James R. Thomson

Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation

Concerted political attention has focused on reducing deforestation, and this remains the cornerstone of most biodiversity conservation strategies. However, maintaining forest cover may not reduce anthropogenic forest disturbances, which are rarely considered in conservation programmes. These disturbances occur both within forests, including selective logging and wildfires, and at the landscape level, through edge, area and isolation effects. Until now, the combined effect of anthropogenic disturbance on the conservation value of remnant primary forests has remained unknown, making it impossible to assess the relative importance of forest disturbance and forest loss. Here we address these knowledge gaps using a large data set of plants, birds and dung beetles (1,538, 460 and 156 species, respectively) sampled in 36 catchments in the Brazilian state of Pará. Catchments retaining more than 69–80% forest cover lost more conservation value from disturbance than from forest loss. For example, a 20% loss of primary forest, the maximum level of deforestation allowed on Amazonian properties under Brazil’s Forest Code, resulted in a 39–54% loss of conservation value: 96–171% more than expected without considering disturbance effects. We extrapolated the disturbance-mediated loss of conservation value throughout Pará, which covers 25% of the Brazilian Amazon. Although disturbed forests retained considerable conservation value compared with deforested areas, the toll of disturbance outside Pará’s strictly protected areas is equivalent to the loss of 92,000–139,000 km2 of primary forest. Even this lowest estimate is greater than the area deforested across the entire Brazilian Amazon between 2006 and 2015 (ref. 10). Species distribution models showed that both landscape and within-forest disturbances contributed to biodiversity loss, with the greatest negative effects on species of high conservation and functional value. These results demonstrate an urgent need for policy interventions that go beyond the maintenance of forest cover to safeguard the hyper-diversity of tropical forest ecosystems.

A social and ecological assessment of tropical land uses at multiple scales: the Sustainable Amazon Network

Science has a critical role to play in guiding more sustainable development trajectories. Here, we present the Sustainable Amazon Network (Rede Amazônia Sustentável, RAS): a multidisciplinary research initiative involving more than 30 partner organizations working to assess both social and ecological dimensions of land-use sustainability in eastern Brazilian Amazonia. The research approach adopted by RAS offers three advantages for addressing land-use sustainability problems: (i) the collection of synchronized and co-located ecological and socioeconomic data across broad gradients of past and present human use; (ii) a nested sampling design to aid comparison of ecological and socioeconomic conditions associated with different land uses across local, landscape and regional scales; and (iii) a strong engagement with a wide variety of actors and non-research institutions. Here, we elaborate on these key features, and identify the ways in which RAS can help in highlighting those problems in most urgent need of attention, and in guiding improvements in land-use sustainability in Amazonia and elsewhere in the tropics. We also discuss some of the practical lessons, limitations and realities faced during the development of the RAS initiative so far.

Effects of removal of a small dam on downstream macroinvertebrate and algal assemblages in a Pennsylvania stream

Abstract Dam removal is often proposed as way to restore ecological integrity to rivers and streams, but ecological responses to dam removals are poorly understood, especially for downstream benthic communities. We examined the responses of benthic macroinvertebrate and algal assemblages in downstream reaches to the removal of a small, run-of-river dam on Manatawny Creek, Pennsylvania. Benthic macroinvertebrates, algae, and habitat characteristics were monitored upstream and downstream of the dam for 4 mo before removal, 3 mo after partial removal (i.e., when the impoundment was largely eliminated but sediment remained trapped behind the remaining structure), and 12 mo after complete dam removal. Macroinvertebrate density, algal biomass, and diatom species richness declined significantly downstream of the dam following complete dam removal, but overall assemblage structure (as indicated by Nonmetric Multidimensional Scaling ordinations) downstream remained similar to upstream control sites throughout the study for both invertebrates and diatoms. Downstream impacts occurred only after the dam structure had been completely removed and sediments had been transported downstream from the former impoundment by high flows. Biotic impacts persisted for the duration of the study (12 mo after complete removal). Our results and other studies of dam removal suggest that downstream sedimentation following dam removal can reduce densities of macroinvertebrates and benthic algae and may reduce benthic diversity, but for small dams such impacts may be relatively minor and will usually be temporary.

