and biological foundation make inference on time and species-specific diversification and niche evolution rates (see Figs 1-3). These models provide the basis in which to study how biotic and abiotic factors have driven niche and species diversification. They integrate paleontological and neontological evidence to understanding the origin and maintenance of biodiversity (Fig 1,2). The fellow applied the diversification models to understand mammal diversification history: using a time-calibrated tree for Mammals, results showed that, contrary to the idea of a suppressed mammalian diversification before the K-Pg mass extinction event (i.e. 66 Mya when most of the dinosaurs went extinct), mammal actually increased their speciation rates before (Fig 3). These developments represent significant mathematical, computational, and biological advancements that will enable examining so far untestable classic evolutionary hypotheses.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The fellow developed a new birth-death model of diversification in which speciation and extinction rates evolve instantaneously according to a Geometric Brownian Motion (GBM) on reconstructed phylogenetic trees including neontological and paleontological information. Rates of speciation and extinction that can vary at any time for any lineage is theoretically expected from the interplay of intrinsic (e.g. species traits such as body size) and extrinsic factors (e.g. environment such as ambient temperature) acting at a given time on species, and opens new modeling and computational possibilities in the study of macroevolutionary dynamics. Before, no mathematical expression nor computational algorithm existed to apply this model. The fellow was able to overcome these obstacles and developed the necessary mathematical and computational tools, provided in an efficient open-source software package, to enable inference of this model using empirical data (Fig 1). The fellow implemented the model in Julia, with a suite of new functions to manipulate, plot and input/output phylogenetic trees, using Data Augmentation within MCMC, achieving high performance. The new model development uncovered a clear signal of an early-rise of modern mammals, suggesting that the angiosperm radiation opened substantial ecological opportunities for these lineages to diversify in the Late Cretaceous and up to the present (Fig 2). Furthermore, the fellow achieved integrating fossil information, allowing for different fossil recovery rates across time, validated the model, and is currently being applied across clades of plants and animals (Fig 3).

Finally, the fellow developed the math and code to jointly infer rates of diversification with trait evolution following a relaxed Brownian motion (biotic variable) and with a fixed dependent function (abiotic variable). This model however, is currently being validated to then perform inference on empirical phylogenetic trees.

Dissemination and engagement: While the COVID pandemic hampered many venues for dissemination and public engagement, the fellow presented the work at conferences and external laboratories, taught three workshops on Julia and flexible diversification methods, mentored two master students, and disseminated current achievements in social media, will continue to do so.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

All models developed and results are beyond the state-of-the-art. The model is efficient and proper and can be applied to empirical trees of thousands of species. The FBDD has been validated and the fellow is currently running it on empirical trees, under various diversification hypotheses. This FBDD model is beyond the state of the art, enabling for the first time species and time specific speciation and extinction rates to change instantaneously. Current development will also achieve the first test of the effect of abiotic and abiotic factors in determining diversification while accounting for unexplained variance.

These models are expected to be widely used in the field of evolutionary field, and the computational, mathematical and probabilistic developments are useful for a wide array of disciplines. A previously lacking efficient Julia package for comparative methods is provided, "Tapestree.jl", open source, and will become the starting point to build-in other models, enabling an efficient toolkit to perform macroevolutionary analyses in a language which is being adopted at a high rate for its numerous advantages. Finally, understanding the evolutionary effects of past climatic fluctuations can shine a light on the consequences of human-driven climate change. The model developed not only estimates past speciation and extinction, but also returns present-time lineage-specific rates of extinction, assigning evolutionary-informed extinction probabilities to species and enabling predictions under future climate change scenarios.

The data augmentation algorithm for the Birth-Death diffusion model

The mammal Birth-Death diffusion: speciation and extinction rates.

The fossilized Birth-Death diffusion model, with number of lineages and trait evolution