The difficulties of systematic reviews

The need for robust evidence to support conservation actions has driven the adoption of systematic approaches to research synthesis in ecology. However, applying systematic review to complex or open questions remains challenging, and this task is becoming more difficult as the quantity of scientific literature increases. We drew on the science of linguistics for guidance as to why the process of identifying and sorting information during systematic review remains so labor intensive, and to provide potential solutions. Several linguistic properties of peer-reviewed corpora-including nonrandom selection of review topics, small-world properties of semantic networks, and spatiotemporal variation in word meaning-greatly increase the effort needed to complete the systematic review process. Conversely, the resolution of these semantic complexities is a common motivation for narrative reviews, but this process is rarely enacted with the rigor applied during linguistic analysis. Therefore, linguistics provides a unifying framework for understanding some key challenges of systematic review and highlights 2 useful directions for future research. First, in cases where semantic complexity generates barriers to synthesis, ecologists should consider drawing on existing methods-such as natural language processing or the construction of research thesauri and ontologies-that provide tools for mapping and resolving that complexity. These tools could help individual researchers classify research material in a more robust manner and provide valuable guidance for future researchers on that topic. Second, a linguistic perspective highlights that scientific writing is a rich resource worthy of detailed study, an observation that can sometimes be lost during the search for data during systematic review or meta-analysis. For example, mapping semantic networks can reveal redundancy and complementarity among scientific concepts, leading to new insights and research questions. Consequently, wider adoption of linguistic approaches may facilitate improved rigor and richness in research synthesis.Australian Research Council. Grant Number: fl12010010

Quantifying shifts in topic popularity over 44 years of austral ecology

The Ecological Society of Australia was founded in 1959, and the society’s journal was first published in 1976. To examine how research published in the society’s journal has changed over this time, we used text mining to quantify themes and trends in the body of work published by the Australian Journal of Ecology and Austral Ecology from 1976 to 2019. We used topic models to identify 30 ‘topics’ within 2778 full-text articles in 246 issues of the journal, followed by mixed modelling to identify topics with above-average or below-average popularity in terms of the number of publications or citations that they contain. We found high inter-decadal turnover in research topics, with an early emphasis on highly specific ecosystems or processes giving way to a modern emphasis on community, spatial and fire ecology, invasive species and statistical modelling. Despite an early focus on Australian research, papers discussing South American ecosystems are now among the fastest-growing and most frequently cited topics in the journal. Topics that were growing fastest in publication rates were not always the same as those with high citation rates. Our results provide a systematic breakdown of the topics that Austral Ecology authors and editors have chosen to research, publish and cite through time, providing a valuable window into the historical and emerging foci of the journal. © 2020 Ecological Society of Australi

Global meta-analysis reveals low consistency of biodiversity congruence relationships

Knowledge of the number and distribution of species is fundamental to biodiversity conservation efforts, but this information is lacking for the majority of species on earth. Consequently, subsets of taxa are often used as proxies for biodiversity; but this assumes that different taxa display congruent distribution patterns. Here we use a global meta-analysis to show that studies of cross-taxon congruence rarely give consistent results. Instead, species richness congruence is highest at extreme spatial scales and close to the equator, while congruence in species composition is highest at large extents and grain sizes. Studies display highest variance in cross-taxon congruence when conducted in areas with dissimilar areal extents (for species richness) or latitudes (for species composition). These results undermine the assumption that a subset of taxa can be representative of biodiversity. Therefore, researchers whose goal is to prioritize locations or actions for conservation should use data from a range of taxa

