Populations and Evolution (q-bio.PE)

Abstract: Binary phylogenetic trees inferred from biological data are central to understanding the shared evolutionary history of organisms. Inferring the placement of latent nodes in a tree by any optimality criterion (e.g., maximum likelihood) is an NP-hard problem, propelling the development of myriad heuristic approaches. Yet, these heuristics often lack a systematic means of uniformly sampling random trees or effectively exploring a tree space that grows factorially, which are crucial to optimisation problems such as machine learning. Accordingly, we present Phylo2Vec, a new parsimonious representation of a phylogenetic tree. Phylo2Vec maps any binary tree with $n$ leaves to an integer vector of length $n$. We prove that Phylo2Vec is both well-defined and bijective to the space of phylogenetic trees. The advantages of Phylo2Vec are twofold: i) easy uniform sampling of binary trees and ii) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for maximum likelihood inference on five real-world datasets and show that a simple hill climbing-based optimisation efficiently traverses the vastness of tree space from a random to an optimal tree.

Abstract: There are two main life cycles in plants, annual and perennial. These life cycles are associated with different traits, which determine ecosystem function. Although life cycles are textbook examples of plant adaptation to different environments, we lack comprehensive knowledge regarding global distributional patterns. Here, we assembled an extensive database of plant life cycle assignments of 235,000 plant species coupled with millions of georeferenced datapoints to map the worldwide biogeography of life cycles. We found that annuals are half as common as initially thought, accounting for only 6% of species. Our analyses indicate annuals are favored in hot and dry regions. However, a more accurate model shows annual species' prevalence is driven by temperature and precipitation in the driest quarter (rather than yearly means), explaining, for example, why some Mediterranean systems have more annuals than deserts. Furthermore, this pattern remains consistent among different families, indicating convergent evolution. Finally, we demonstrate that increasing climate variability and anthropogenic disturbance increase annual favorability. Considering future climate change, we predict an increase in annual prevalence for 81% of the world's ecoregions by 2100. Overall, our analyses raise concerns for ecosystem services provided by perennials as ongoing changes are leading to a more annuals-dominated world.