种群与进化
Evolutionary intermediates connect observed proteins, but the sequence of steps that produced them is rarely recoverable from extant data alone. Here we ask what can, and cannot, be inferred about such intermediates from the endpoints.…
Efficient evaluation of sequence data likelihoods and their high-dimensional gradients on phylogenetic trees improves inference under both maximum-likelihood and Bayesian frameworks. Here, we present BEAGLE 4.1, a high-performance library…
Recent progress in diverse intelligence has shown simple learning capacities below the organism level - single cells and even molecular networks. However, there are still many knowledge gaps around learning capacity above the organism…
We extend the ``Brownian bees'' model of Berestycki et al. (2021, 2022) to cooperative reproduction, $kA\to(k{+}1)A$, of a population of $N$ symmetric random walkers with removal, at each birth event, of the particle farthest from the…
We study the temporal dynamics of the first two empirical moments of Brownian traits on phylogenetic trees. For a fixed tree, we characterize the distributions of their empirical mean and empirical variance across all lineages extant at any…
The Shigesada-Kawasaki-Teramoto (SKT) model has become a classical modelling framework for studying spatial segregation and cross-diffusion-driven pattern formation in competing populations. This model assumes phenotypic homogeneity, but…
When competing species grow into new territory, the population is dominated by descendants of successful ancestors at the expansion front. Successful ancestry depends on both the reproductive advantage (fitness), as well as ability and…
Fish migration is a collective phenomenon that has multiple timescales, ranging from daily to intraday (hourly or even finer). We propose a unified mathematical approach using diffusion bridges, nonlinear stochastic differential equations…
PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…
Convergent evolution provides a useful framework for testing whether independent origins of similar traits share common genetic mechanisms. Evolutionary Sparse Learning with Paired Species Contrast (ESL-PSC) is an approach to identify genes…
Species sharing a habitat will co-evolve to make use of the available resources, as consumption is modulated by competition and negative feedback loops between consumers and resources. The dietary range of a given species determines the…
Chronic Wasting Disease (CWD) is a neurological disease impacting deer, elk, moose, and other cervid populations and is caused by a misfolded protein known as a prion. CWD is difficult to control due to the persistence of prions in the…
We study an ecology-inspired model for a population of bounded size, whose dynamics is governed by random birth, death, and immigration events. Stochastic fluctuations in the number of individuals give rise to a succession of alternating…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
In stochastic evolutionary dynamics, the replacement of an existing genotype or cultural trait by a newly introduced mutant is typically characterized by the quantities of fixation probability and fixation time. But in a structured…
Species populations often modify their environment as they grow. When environmental feedback operates more slowly than population growth, the system can undergo boom-bust dynamics, where the population overshoots its carrying capacity and…
Discrete dynamical models underpin systems biology, but we still lack substrate-agnostic diagnostics for identifying finite-horizon dynamical signatures that may be relevant to open-ended evolution (OEE), such as the recurrent production of…
In an emerging pandemic, policymakers need to make important decisions with limited information, for example choosing between a mitigation, suppression or elimination strategy. These strategies may require trade-offs to be made between the…
We show that a simple nonlinear differential equation (originally studied in the physics of disordered systems) is able to mathematically describe the global population growth over the past 12000 years. Different regimes of population…
The regularity of ecosystem size spectra is one of the most intriguing and relevant phenomena on our planet. Pelagic size spectra generally show a log-linearly downtrending shape, following a power-law distribution. A constant log-linear…