Evaluating the legacy of landscape history: extinction debt and species credit in bird and small mammal assemblages in the Brazilian Atlantic Forest

Ongoing over-exploitation and delayed responses to environmental change highlight the urgency for action to promote vertebrate recoveries by 2030

To safeguard nature, we must understand the drivers of biodiversity loss. Time-delayed biodiversity responses to environmental changes (ecological lags) are often absent from models of biodiversity change, despite their well-documented existence. We quantify how lagged responses to climate and land-use change have influenced mammal and bird populations around the world, while incorporating effects of direct exploitation and conservation interventions. Ecological lag duration varies between drivers, vertebrate classes and body size groupings-e.g. lags linked to climate-change impacts are 13 years for small birds, rising to 40 years for larger species. Past warming and land conversion generally combine to predict population declines; however, such conditions are associated with population increases for small mammals. Positive effects of management (>+4% annually for large mammals) and protected areas (>+6% annually for large birds) on population trends contrast with the negative impact of exploitation (<-7% annually for birds), highlighting the need to promote sustainable use. Model projections suggest a future with winners (e.g. large birds) and losers (e.g. medium-sized birds), with current/recent environmental change substantially influencing abundance trends to 2050. Without urgent action, including effective conservation interventions and promoting sustainable use, ambitious targets to stop declines by 2030 may already be slipping out of reach.

Moving-habitat models: A numerical approach

As the global climate changes, biological populations have to adapt in place or move in space to stay within their preferred temperature regime. Empirical evidence suggests that shifting speeds of temperature isoclines are location and elevation dependent and may accelerate over time. We present a mathematical tool to study transient behaviour of population dynamics within such moving habitats to discern between populations at high and low risk of extinction. We introduce a system of reaction-diffusion equations to study the impact of varying shifting speeds on the persistence and distribution of a single species. Our model includes habitat dependent movement behaviour and habitat preference of individuals. These assumptions result in a jump in density across habitat types and generalize previous studies. We build and validate a numerical finite difference scheme to solve the resulting equations. Our numerical scheme uses a coordinate system where the location of the moving suitable habitat is fixed in space and a modification of a finite difference scheme to capture the jump in density. We explore a variety of shifting-speed scenarios and contribute insights into the mechanisms that support population persistence through time in shifting habitats. One common finding is that a strong bias for the suitable habitat helps the population persist at faster shifting speeds, yet sustains a smaller total population at slower shifting speeds.

Bird Extinctions in Brazil’s Atlantic Forest and How They Can Be Prevented

Bird species extinctions in the Atlantic Forest of Brazil have been predicted since the early 1990s, but it has become accepted wisdom that none have yet been documented. We revisit this question in light of updates to the global Red List, and conclude that between five and seven bird species have likely been driven to extinction in the wild in this biome in recent decades, plus a further two species that occurred elsewhere in Brazil. These extinctions were the result of habitat loss in combination with other threats. A further nine Atlantic Forest bird species are Critically Endangered, plus six from elsewhere in Brazil. We review growing efforts to help these species avoid extinction using a range of tools including multi-stakeholder planning, advocacy, habitat protection and restoration on public and private land, focussed research, and intensive population management, drawing on examples from the most threatened Atlantic Forest endemics. Conservation organisations, local communities, government agencies, zoos, international funders, universities and others are working together to prevent these species from disappearing. While the political environment in Brazil has rarely been more hostile to conservation, there are also some positive trends. Rates of deforestation in the Atlantic Forest have fallen, forest restoration and recovery is increasing, and an unprecedented number of ordinary people are taking an interest in birds and participating in citizen science. With dedication, collaboration, sufficient resources, and a focus on evidence-informed solutions, we are hopeful that many of the Critically Endangered species can be pulled back from the brink of extinction.

