Languages change over time, driven by creation of new words and cultural pressure to optimize communication. Programming languages resemble written language but communicate primarily with computer ...hardware rather than a human audience. I tested whether there were detectable changes over time in use of R, a mature, open-source programming language used for scientific computing. Across 393 142 GitHub repositories published between 2014 and 2021, I extracted 143 409 288 R functions, programming 'verbs', pairing linguistic and ecological analyses to detect change to diversity and composition of functions used over time. I found the number of R functions in use increased and underwent substantial change, driven primarily by the popularity of the 'tidyverse' collection of community-written extensions. I provide evidence that users can change the nature of programming languages, with patterns that match known processes from natural languages and genetic evolution. In R, there appear to be selective pressures for increased analytic complexity and R functions in decline that are not yet extinct (extinction debts). R's evolution towards the tidyverse may also represent the start of a division into two distinct dialects, which may impact the readability and continuity of analytic and scientific inquiries codified in R, as well as the language's future.
1. Community ecology is frequently invoked as complementary to and useful for guiding ecological restoration. While the conceptual literature is devoted to this unification, first-hand accounts from ...practitioners and ecologists suggest that integration may be weak in practice. To date, there have been no analyses of how extensively community ecology theory appears in the empirical restoration literature. 2. We address this knowledge gap with the first quantitative assessment of the extent to which community ecology concepts appear in empirical restoration literature by analysing the use of community ecology theories, concepts and conceptually derived tools in the design and interpretation of 1,000+ experimental ecological restoration studies over time (20 years) across all global regions. We also gauge general trends in author demographics, focal ecosystems and taxa targeted by these studies. 3. We found that the incorporation of community ecology into restoration research has increased significantly in recent years. 4. Community assembly and succession theories were the community ecology concepts integrated most often, while the functional traits framework and evolutionary theory have increased in usage recently. 5. Synthesis and applications. Restoration endeavours are increasingly infused with elements of community ecology. Our results highlight the widespread application of deterministic models of community structure in restoration design and the rise of ecosystem service and function-focused restoration. With this diagnostic summary of these applications, ecologists and restoration practitioners can move forward while directly exploring underdeveloped synergies between theory and practice.
Anthropogenic disturbance and climate change can result in dramatic increases in the emergence of new, ecologically novel, communities of organisms. We used a standardised framework to detect local ...novel communities in 2135 pollen time series over the last 25,000 years. Eight thousand years of post‐glacial warming coincided with a threefold increase in local novel community emergence relative to glacial estimates. Novel communities emerged predominantly at high latitudes and were linked to global and local temperature change across multi‐millennial time intervals. In contrast, emergence of locally novel communities in the last 200 years, although already on par with glacial retreat estimates, occurred at midlatitudes and near high human population densities. Anthropogenic warming does not appear to be strongly associated with modern local novel communities, but may drive widespread emergence in the future, with legacy effects for millennia after warming abates.
Eight thousand years of post‐glacial warming coincided with a threefold increase in how often locally new, ecologically novel, communities emerged, relative to glacial estimates, predominantly at high latitudes and with multi‐millennial time lags. In contrast, emergence of locally novel communities in the last 200 years, although already on par with glacial retreat estimates, occurred at midlatitudes and near high human population densities. Anthropogenic warming does not appear to be strongly associated with modern local novel communities, but may drive widespread emergence in the future, with legacy effects for millennia after warming abates.
Aim
Understanding biodiversity–ecosystem function (BEF) relationships in forest systems is crucial for effective forest management and restoration, yet testing these relationships is often limited by ...biased diversity patterns in forestry plantings (biased towards commercially valuable species) and uncontrollable diversity in mature natural forests. Multispecies reforestation plantings present a valuable opportunity to investigate BEF relationships in woody systems, especially across large environmental gradients.
Location
Reforestation plantings across the arable region of Australia.
Time period
1951–2012.
Major taxa studied
Three hundred and sixty‐four woody plant species.
Methods
We examined relationships between productivity and diversity using inventory data from 977 plots in 386 multispecies reforestation plantings. Diversity was estimated using observed species richness and three functional diversity indices calculated from four functional traits: specific leaf area, wood density, seed mass and maximum attainable height. We modelled how plot‐level biomass accumulation (a productivity proxy) correlated with these diversity indices, as well as age since planting, plant density and three environmental variables: solar radiation, moisture availability and soil sand content. These models were fitted across Australia and, separately, within eight groups of plantings with similar environmental conditions.
