Search

A large number of published ecological studies fail to include basic information about the climate data used. In the interest of reproducibility and transparency, we offer recommendations for best practices that we urge Editors, authors, and reviewers to adopt in future publications.

Stochastic diffusion is the noisy and uncertain process through which dynamics like epidemics, or agents like animal species, disperse over a larger area. Understanding these processes is becoming increasingly important as we attempt to better prepare for potential pandemics and as species ranges shift in response to climate change. Unfortunately, modeling of stochastic diffusion is mostly done through inaccurate deterministic tools that fail to capture the random nature of dispersal or else through expensive computational simulations. In particular, standard tools fail to fully capture the heterogeneity of the area over which this diffusion occurs. Rural areas with low population density require different epidemic models than urban areas; likewise, the edges of a species range require us to explicitly track low integer numbers of individuals rather than vague averages. In this work, we introduce a series of new tools called "mean-FLAME" models that track stochastic dispersion using approximate master equations that explicitly follow the probability distribution of an area of interest over all of its possible states, up to states that are active enough to be approximated using a mean-field model. In one limit, this approach is locally exact if we explicitly track enough states, and in the other limit collapses back to traditional deterministic models if we track no state explicitly. Applying this approach, we show how deterministic tools fail to capture the uncertainty around the speed of nonlinear dynamical processes. This is especially true for marginal areas that are close to unsuitable for diffusion, like the edge of a species range or epidemics in small populations. Capturing the uncertainty in such areas is key to producing accurate forecasts and guiding potential interventions.

Understanding the topographic basis for microclimatic variation remains fundamental to predicting the site level effects of warming air temperatures. Quantifying diurnal fluctuation and seasonal extremes in relation to topography offers insight into the potential relationship between site level conditions and changes in regional climate. The present study investigated an annual understory temperature regime for 50 sites distributed across a topographically diverse area (>12 km2) comprised of mixed evergreen-deciduous woodland vegetation typical of California coastal ranges. We investigated the effect of topography and tree cover on site-to-site variation in near-surface temperatures using a combination of multiple linear regression and multivariate techniques. Sites in topographically depressed areas (e.g., valley bottoms) exhibited larger seasonal and diurnal variation. Elevation (at 10 m resolution) was found to be the primary driver of daily and seasonal variations, in addition to hillslope position, canopy cover and northness. The elevation effect on seasonal mean temperatures was inverted, reflecting large-scale cold-air pooling in the study region, with elevated minimum and mean temperature at higher elevations. Additionally, several of our sites showed considerable buffering (dampened diurnal and seasonal temperature fluctuations) compared to average regional conditions measured at an on-site weather station. Results from this study help inform efforts to extrapolate temperature records across large landscapes and have the potential to improve our ecological understanding of fine-scale seasonal climate variation in coastal range environments., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 John et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

It has been proposed that climate adaptation research can benefit from an evolutionary approach. But related empirical research is lacking. We advance the evolutionary study of climate adaptation with two case studies from contemporary United States agriculture. First, we define 'cultural adaptation to climate change' as a mechanistic process of population-level cultural change. We argue this definition enables rigorous comparisons, yields testable hypotheses from mathematical theory and distinguishes adaptive change, non-adaptive change and desirable policy outcomes. Next, we develop an operational approach to identify 'cultural adaptation to climate change' based on established empirical criteria. We apply this approach to data on crop choices and the use of cover crops between 2008 and 2021 from the United States. We find evidence that crop choices are adapting to local trends in two separate climate variables in some regions of the USA. But evidence suggests that cover cropping may be adapting more to the economic environment than climatic conditions. Further research is needed to characterize the process of cultural adaptation, particularly the routes and mechanisms of cultural transmission. Furthermore, climate adaptation policy could benefit from research on factors that differentiate regions exhibiting adaptive trends in crop choice from those that do not. This article is part of the theme issue 'Climate change adaptation needs a science of culture'.

