Emerging strains of watermelon mosaic virus in Southeastern France: model-based estimation of the dates and places of introduction

Coupling Genetic and Demographic Data to Reveal Dispersal Processes in Emperor Penguins

Dispersal is a ubiquitous phenomenon that affects the dynamics of the population and the evolution of natural populations; however, it is challenging to measure in most species. Furthermore, the influence of informed dispersal behaviors, referring to the nonrandom selection of breeding habitats by individuals, on species' responses to rapid global change is substantial but difficult to comprehend. Here, we present a modeling framework to assess the dispersal characteristics and behaviors of a metapopulation when observations provide information on its neutral genetic structure for a restricted sampling of locations. Our mechanistic-statistical model couples a deterministic model capturing the spatio-temporal dynamics of four genetic clusters across all breeding colonies by integrating demographic processes with genetic projections, with a probabilistic observation model describing the probability to sample an individual from a given genetic cluster. We apply this new framework to the emperor penguin, a species living in Antarctica and currently experiencing habitat loss. The model estimates the species' dispersal distance, rates of emigration, and behaviors associated with dispersal (informed or random). By incorporating these estimations with satellite censuses of breeding colonies, we can identify environmental and demographic factors that influence the dispersal of emperor penguins. Finally, we provide new global population forecasts for emperor penguins that can inform conservation actions in Antarctica.

Phylodynamics and phylogeography of watermelon mosaic virus: Multiple local invasion routes in southern France and recombination-driven limits to global analysis

Watermelon mosaic virus (WMV) is a major plant pathogen, infecting over 170 plant species, including cucurbits and legumes. Though mostly propagated locally by aphids in a non-persistent manner, long-range dispersal can occur through human-induced plant or vector movements. Understanding patterns of local and global spread of WMV is crucial to help formulate adequate control strategies. We used phylodynamic methods based on partial and whole-genome sequences collected in France between 2000 and 2017 to reconstruct the introduction of new lineages in the past 30 years and their subsequent diffusion in the country. We identified at least 11 different introduction events, hailing from different parts of the global diversity of WMV, highlighting the critical role international exchanges play in the spread of plant pathogens. For three of these lineages, we estimated the time and location of their introduction in the mid-1990s in the south of France and the speed at which they spread in this specific landscape. We also showed that the highly recombinogenic nature of WMV, as with most potyviruses, makes the use of whole genomes necessary to classify these viruses on a global scale and must be taken into consideration to reconstruct viral evolutionary history. Our results demonstrate how genomic sequencing of plant viruses can help reconstruct specific viral outbreaks and understand global circulation patterns of plant pathogens.

Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion

Plant invasions generate massive ecological and economic costs worldwide. Predicting their spatial dynamics is crucial to the design of effective management strategies and the prevention of invasions. Earlier studies highlighted the crucial role of long-distance dispersal in explaining the speed of many invasions. In addition, invasion speed depends highly on the duration of its lag phase, which may depend on the scaling of fecundity with age, especially for woody plants, even though empirical proof is still rare. Bayesian dynamic species distribution models enable the fitting of process-based models to partial and heterogeneous observations using a state-space modeling approach, thus offering a tool to test such hypotheses on past invasions over large spatial scales. We use such a model to explore the roles of long-distance dispersal and age-structured fecundity in the transient invasion dynamics of Plectranthus barbatus, a woody plant invader in South Africa. Our lattice-based model accounts for both short and human-mediated long-distance dispersal, as well as age-structured fecundity. We fitted our model on opportunistic occurrences, accounting for the spatio-temporal variations of the sampling effort and the variable detection rates across datasets. The Bayesian framework enables us to integrate a priori knowledge on demographic parameters and control identifiability issues. The model revealed a massive wave of spatial spread driven by human-mediated long-distance dispersal during the first decade and a subsequent drastic population growth, leading to a global equilibrium in the mid-1990s. Without long-distance dispersal, the maximum population would have been equivalent to 30% of the current equilibrium population. We further identified the reproductive maturity at three years old, which contributed to the lag phase before the final wave of population growth. Our results highlighted the importance of the early eradication of weedy horticultural alien plants around urban areas to hamper and delay the invasive spread.