Results
We found no correlation between diversity and productivity, regardless of the diversity metric or spatial scale used (continent‐wide or within environment groups). Instead, productivity was best explained by local environmental conditions and plant density.
Main conclusions
A positive relationship between diversity and productivity was not evident in planted forests across a wide range of Australian woodland and forest systems, at least in the first few decades of growth. Our findings suggest that the positive relationship between diversity and productivity commonly reported in experimental settings should not be assumed for all systems and conditions.
Functional traits are proxies for a species' ecology and physiology and are often correlated with plant vital rates. As such they have the potential to guide species selection for restoration ...projects. However, predictive trait‐based models often only explain a small proportion of plant performance, suggesting that commonly measured traits do not capture all important ecological differences between species. Some residual variation in vital rates may be evolutionarily conserved and captured using taxonomic groupings alongside common functional traits. We tested this hypothesis using growth rate data for 17,299 trees and shrubs from 80 species of Eucalyptus and 43 species of Acacia, two hyper‐diverse and co‐occurring genera, collected from 497 neighborhood plots in 137 Australian mixed‐species revegetation plantings. We modeled relative growth rates of individual plants as a function of environmental conditions, species‐mean functional traits, and neighbor density and diversity, across a moisture availability gradient. We then assessed whether the strength and direction of these relationships differed between the two genera. We found that the inclusion of genus‐specific relationships offered a significant but modest improvement to model fit (1.6%–1.7% greater R2 than simpler models). More importantly, almost all correlates of growth rate differed between Eucalyptus and Acacia in strength, direction, or how they changed along the moisture gradient. These differences mapped onto physiological differences between the genera that were not captured solely by measured functional traits. Our findings suggest taxonomic groupings can capture or mediate variation in plant performance missed by common functional traits. The inclusion of taxonomy can provide a more nuanced understanding of how functional traits interact with abiotic and biotic conditions to drive plant performance, which may be important for constructing trait‐based frameworks to improve restoration outcomes.
Mangroves store large amounts of organic carbon (C) in their soils and are important in the global C cycle. These C stocks have been attributed to the below-ground productivity of mangroves, yet ...there is limited knowledge about the environmental factors that influence mangrove root growth. Thus, this study aimed to assess the role of variation in soil bulk density (BD) on the early development of mangroves. Seedlings of four mangrove species were grown in a pot-experiment in soils with a BD ranging from 0.2 to 1.2 g cm⁻³. Nine functional above- and below-ground plant traits were measured. Above- and below-ground traits of mangrove seedlings were influenced by variation in soil BD, but the effect was species specific. The reaction norms for most plant traits of Bruguiera gymnorrhiza and Rhizophora stylosa suggested a growth optimum at a specific soil BD (0.6 and 0.4 g cm⁻³, respectively), whilst the reaction norm of Avicennia marina was highly variable among traits, and Ceriops australis showed a very limited response. Moreover, A. marina was the most plastic species above-ground, while R. stylosa was the most plastic species below-ground. Ceriops australis was the least plastic species. Hence, soil BD is an environmental factor that influences mangrove root traits and seedling establishment, and may therefore affect mangrove species distributions and ecosystem C stocks.
Globalisation has resulted in the spread of infectious plant diseases to new regions and host species and the novel disease caused by myrtle rust poses a global threat to naïve hosts in the Myrtaceae ...family of plants. This study uses a focal species,
Tristaniopsis exiliflora,
to explore the climatic and microclimatic preference of the myrtle rust disease (
Austropuccinia psidii
). Populations of
T. exiliflora
were sampled across the species distribution in Far North Queensland, Australia, modelling
A. psidii
severity as a function of macro- and micro-environmental variables. Disease severity was found to increase with annual precipitation and foliage projective cover, and decrease with maximum temperature and valley confinement. A subsampled population found that individuals with lower canopy heights experienced more severe disease. Our results suggest that, in tropical environments with seasonal rainfall,
A. psidii
virulence is reduced when mean annual rainfall is less than 1500 mm and virulence is substantially reduced when maximum temperatures exceed 32 °C. The climatic drivers identified in this study align with optimal in vitro conditions for
A. psidii
germination and development
.