A strategy for wildlife management in depopulating rural areas of Japan

Former ranges of wild animals have been reestablished in many developed countries. However, this reestablishment has led to increasing human-wildlife conflict in agroforest ecosystems. In Japan, human-wildlife conflict, such as crop raiding by and ecological impacts of wild ungulates and primates, is a serious problem in depopulated rural areas due to these animal range expansions and increased abundances. Japan's human population is predicted to decline by 24% by 2050, and approximately 20% of agricultural settlements will become completely depopulated. In this scenario, anthropogenic pressures on wildlife (e.g., hunting and habitat alteration) will continue to decrease and human-wildlife conflict will increase due to increasing wildlife recovery. Japan's local governments plan to slow range recovery, prevent species reestablishment, or remove recolonizing large mammals through lethal control. This strategy, however, is not cost-effective, and workforce shortages in depopulated communities make it infeasible. Moreover, the suppression of wildlife prevents the recovery of ecological functions and thus would degrade regional biodiversity. The declining pressure on wildlife that accompanies human depopulation will prevent the restoration of any past states of human-wildlife interaction. We suggest human-used areas in rural landscapes be aggregated in compact cities and that in transition zones between human settlements and depopulated lands that land-sharing approaches be applied. Concentrating management efforts in compact cities may effectively decrease human-wildlife conflict, rather than intensifying human pressures. Reforestation of depopulated lands may lead to recovery of wildlife habitats, their ecosystem functions, and regional biodiversity due to minimization of negative anthropogenic effects (land-sparing approach). Balancing resolution of human-wildlife conflict and ecological rewilding could become a new, challenging task for regional wildlife managers.

Cold War spy satellite images reveal long-term declines of a philopatric keystone species in response to cropland expansion

Agricultural expansion drives biodiversity loss globally, but impact assessments are biased towards recent time periods. This can lead to a gross underestimation of species declines in response to habitat loss, especially when species declines are gradual and occur over long time periods. Using Cold War spy satellite images (Corona), we show that a grassland keystone species, the bobak marmot (Marmota bobak), continues to respond to agricultural expansion that happened more than 50 years ago. Although burrow densities of the bobak marmot today are highest in croplands, densities declined most strongly in areas that were persistently used as croplands since the 1960s. This response to historical agricultural conversion spans roughly eight marmot generations and suggests the longest recorded response of a mammal species to agricultural expansion. We also found evidence for remarkable philopatry: nearly half of all burrows retained their exact location since the 1960s, and this was most pronounced in grasslands. Our results stress the need for farsighted decisions, because contemporary land management will affect biodiversity decades into the future. Finally, our work pioneers the use of Corona historical Cold War spy satellite imagery for ecology. This vastly underused global remote sensing resource provides a unique opportunity to expand the time horizon of broad-scale ecological studies.

Ecological time lags and the journey towards conservation success

Global conservation targets to reverse biodiversity declines and halt species extinctions are not being met despite decades of conservation action. However, a lack of measurable change in biodiversity indicators towards these targets is not necessarily a sign that conservation has failed; instead, temporal lags in species' responses to conservation action could be masking our ability to observe progress towards conservation success. Here we present our perspective on the influence of ecological time lags on the assessment of conservation success and review the principles of time lags and their ecological drivers. We illustrate how a number of conceptual species may respond to change in a theoretical landscape and evaluate how these responses might influence our interpretation of conservation success. We then investigate a time lag in a real biodiversity indicator using empirical data and explore alternative approaches to understand the mechanisms that drive time lags. Our proposal for setting and evaluating conservation targets is to use milestones, or interim targets linked to specific ecological mechanisms at key points in time, to assess whether conservation actions are likely to be working. Accounting for ecological time lags in biodiversity targets and indicators will greatly improve the way that we evaluate conservation successes.