Using species distribution models to infer potential climate change-induced range shifts of freshwater fish in south-eastern Australia

There are few quantitative predictions for the impacts of climate change on freshwater fish in Australia. We developed species distribution models (SDMs) linking historical fish distributions for 43 species from Victorian streams to a suite of hydro-climatic and catchment predictors, and applied these models to explore predicted range shifts under future climate-change scenarios. Here, we present summary results for the 43 species, together with a more detailed analysis for a subset of species with distinct distributions in relation to temperature and hydrology. Range shifts increased from the lower to upper climate-change scenarios, with most species predicted to undergo some degree of range shift. Changes in total occupancy ranged from –38% to +63% under the lower climate-change scenario to –47% to +182% under the upper climate-change scenario. We do, however, caution that range expansions are more putative than range contractions, because the effects of barriers, limited dispersal and potential life-history factors are likely to exclude some areas from being colonised. As well as potentially informing more mechanistic modelling approaches, quantitative predictions such as these should be seen as representing hypotheses to be tested and discussed, and should be valuable for informing long-term strategies to protect aquatic biota.

Predicting landscape-genetic consequences of habitat loss, fragmentation and mobility for multiple species of woodland birds.

Inference concerning the impact of habitat fragmentation on dispersal and gene flow is a key theme in landscape genetics. Recently, the ability of established approaches to identify reliably the differential effects of landscape structure (e.g. land-cover composition, remnant vegetation configuration and extent) on the mobility of organisms has been questioned. More explicit methods of predicting and testing for such effects must move beyond post hoc explanations for single landscapes and species. Here, we document a process for making a priori predictions, using existing spatial and ecological data and expert opinion, of the effects of landscape structure on genetic structure of multiple species across replicated landscape blocks. We compare the results of two common methods for estimating the influence of landscape structure on effective distance: least-cost path analysis and isolation-by-resistance. We present a series of alternative models of genetic connectivity in the study area, represented by different landscape resistance surfaces for calculating effective distance, and identify appropriate null models. The process is applied to ten species of sympatric woodland-dependant birds. For each species, we rank a priori the expectation of fit of genetic response to the models according to the expected response of birds to loss of structural connectivity and landscape-scale tree-cover. These rankings (our hypotheses) are presented for testing with empirical genetic data in a subsequent contribution. We propose that this replicated landscape, multi-species approach offers a robust method for identifying the likely effects of landscape fragmentation on dispersal.

Regime shifts, thresholds and multiple stable states in freshwater ecosystems; a critical appraisal of the evidence

The concepts of ecosystem regime shifts, thresholds and alternative or multiple stable states are used extensively in the ecological and environmental management literature. When applied to aquatic ecosystems, these terms are used inconsistently reflecting differing levels of supporting evidence among ecosystem types. Although many aquatic ecosystems around the world have become degraded, the magnitude and causes of changes, relative to the range of historical variability, are poorly known. A working group supported by the Australian Centre for Ecological Analysis and Synthesis (ACEAS) reviewed 135 papers on freshwater ecosystems to assess the evidence for pressure-induced non-linear changes in freshwater ecosystems; these papers used terms indicating sudden and non-linear change in their titles and key words, and so was a positively biased sample. We scrutinized papers for study context and methods, ecosystem characteristics and focus, types of pressures and ecological responses considered, and the type of change reported (i.e., gradual, non-linear, hysteretic or irreversible change). There was little empirical evidence for regime shifts and changes between multiple or alternative stable states in these studies although some shifts between turbid phytoplankton-dominated states and clear-water, macrophyte-dominated states were reported in shallow lakes in temperate climates. We found limited understanding of the subtleties of the relevant theoretical concepts and encountered few mechanistic studies that investigated or identified cause-and-effect relationships between ecological responses and nominal pressures. Our results mirror those of reviews for estuarine, nearshore and marine aquatic ecosystems, demonstrating that although the concepts of regime shifts and alternative stable states have become prominent in the scientific and management literature, their empirical underpinning is weak outside of a specific environmental setting. The application of these concepts in future research and management applications should include evidence on the mechanistic links between pressures and consequent ecological change. Explicit consideration should also be given to whether observed temporal dynamics represent variation along a continuum rather than categorically different states.

Integrating plant- and animal- based perspectives for more effective restoration of biodiversity

Ecological restoration of modified and degraded landscapes is an important challenge for the 21st century, with potential for major gains in the recovery of biodiversity. However, there is a general lack of agreement between plant- and animal-based approaches to restoration, both in theory and practice. Here, we review these approaches, identify limitations from failing to effectively integrate their different perspectives, and suggest ways to improve outcomes for biodiversity recovery in agricultural landscapes. We highlight the need to strengthen collaboration between plant and animal ecologists, to overcome disciplinary and cultural differences, and to achieve a more unified approach to restoration ecology. Explicit consideration of key ecosystem functions, the need to plan at multiple spatial and temporal scales, and the importance of plant–animal interactions can provide a bridge between plant- and animal-based methods. A systematic approach to restoration planning is critical to achieving effective biodiversity outcomes while meeting long-term social and economic needs.