This suggests that climatic conditions are regulating myrtle rust in natural ecosystems at a broader scale, and that increased conservation efforts should focus on species with narrow climatic distributions and highly susceptible regions such as the Wet Tropics World Heritage Area.
The clearing of natural vegetation for agriculture has reduced the capacity of natural systems to provide ecosystem functions. Ecological restoration can restore desirable ecosystem functions, such ...as creating habitat for animal conservation and carbon sequestration as woody biomass. In order to maintain these beneficial ecosystem functions, restoration projects need to mature into self‐perpetuating communities. Here we compared the ecological attributes of two types of restoration, “active” tree plantings with “passive” natural forest regeneration (“natural regrowth”) to existing remnant vegetation in a cleared agricultural landscape. Specifically, we measured differences between forest categories in factors that may predict future restoration failure or ecosystem collapse: aboveground plant biomass and biomass accrual over time (for regrowing stands), plant density and size class distributions, and diversity of functional groups based on seed dispersal and growth strategy traits. We found that natural regrowth and planted forests were similar in many ecological characteristics, including biomass accrual. Despite this, planted stands contained fewer tree recruit and shrub individuals, which may be due to limited recruitment in plantings. If this continues, these forests may be at risk of collapsing into nonforest states after mature trees senesce. Lower shrub density and richness of mid‐story trees may lead to lower structural complexity in planting plots, and alongside lower richness of fleshy‐fruited plant species may reduce animal resources and animal use of the restored stand. In our study region, natural regrowth may result in restored woodland communities with greater conservation and carbon mitigation value.
The stable coexistence of very similar species has perplexed ecologists for decades and has been central to the development of coexistence theory. According to modern coexistence theory, species can ...coexist stably (i.e. persist indefinitely with no long-term density trends) as long as species’ niche differences exceed competitive ability differences, even if these differences are very small. Recent studies have directly quantified niche and competitive ability differences in experimental communities at small spatial scales, but provide limited information about stable coexistence across spatial scales in heterogeneous natural communities. In this study, we use experimental and observational approaches to explore evidence for niche and competitive ability differences between two closely related, ecologically similar and widely coexisting annual forbs: Trachymene cyanopetala and T. ornata. We experimentally tested for stabilizing niche differences and competitive ability differences between these species by manipulating species’ frequencies, under both well-watered and water-stressed conditions. We considered these experimental results in light of extensive field observations to explore evidence of niche segregation at a range of spatial scales. We found little evidence of intra-specific stabilization or competitive ability differences in laboratory experiments while observational studies suggested niche segregation across pollinator assemblages and small-scale microclimate heterogeneity. Though we did not quantify long-term stabilization of coexisting populations of these species, results are consistent with expectations for stable coexistence of similar species via a spatial storage effect allowing niche differences to overcome even small (to absent) competitive ability differences.
Climate change, land clearing and invasive species are affecting ecosystems in concert, so effective management requires knowledge sharing and collaboration across multiple fields of applied ...ecological research.
We provide an examination of the growth and interconnectivity of four major subfields of applied ecology: climate change biology, conservation biology, invasion biology and restoration ecology; estimated using citations from the entire population of peer‐reviewed journal articles published between 1990 and 2017.
Over this period applied ecological research has grown from 2% of new ecology papers to over 20%. The subfields each represented c. 6% of new ecology publications in 2017, with the exception of restoration ecology at c. 3%. Inter‐subfield citation probabilities also increased consistently over our study period.
Despite these positive trends, we identified apparent barriers to future integration of these research areas. While the probability that citations in one subfield would include at least one paper from another subfield was high, the magnitude of cross‐subfield citations was low. Subfields also exhibited segregated publishing habits, asynchronous research foci and a strong preference for citing application over theory.
Synthesis and applications. Despite strong overall growth in applied ecological research, segregation of subfields in papers and journals may limit opportunities to identify co‐benefits and complementary theoretical frameworks. This has the potential to result in suboptimal ecological management outcomes.
Despite strong overall growth in applied ecological research, segregation of subfields in papers and journals may limit opportunities to identify co‐benefits and complementary theoretical frameworks. This has the potential to result in suboptimal ecological management outcomes.
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