Medium and large mammals in a Cerrado fragment in Southeast Goiás, Brazil: inventory and immediate effects of habitat reduction on species richness and composition

Abstract: The reduction and fragmentation of remnant vegetation habitats has been one of the main threats to Cerrado biodiversity. The aim of the present study is to make an inventory of medium and large mammal species in a Cerrado remnant and to assess deforestation influence on part of this fragment on the richness and composition of mammal species. The study was conducted in a Cerrado fragment in southeast Goias State, Ipameri County. Data were collected during three different periods (P1, January-June, 2014; P2, December, 2016 - June, 2017; P3, July-December, 2017) through direct (visual, vocal and camera-trap records) and indirect methods (foot prints, animal burrows and other traces) in order to register the mammal species. Jackknife 1 estimator was used to estimate species richness during each of the three sampled periods and for the complete collection period; species similarity between periods was assessed through the Jaccard's Index of Similarity (Cj). Species richness between periods was performed through inference by overlapping confidence intervals (CI). Twenty-nine species were recorded during the assessed period, five of them were listed as endangered in Brazil. There was no significant change in species richness between the assessed periods: species richness of 25 species was observed in Period 1 (P1), the richness of 32 species was estimated (CI = 4.58); 23 species were recorded in Period 2 (P2), and the richness of 30 species was estimated (CI = 4.39), the richness of 23 species was observed in Period 3 (P3) and the richness of 28 species was estimated (CI = 4.70). Similarity in species composition between the assessed periods recorded Cj = 0.71 (71%) between P1 and P2, Cj = 0.66 (66%) between P1 and P3, and Cj = 0.77 between P2 and P3. Fragment deforestation did not influence the richness and composition of medium and large mammal species (within a period of 2~3 years) when the three periods were compared; however, the absence of changes in the community can be the result of time-lag, therefore, we cannot put aside the likelihood of mid and long-term effects.

Time-lagged response of carabid species richness and composition to past management practices and landscape context of semi-natural field margins

Field margins are key features for the maintenance of biodiversity and associated ecosystem services in agricultural landscapes. Little is known about the effects of management practices of old semi-natural field margins, and their historical dimension regarding past management practices and landscape context is rarely considered. In this paper, the relative influence of recent and past management practices and landscape context (during the last five years) were assessed on the local biodiversity (species richness and composition) of carabid assemblages of field margins in agricultural landscapes of northwestern France. The results showed that recent patterns of carabid species richness and composition were best explained by management practices and landscape context measured four or five years ago. It suggests the existence of a time lag in the response of carabid assemblages to past environmental conditions of field margins. The relative contribution of past management practices and past landscape context varied depending on the spatial scale at which landscape context was taken into account. Carabid species richness was higher in grazed or sprayed field margins probably due to increased heterogeneity in habitat conditions. Field margins surrounded by grasslands and crops harbored species associated with open habitats whilst forest species dominated field margins surrounded by woodland. Landscape effect was higher at fine spatial scale, within 50 m around field margins. The present study highlights the importance of considering time-lagged responses of biodiversity when managing environment. It also suggests that old semi-natural field margins should not be considered as undisturbed habitats but more as management units being part of farming activities in agricultural landscapes, as for arable fields.

Long-term monitoring reveals an avian species credit in secondary forest patches of Costa Rica

Degraded and secondary forests comprise approximately 50% of remaining tropical forest. Bird community characteristics and population trends in secondary forests are infrequently studied, but secondary forest may serve as a “safety net” for tropical biodiversity. Less understood is the occurrence of time-delayed, community-level dynamics such as an extinction debt of specialist species or a species credit resulting from the recolonization of forest patches by extirpated species. We sought to elucidate patterns and magnitudes of temporal change in avian communities in secondary forest patches in Southern Costa Rica biannually over a 10 year period during the late breeding season and mid-winter. We classified birds caught in mist nets or recorded in point counts by residency status, and further grouped them based on preferred habitat, sensitivity to disturbance, conservation priority, foraging guild, and foraging strata. Using hierarchical, mixed-effects models we tested for trends among species that share traits. We found that permanent-resident species increased over time relative to migrants. In both seasons, primary forest species generally increased while species typical of secondary forest, scrub, or edge declined. Species relatively sensitive to habitat disturbance increased significantly over time, whereas birds less sensitive to disturbance decreased. Similarly, generalists with higher habitat breadth scores declined. Because, we found very few changes in vegetation characteristics in secondary forest patches, shifts in the avian community toward primary forest species represent a species credit and are likely related to vegetation changes in the broader landscape. We suggest that natural regeneration and maturation of secondary forests should be recognized as a positive conservation development of potential benefit even to species typical of primary forest.