Reforestation with native mixed‐species plantings in a temperate continental climate effectively sequesters and stabilizes carbon within decades

Reforestation has large potential for mitigating climate change through carbon sequestration. Native mixed-species plantings have a higher potential to reverse biodiversity loss than do plantations of production species, but there are few data on their capacity to store carbon. A chronosequence (5-45 years) of 36 native mixed-species plantings, paired with adjacent pastures, was measured to investigate changes to stocks among C pools following reforestation of agricultural land in the medium rainfall zone (400-800 mm yr(-1)) of temperate Australia. These mixed-species plantings accumulated 3.09 ± 0.85 t C ha(-1) yr(-1) in aboveground biomass and 0.18 ± 0.05 t C ha(-1) yr(-1) in plant litter, reaching amounts comparable to those measured in remnant woodlands by 20 years and 36 years after reforestation respectively. Soil C was slower to increase, with increases seen only after 45 years, at which time stocks had not reached the amounts found in remnant woodlands. The amount of trees (tree density and basal area) was positively associated with the accumulation of carbon in aboveground biomass and litter. In contrast, changes to soil C were most strongly related to the productivity of the location (a forest productivity index and soil N content in the adjacent pasture). At 30 years, native mixed-species plantings had increased the stability of soil C stocks, with higher amounts of recalcitrant C and higher C:N ratios than their adjacent pastures. Reforestation with native mixed-species plantings did not significantly change the availability of macronutrients (N, K, Ca, Mg, P, and S) or micronutrients (Fe, B, Mn, Zn, and Cu), content of plant toxins (Al, Si), acidity, or salinity (Na, electrical conductivity) in the soil. In this medium rainfall area, native mixed-species plantings provided comparable rates of C sequestration to local production species, with the probable additional benefit of providing better quality habitat for native biota. These results demonstrate that reforestation using native mixed-species plantings is an effective alternative for carbon sequestration to standard monocultures of production species in medium rainfall areas of temperate continental climates, where they can effectively store C, convert C into stable pools and provide greater benefits for biodiversity.

Building a Regionally Connected Reserve Network in a Changing and Uncertain World

Habitat connectivity is required at large spatial scales to facilitate movement of biota in response to climatic changes and to maintain viable populations of wide-ranging species. Nevertheless, it may require decades to acquire habitat linkages at such scales, and areas that could provide linkages are often developed before they can be reserved. Reserve scheduling methods usually consider only current threats, but threats change over time as development spreads and reaches presently secure areas. We investigated the importance of considering future threats when implementing projects to maintain habitat connectivity at a regional scale. To do so, we compared forward-looking scheduling strategies with strategies that consider only current threats. The strategies were applied to a Costa Rican case study, where many reserves face imminent isolation and other reserves will probably become isolated in the more distant future. We evaluated strategies in terms of two landscape-scale connectivity metrics, a pure connectivity metric and a metric of connected habitat diversity. Those strategies that considered only current threats were unreliable because they often failed to complete planned habitat linkage projects. The most reliable and effective strategies considered the future spread of development and its impact on the likelihood of completing planned habitat linkage projects. Our analyses highlight the critical need to consider future threats when building connected reserve networks over time.

Finding needles (or ants) in haystacks: predicting locations of invasive organisms to inform eradication and containment

To eradicate or effectively contain a biological invasion, all or most reproductive individuals of the invasion must be found and destroyed. To help find individual invading organisms, predictions of probable locations can be made with statistical models. We estimated spread dynamics based on time-series data and then used model-derived predictions of probable locations of individuals. We considered one of the largest data sets available for an eradication program: the campaign to eradicate the red imported fire ant (Solenopsis invicta) from around Brisbane, Australia. After estimating within-site growth (local growth) and intersite dispersal (saltatory spread) of fire ant nests, we modeled probabilities of fire ant presence for >600000 1-ha sites, including uncertainties about fire ant population and spatial dynamics. Such a high level of spatial detail is required to assist surveillance efforts but is difficult to incorporate into common modeling methods because of high computational costs. More than twice as many fire ant nests would have been found in 2008 using predictions made with our method rather than those made with the method currently used in the study region. Our method is suited to considering invasions in which a large area is occupied by the invader at low density. Improved predictions of such invasions can dramatically reduce the area that needs to be searched to find the majority of individuals, assisting containment efforts and potentially making eradication a realistic goal for many invasions previously thought to be ineradicable.