Wind disperses the pollen and seeds of many plants, but little is known about whether and how it shapes large-scale landscape genetic patterns. We address this question by a synthesis and reanalysis of genetic data from more than 1,900 populations of 97 tree and shrub species around the world, using a newly developed framework for modeling long-term landscape connectivity by wind currents. We show that wind shapes three independent aspects of landscape genetics in plants with wind pollination or seed dispersal: populations linked by stronger winds are more genetically similar, populations linked by directionally imbalanced winds exhibit asymmetric gene flow ratios, and downwind populations have higher genetic diversity. For each of these distinct hypotheses, partial correlations between the respective wind and genetic metrics (controlling for distance and climate) are positive for a significant majority of wind-dispersed or wind-pollinated genetic data sets and increase significantly across functional groups expected to be increasingly influenced by wind. Together, these results indicate that the geography of both wind strength and wind direction play important roles in shaping large-scale genetic patterns across the world's forests. These findings have implications for various aspects of basic plant ecology and evolution, as well as the response of biodiversity to future global change., Competing Interests: The authors declare no competing interest.

Quantitative knowledge of xylem physical tolerance limits to dehydration is essential to understanding plant drought tolerance but is lacking in many long-vessel angiosperms. We examine the hypothesis that a fundamental association between sustained xylem water transport and downstream tissue function should select for xylem that avoids embolism in long-vessel trees by quantifying xylem capacity to withstand air entry of western North American oaks ( Quercus spp.). Optical visualization showed that 50% of embolism occurs at water potentials below -2.7 MPa in all 19 species, and -6.6 MPa in the most resistant species. By mapping the evolution of xylem vulnerability to embolism onto a fossil-dated phylogeny of the western North American oaks, we found large differences between clades (sections) while closely related species within each clade vary little in their capacity to withstand air entry. Phylogenetic conservatism in xylem physical tolerance, together with a significant correlation between species distributions along rainfall gradients and their dehydration tolerance, suggests that closely related species occupy similar climatic niches and that species' geographic ranges may have shifted along aridity gradients in accordance with their physical tolerance. Such trends, coupled with evolutionary associations between capacity to withstand xylem embolism and other hydraulic-related traits, yield wide margins of safety against embolism in oaks from diverse habitats. Evolved responses of the vascular system to aridity support the embolism avoidance hypothesis and reveal the importance of quantifying plant capacity to withstand xylem embolism for understanding function and biogeography of some of the Northern Hemisphere's most ecologically and economically important plants., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Premise of the Study: Herbarium specimens are increasingly used as records of plant flowering phenology. However, most herbarium-based studies on plant phenology focus on taxa from temperate regions. Here, we explore flowering phenologic responses to climate in the subtropical plant genus Protea (Proteaceae), an iconic group of plants that flower year-round and are endemic to subtropical Africa., Methods: We present a novel, circular sliding window approach to investigate phenological patterns developed for species with year-round flowering. We employ our method to evaluate the extent to which site-to-site and year-to-year variation in temperature and precipitation affect flowering dates using a database of 1727 herbarium records of 25 Protea species. We also explore phylogenetic conservatism in flowering phenology., Results: We show that herbarium data combined with our sliding window approach successfully captured independently reported flowering phenology patterns ( r = 0.93). Both warmer sites and warmer years were associated with earlier flowering of 3-5 days/°C, whereas precipitation variation had no significant effect on flowering phenology. Although species vary widely in phenological responsiveness, responses are phylogenetically conserved, with closely related species tending to shift flowering similarly with increasing temperature., Discussion: Our results point to climate-responsive phenology for this important plant genus and indicate that the subtropical, aseasonally flowering genus Protea has temperature-driven flowering responses that are remarkably similar to those of better-studied northern temperate plant species, suggesting a generality across biomes that has not been described elsewhere.