The use and utility of surrogates in biodiversity monitoring programmes

**Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record*

Novel bird responses to successive, large-scale, landscape transformations

Transformation of intact vegetation into new kinds and configurations of human-modified habitats is a well-established driver of biodiversity loss. Following initial conversion, many human-dominated landscapes are then subject to further large-scale changes in land use. The impacts on biodiversity of repeated changes in land use remain poorly known, particularly how changes in the matrix interact with initial patterns of vegetation clearing. We used an 18-yr study of birds in remnant patches of endangered temperate woodland in south-eastern Australia to quantify the spatial and temporal effects of successive land use transformation in the surrounding landscape. We examined bird response to (1) initial patterns of landscape modification (creating semi-cleared grazing land dominated by pastures that surrounded remnant woodland patches), (2) subsequent establishment and maturation of exotic tree plantations on the pastures surrounding woodland patches, and (3) additive and interactive effects of both types of landscape transformation. The majority of the 57 bird species modeled responded to conversion of grazing land to exotic plantations, either independently from initial patterns of landscape transformation (20 species), or interactively (18 species) or additively (15 species) with initial landscape transformation. The occurrence of only one species (the Common Bronzewing) was related to patterns of initial transformation but not subsequent transformation due to plantation establishment. Thus, despite many characteristics of the woodland patches within the plantation remaining largely unaltered throughout our 18-yr investigation, the matrix had a profound effect on the kinds of species inhabiting them, with such impacts often magnified over time as the matrix continued to change. Plantation establishment triggered new regional-level spatial processes with effects on birds detected in woodland patches up to 2 km away from the plantation. Matrix conversion selected for species with different traits (size, diet and movement patterns) compared to the initial transformation, suggesting it is acting as a different filter on the bird community. New kinds of landscape transformation (such as plantation establishment on previously cleared land) can radically affect the species that have persisted for many decades in previously modified landscapes. This highlights the challenges, but also opportunities, for conserving taxa in ever changing human-dominated environments. © 2019 by the Ecological Society of America. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record*

Two roles for ecological surrogacy : indicator surrogates and management surrogates

Ecological surrogacy - here defined as using a process or element (e.g., species, ecosystem, or abiotic factor) to represent another aspect of an ecological system - is a widely used concept, but many applications of the surrogate concept have been controversial. We argue that some of this controversy reflects differences among users with different goals, a distinction that can be crystalized by recognizing two basic types of surrogate. First, many ecologists and natural resource managers measure "indicator surrogates" to provide information about ecological systems. Second, and often overlooked, are "management surrogates" (e.g., umbrella species) that are primarily used to facilitate achieving management goals, especially broad goals such as "maintain biodiversity" or "increase ecosystem resilience." We propose that distinguishing these two overarching roles for surrogacy may facilitate better communication about project goals. This is critical when evaluating the usefulness of different surrogates, especially where a potential surrogate might be useful in one role but not another. Our classification for ecological surrogacy applies to species, ecosystems, ecological processes, abiotic factors, and genetics, and thus can provide coherence across a broad range of uses. © 2015 Elsevier Ltd. All rights reserved. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton" is provided in this record*

How practitioners integrate decision triggers with existing metrics in conservation monitoring

Decision triggers are defined thresholds in the status of monitored variables that indicate when to undertake management, and avoid undesirable ecosystem change. Decision triggers are frequently recommended to conservation practitioners as a tool to facilitate evidence-based management practices, but there has been limited attention paid to how practitioners are integrating decision triggers into existing monitoring programs. We sought to understand whether conservation practitioners’ use of decision triggers was influenced by the type of variables in their monitoring programs. We investigated this question using a practitioner-focused workshop involving a structured discussion and review of eight monitoring programs. Among our case studies, direct measures of biodiversity (e.g. native species) were more commonly monitored, but less likely to be linked to decision triggers (10% with triggers) than measures being used as surrogates (54% with triggers) for program objectives. This was because decision triggers were associated with management of threatening processes, which were often monitored as a surrogate for a biodiversity asset of interest. By contrast, direct measures of biodiversity were more commonly associated with informal decision processes that led to activities such as management reviews or external consultation. Workshop participants were in favor of including more formalized decision triggers in their programs, but were limited by incomplete ecological knowledge, lack of appropriately skilled staff, funding constraints, and/or uncertainty regarding intervention effectiveness. We recommend that practitioners consider including decision triggers for discussion activities (such as external consultation) in their programs as more than just early warning points for future interventions, particularly for direct measures. Decision triggers for discussions should be recognized as a critical feature of monitoring programs where information and operational limitations inhibit the use of decision triggers for interventions. © 2018 Elsevier Ltd. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record*

Tests of predictions associated with temporal changes in Australian bird populations

