Oak habitat recovery on California's largest islands: Scenarios for the role of corvid seed dispersal

The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species

Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this species is endangered by threats such as non-native plants, grazing animals, and human removal. Efforts for conservation and restoration of island oak currently underway could benefit from information about its range-wide genetic structure and evolutionary history. Here we present a high-quality genome assembly for Q. tomentella, assembled using PacBio HiFi and Omni-C sequencing, developed as part of the California Conservation Genomics Project (CCGP). The resulting assembly has a length of 781 Mb, with a contig N50 of 22.0 Mb and a scaffold N50 of 63.4 Mb. This genome assembly will provide a resource for genomics-informed conservation of this rare oak species. Additionally, this reference genome will be the first one available for a species in Quercus section Protobalanus, a unique oak clade present only in western North America.

Unlocking ensemble ecosystem modelling for large and complex networks

The potential effects of conservation actions on threatened species can be predicted using ensemble ecosystem models by forecasting populations with and without intervention. These model ensembles commonly assume stable coexistence of species in the absence of available data. However, existing ensemble-generation methods become computationally inefficient as the size of the ecosystem network increases, preventing larger networks from being studied. We present a novel sequential Monte Carlo sampling approach for ensemble generation that is orders of magnitude faster than existing approaches. We demonstrate that the methods produce equivalent parameter inferences, model predictions, and tightly constrained parameter combinations using a novel sensitivity analysis method. For one case study, we demonstrate a speed-up from 108 days to 6 hours, while maintaining equivalent ensembles. Additionally, we demonstrate how to identify the parameter combinations that strongly drive feasibility and stability, drawing ecological insight from the ensembles. Now, for the first time, larger and more realistic networks can be practically simulated and analysed.

Understanding mast seeding for conservation and land management

Masting, the intermittent and synchronous production of large seed crops, can have profound consequences for plant populations and the food webs that are built on their seeds. For centuries, people have recorded mast crops because of their importance in managing wildlife populations. In the past 30 years, we have begun to recognize the importance of masting in conserving and managing many other aspects of the environment: promoting the regeneration of forests following fire or other disturbance, conserving rare plants, conscientiously developing the use of edible seeds as non-timber forest products, coping with the consequences of extinctions on seed dispersal, reducing the impacts of plant invasions with biological control, suppressing zoonotic diseases and preventing depredation of endemic fauna. We summarize current instances and future possibilities of a broad set of applications of masting. By exploring in detail several case studies, we develop new perspectives on how solutions to pressing conservation and land management problems may benefit by better understanding the dynamics of seed production. A lesson common to these examples is that masting can be used to time management, and often, to do this effectively, we need models that explicitly forecast masting and the dynamics of seed-eating animals into the near-term future. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

The effects of ENSO and the North American monsoon on mast seeding in two Rocky Mountain conifer species

We aimed to disentangle the patterns of synchronous and variable cone production (i.e. masting) and its relationship to climate in two conifer species native to dry forests of western North America. We used cone abscission scars to reconstruct ca 15 years of recent cone production in Pinus edulis and Pinus ponderosa, and used redundancy analysis to relate time series of annual cone production to climate indices describing the North American monsoon and the El Niño Southern Oscillation (ENSO). We show that the sensitivity to climate and resulting synchrony in cone production varies substantially between species. Cone production among populations of P. edulis was much more spatially synchronous and more closely related to large-scale modes of climate variability than among populations of P. ponderosa. Large-scale synchrony in P. edulis cone production was associated with the North American monsoon and we identified a dipole pattern of regional cone production associated with ENSO phase. In P. ponderosa, these climate indices were not strongly associated with cone production, resulting in asynchronous masting patterns among populations. This study helps frame our understanding of mast seeding as a life-history strategy and has implications for our ability to forecast mast years in these species. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

A guide to ecosystem models and their environmental applications

Applied ecology has traditionally approached management problems through a simplified, single-species lens. Repeated failures of single-species management have led us to a new paradigm - managing at the ecosystem level. Ecosystem management involves a complex array of interacting organisms, processes and scientific disciplines. Accounting for interactions, feedback loops and dependencies between ecosystem components is therefore fundamental to understanding and managing ecosystems. We provide an overview of the main types of ecosystem models and their uses, and discuss challenges related to modelling complex ecological systems. Existing modelling approaches typically attempt to do one or more of the following: describe and disentangle ecosystem components and interactions; make predictions about future ecosystem states; and inform decision making by comparing alternative strategies and identifying important uncertainties. Modelling ecosystems is challenging, particularly when balancing the desire to represent many components of an ecosystem with the limitations of available data and the modelling objective. Explicitly considering different forms of uncertainty is therefore a primary concern. We provide some recommended strategies (such as ensemble ecosystem models and multi-model approaches) to aid the explicit consideration of uncertainty while also meeting the challenges of modelling ecosystems.