Biodiversity is often described as having multiple facets, including species richness, functional diversity and phylogenetic diversity. In this paper, we argue that phylogenetic diversity itself has three distinct facets-lineage diversification, character divergence and survival time-that can be quantified using distinct branch length metrics on an evolutionary tree. Each dimension is related to different processes of macroevolution, has different spatial patterns and is tied to distinct goals for conserving biodiversity and protecting its future resilience and evolutionary potential. We compared the landscapes identified as top conservation priorities by each of these three metrics in a conservation gap analysis for California, a world biodiversity hotspot, using herbarium data on the biogeography and evolutionary relationships of more than 5000 native plant species. Our analysis incorporated a novel continuous metric of current land protection status, fine-scale data on landscape intactness and an optimization algorithm used to identify complementary priority sites containing concentrations of taxa that are evolutionarily unique, vulnerable due to small range size and/or poorly protected across their ranges. Top conservation priorities included pockets of coastal and northern California that ranked highly for all three phylodiversity dimensions and for species richness, as well as sites uniquely identified by each metric whose value may depend on whether properties such as genetic divergence, high net diversification or independent survival experience are most desirable in an Anthropocene flora.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'., (© 2018 The Author(s).)

Background: California is a world floristic biodiversity hotspot where the terms neo- and paleo-endemism were first applied. Using spatial phylogenetics, it is now possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism, by combining spatial information from museum collections and DNA-based phylogenies. Here we used a distributional dataset of 1.39 million herbarium specimens, a phylogeny of 1083 operational taxonomic units (OTUs) and 9 genes, and a spatial randomization test to identify regions of significant phylogenetic diversity, relative phylogenetic diversity, and phylogenetic endemism (PE), as well as to conduct a categorical analysis of neo- and paleo-endemism (CANAPE)., Results: We found (1) extensive phylogenetic clustering in the South Coast Ranges, southern Great Valley, and deserts of California; (2) significant concentrations of short branches in the Mojave and Great Basin Deserts and the South Coast Ranges and long branches in the northern Great Valley, Sierra Nevada foothills, and the northwestern and southwestern parts of the state; (3) significant concentrations of paleo-endemism in Northwestern California, the northern Great Valley, and western Sonoran Desert, and neo-endemism in the White-Inyo Range, northern Mojave Desert, and southern Channel Islands. Multiple analyses were run to observe the effects on significance patterns of using different phylogenetic tree topologies (uncalibrated trees versus time-calibrated ultrametric trees) and using different representations of OTU ranges (herbarium specimen locations versus species distribution models)., Conclusions: These analyses showed that examining the geographic distributions of branch lengths in a statistical framework adds a new dimension to California floristics that, in comparison with climatic data, helps to illuminate causes of endemism. In particular, the concentration of significant PE in more arid regions of California extends previous ideas about aridity as an evolutionary stimulus. The patterns seen are largely robust to phylogenetic uncertainty and time calibration but are sensitive to the use of occurrence data versus modeled ranges, indicating that special attention toward improving geographic distributional data should be top priority in the future for advancing understanding of spatial patterns of biodiversity.

Premise of the Study: California's vascular flora is the most diverse and threatened in temperate North America. Previous studies of spatial patterns of Californian plant diversity have been limited by traditional metrics, non-uniform geographic units, and distributional data derived from floristic descriptions for only a subset of species., Methods: We revisited patterns of sampling intensity, species richness, and relative endemism in California based on equal-area spatial units, the full vascular flora, and specimen-based distributional data. We estimated richness, weighted endemism (inverse range-weighting of species), and corrected weighted endemism (weighted endemism corrected for richness), and performed a randomization test for significantly high endemism., Key Results: Possible biases in herbarium data do not obscure patterns of high richness and endemism at the spatial resolution studied. High species richness was sometimes associated with significantly high endemism (e.g., Klamath Ranges) but often not. In Stebbins and Major's (1965) main endemism hotspot, Southwestern California, species richness is high across much of the Peninsular and Transverse ranges but significantly high endemism is mostly localized to the Santa Rosa and San Bernardino mountains. In contrast, species richness is low in the Channel Islands, where endemism is significantly high, as also found for much of the Death Valley region., Conclusions: Measures of taxonomic richness, even with greater weighting of range-restricted taxa, are insufficient for identifying areas of significantly high endemism that warrant conservation attention. Differences between our findings and those in previous studies appear to mostly reflect the source and scale of distributional data, and recent analytical refinements., (© 2017 Botanical Society of America.)