Global biodiversity loss is the cumulative result of local species declines. To combat biodiversity loss, detailed information on the temporal trends of at-risk species at local scales is needed. Here we report the results of a 13-year study of temporal change in bird occupancy in one of the most heavily modified biomes worldwide; the temperate woodlands of south-eastern Australia. We sought to determine if temporal changes in bird species were different between three broad native vegetation types (old-growth woodland, regrowth woodland and restoration plantings) and between species traits (body size, migratory status, rarity, woodland dependency, or diet). We found evidence of decline for over a quarter of all bird species for which we had sufficient data for detailed analysis (30 out of 108 species). In contrast, only 14 species increased significantly. Temporal change of birds was linked to life-history attributes, with patterns often being habitat-dependent. Nectarivores and large-bodied birds declined across all vegetation types, whereas small-bodied species increased, particularly in restoration plantings. Contrasting with patterns documented elsewhere, resident but not migratory species declined, with this trend strongest in restoration plantings. Finally, our analyses showed that, as a group, common birds tended to decline whereas rare birds tended to increase, with effects for both most pronounced in restoration plantings. Our results highlight the benefit of targeted restoration planting for some species, but also demonstrate that many common species that have long-persisted in human-dominated landscapes are experiencing severe declines. © 2018 Elsevier Ltd. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record*

Visualization of species pairwise associations: A case study of surrogacy in bird assemblages

Quantifying and visualizing species associations are important to many areas of ecology and conservation biology. Species networks are one way to analyze species associations, with a growing number of applications such as food webs, nesting webs, plant-animal mutualisms, and interlinked extinctions. We present a new method for assessing and visualizing patterns of co-occurrence of species. The method depicts interactions and associations in an analogous way with existing network diagrams for studying pollination and trophic interactions, but adds the assessment of sign, strength, and direction of the associations. This provides a distinct advantage over existing methods of quantifying and visualizing co-occurrence. We demonstrate the utility of our new approach by showing differences in associations among woodland bird species found in different habitats and by illustrating the way these can be interpreted in terms of underlying ecological mechanisms. Our new method is computationally feasible for large assemblages and provides readily interpretable effects with standard errors. It has wide applications for quantifying species associations within ecological communities, examining questions about particular species that occur with others, and how their associations can determine the structure and composition of communities

Spatiotemporal effects of logging and fire on tall, wet temperate eucalypt forest birds

Forests globally are subject to disturbances such as logging and fire that create complex temporal variation in spatial patterns of forest cover and stand age. However, investigations that quantify temporal changes in biodiversity in response to multiple forms of disturbance in space and time are relatively uncommon. Over a 10-yr period, we investigated the response of bird species to spatiotemporal changes in forest cover associated with logging and wildfire in the mountain ash (Eucalyptus regnans) forests of southeastern Australia. Specifically, we examined how bird occurrence changed with shifts in the proportion of area burned or logged in a 4.5 km radius surrounding our 88 long-term field survey sites, each measuring 1 ha in size. Overall species richness was greatest in older forest patches, but declined as the amount of fire around each site increased. At the individual species level, 31 of the 37 bird species we modeled exhibited a negative response to the amount of fire in the surrounding landscape, while one species responded positively to fire. Only nine species exhibited signs of recovery in the 6 yr of surveys following the fire. Five species were more likely to be detected as the proportion of logged forest surrounding a site increased, suggesting a possible "concentration effect" with displaced birds moving into unlogged areas following harvesting of adjacent areas. We also identified relationships between the coefficients of life history attributes and spatiotemporal changes in forest cover and stand age. Large-bodied birds and migratory species were associated with landscapes subject to large amounts of fire in 2009. There were associations between old growth stands and small-bodied bird species and species that were not insectivores. Our study shows that birds in mountain ash forests are strongly associated with old growth stands and exhibit complex, time-dependent, and species-specific responses to landscape disturbance. Despite logging and fire both being high-severity perturbations, no bird species exhibited similar responses to fire and logging in the landscape surrounding our sites. Thus, species responses to one kind of landscape-scale disturbance are not readily predictable based on an understanding of the responses to another kind of (albeit superficially similar) disturbance.Threatened Species Recovery Hub of the National Environmental Science Program, Parks Victoria, and Victorian Government Department of Environment, Land, Water and Plannin