Trophic Niche Differentiation in Rodents and Marsupials Revealed by Stable Isotopes

Tropical rainforests support the greatest diversity of small mammals in the world, yet we have little understanding about the mechanisms that promote the coexistence of species. Diet partitioning can favor coexistence by lessening competition, and interspecific differences in body size and habitat use are usually proposed to be associated with trophic divergence. However, the use of classic dietary methods (e.g. stomach contents) is challenging in small mammals, particularly in community-level studies, thus we used stable isotopes (δ¹³C and δ¹⁵N) to infer about trophic niche. We investigated i) how trophic niche is partitioned among rodent and marsupial species in three Atlantic forest sites and ii) if interspecific body size and locomotor habit inequalities can constitute mechanisms underlying the isotopic niche partitioning. We found that rodents occupied a broad isotopic niche space with species distributed in different trophic levels and relying on diverse basal carbon sources (C3 and C4 plants). Surprisingly, on the other hand, marsupials showed a narrow isotopic niche, both in δ¹³C and δ¹⁵N dimensions, which is partially overlapped with rodents, contradicting their description as omnivores and generalists proposed classic dietary studies. Although body mass differences did not explained the divergence in isotopic values among species, groups of species with different locomotor habit presented clear differences in the position of the isotopic niche space, indicating that the use of different forest strata can favor trophic niche partitioning in small mammals communities. We suggest that anthropogenic impacts, such as habitat modification (logging, harvesting), can simplify the vertical structure of ecosystems and collapse the diversity of basal resources, which might affect negatively small mammals communities in Atlantic forests.

Time-Lag in Responses of Birds to Atlantic Forest Fragmentation: Restoration Opportunity and Urgency

There are few opportunities to evaluate the relative importance of landscape structure and dynamics upon biodiversity, especially in highly fragmented tropical landscapes. Conservation strategies and species risk evaluations often rely exclusively on current aspects of landscape structure, although such limited assumptions are known to be misleading when time-lag responses occur. By relating bird functional-group richness to forest patch size and isolation in ten-year intervals (1956, 1965, 1978, 1984, 1993 and 2003), we revealed that birds with different sensitivity to fragmentation display contrasting responses to landscape dynamics in the Brazilian Atlantic Forest. For non-sensitive groups, there was no time-lag in response: the recent degree of isolation best explains their variation in richness, which likely relates to these species' flexibility to adapt to changes in landscape structure. However, for sensitive bird groups, the 1978 patch area was the best explanatory variable, providing evidence for a 25-year time-lag in response to habitat reduction. Time-lag was more likely in landscapes that encompass large patches, which can support temporarily the presence of some sensitive species, even when habitat cover is relatively low. These landscapes potentially support the most threatened populations and should be priorities for restoration efforts to avoid further species loss. Although time-lags provide an opportunity to counteract the negative consequences of fragmentation, it also reinforces the urgency of restoration actions. Fragmented landscapes will be depleted of biodiversity if landscape structure is only maintained, and not improved. The urgency of restoration action may be even higher in landscapes where habitat loss and fragmentation history is older and where no large fragment remained to act temporarily as a refuge.

Assessing coexisting plant extinction debt and colonization credit in a grassland-forest change gradient

Changes in species richness along the ecological succession gradient may be strongly determined by coexisting extinction debts of species from the original habitats and colonization credits of those from the replacing habitats. The magnitude of these processes and their causes remain largely unknown. We explored the extinction debt and colonization credit for grassland and forest specialist plants, respectively, and the local and landscape factors associated to the richness of these species groups in a 50-year process of forest encroachment into semi-natural Mediterranean grasslands. A set of sampling plots of persistent grasslands and forests and their transitional habitat (wooded grasslands) was selected within fixed-area sites distributed across the landscape. Our results confirm the extinction debt and suggest colonization credit (according to observed trends and model predictions) in wooded grasslands when compared to persistent forests, despite wooded grasslands and persistent forests having similar tree cover. Grassland connectivity and solar radiation had opposing effects on the richness of both grassland and forest specialists, and it is possible that the availability of seed sources from old forests may have accelerate the payment of colonization credit in the wooded grasslands. These results suggest that extinction debt and colonization credit have driven species turnover during the 50 years of forest encroachment, but at different rates, and that local and landscape factors have opposing effects on these two phenomena. They also highlight the importance of documenting biodiversity time lags following habitat change when they are still in progress in order to timely and adequately manage habitats of high conservation value such as the grasslands studied here.

Experiences from the Brazilian Atlantic Forest: ecological findings and conservation initiatives

The Brazilian Atlantic Forest hosts one of the world's most diverse and threatened tropical forest biota. In many ways, its history of degradation describes the fate experienced by tropical forests around the world. After five centuries of human expansion, most Atlantic Forest landscapes are archipelagos of small forest fragments surrounded by open-habitat matrices. This 'natural laboratory' has contributed to a better understanding of the evolutionary history and ecology of tropical forests and to determining the extent to which this irreplaceable biota is susceptible to major human disturbances. We share some of the major findings with respect to the responses of tropical forests to human disturbances across multiple biological levels and spatial scales and discuss some of the conservation initiatives adopted in the past decade. First, we provide a short description of the Atlantic Forest biota and its historical degradation. Secondly, we offer conceptual models describing major shifts experienced by tree assemblages at local scales and discuss landscape ecological processes that can help to maintain this biota at larger scales. We also examine potential plant responses to climate change. Finally, we propose a research agenda to improve the conservation value of human-modified landscapes and safeguard the biological heritage of tropical forests.

Assessing the utility of statistical adjustments for imperfect detection in tropical conservation science

In recent years, there has been a fast development of models that adjust for imperfect detection. These models have revolutionized the analysis of field data, and their use has repeatedly demonstrated the importance of sampling design and data quality. There are, however, several practical limitations associated with the use of detectability models which restrict their relevance to tropical conservation science.

We outline the main advantages of detectability models, before examining their limitations associated with their applicability to the analysis of tropical communities, rare species and large‐scale data sets. Finally, we discuss whether detection probability needs to be controlled before and/or after data collection.

Models that adjust for imperfect detection allow ecologists to assess data quality by estimating uncertainty and to obtain adjusted ecological estimates of populations and communities. Importantly, these models have allowed informed decisions to be made about the conservation and management of target species.

Data requirements for obtaining unadjusted estimates are substantially lower than for detectability‐adjusted estimates, which require relatively high detection/recapture probabilities and a number of repeated surveys at each location. These requirements can be difficult to meet in large‐scale environmental studies where high levels of spatial replication are needed, or in the tropics where communities are composed of many naturally rare species. However, while imperfect detection can only be adjusted statistically, covariates of detection probability can also be controlled through study design. Using three study cases where we controlled for covariates of detection probability through sampling design, we show that the variation in unadjusted ecological estimates from nearly 100 species was qualitatively the same as that obtained from adjusted estimates. Finally, we discuss that the decision as to whether one should control for covariates of detection probability through study design or statistical analyses should be dependent on study objectives.

Synthesis and applications. Models that adjust for imperfect detection are an important part of an ecologist's toolkit, but they should not be uniformly adopted in all studies. Ecologists should never let the constraints of models dictate which questions should be pursued or how the data should be analysed, and detectability models are no exception. We argue for pluralism in scientific methods, particularly where cost‐effective applied ecological science is needed to inform conservation policy at a range of different scales and in many different systems.

Models that adjust for imperfect detection are an important part of an ecologist's toolkit, but they should not be uniformly adopted in all studies. Ecologists should never let the constraints of models dictate which questions should be pursued or how the data should be analysed, and detectability models are no exception. We argue for pluralism in scientific methods, particularly where cost‐effective applied ecological science is needed to inform conservation policy at a range of different scales and in many different systems.