Winner-Loser Species Replacements in Human-Modified Landscapes

Plant virus community structuring is shaped by habitat heterogeneity and traits for host plant resource utilisation

Host plants provide resources critical to viruses and the spatial structuring of plant communities affects the niches available for colonisation and disease emergence. However, large gaps remain in the understanding of mechanisms that govern plant-virus disease ecology across heterogeneous plant assemblages. We combine high-throughput sequencing, network, and metacommunity approaches to test whether habitat heterogeneity in plant community composition corresponded with virus resource utilisation traits of transmission mode and host range. A majority of viruses exhibited habitat specificity, with communities connected by key generalist viruses and potential host reservoirs. There was an association between habitat heterogeneity and virus community structuring, and between virus community structuring and resource utilisation traits of host range and transmission. The relationship between virus species distributions and virus trait responses to habitat heterogeneity was scale-dependent, being stronger at finer (site) than larger (habitat) spatial scales. Results indicate that habitat heterogeneity has a part in plant virus community assembly, and virus community structuring corresponds to virus trait responses that vary with the scale of observation. Distinctions in virus communities caused by plant resource compartmentalisation can be used to track trait responses of viruses to hosts important in forecasting disease emergence.

Using historical habitat loss to predict contemporary mammal extirpations in Neotropical forests

Understanding which species will be extirpated in the aftermath of large-scale human disturbance is critical to mitigating biodiversity loss, particularly in hyperdiverse tropical biomes. Deforestation is the strongest driver of contemporary local extinctions in tropical forests but may occur at different tempos. The 2 most extensive tropical forest biomes in South America-the Atlantic Forest and the Amazon-have experienced historically divergent pathways of habitat loss and biodiversity decay, providing a unique case study to investigate rates of local species persistence on a single continent. We quantified medium- to large-bodied mammal species persistence across these biomes to elucidate how landscape configuration affects their persistence and associated ecological functions. We collected occurrence data for 617 assemblages of medium- to large-bodied mammal species (>1 kg) in the Atlantic Forest and the Amazon. Analyzing natural habitat cover based on satellite data (1985-2022), we employed descriptive statistics and generalized linear models (GLMs) to investigate ecospecies occurrence patterns in relation to habitat cover across the landscapes. The subregional erosion of Amazonian mammal assemblage diversity since the 1970s mirrors that observed since the colonial conquest of the Atlantic Forest, given that 52.8% of all Amazonian mammals are now on a similar trajectory. Four out of 5 large mammals in the Atlantic Forest were prone to extirpation, whereas 53% of Amazonian mammals were vulnerable to extirpation. Greater natural habitat cover increased the persistence likelihood of ecospecies in both biomes. These trends reflected a median local species loss 63.9% higher in the Atlantic Forest than in the Amazon, which appears to be moving toward a turning point of forest habitat loss and degradation. The contrasting trajectories of species persistence in the Amazon and Atlantic Forest domains underscore the importance of considering historical habitat loss pathways and regional biodiversity erosion in conservation strategies. By focusing on landscape configuration and identifying essential ecological functions associated with large vertebrate species, conservation planning and management practices can be better informed.

Land-use homogenization reduces the occurrence and diversity of frugivorous birds in a tropical biodiversity hotspot

Understanding how human-modified landscapes maintain biodiversity and provide ecosystem services is crucial for establishing conservation practices. Given that responses to land-use are species-specific, it is crucial to understand how land-use changes may shape patterns of species diversity and persistence in human-modified landscapes. Here, we used a comprehensive data set on bird distribution from the Brazilian Atlantic Forest to understand how species richness and individual occurrences of frugivorous bird species responded to land-use spatial predictors and, subsequently, assess how ecological traits and phylogeny modulated these responses. Using Bayesian hierarchical modeling, we reveal that the richness of frugivorous birds was positively associated with the amount of native forest and negatively with both agriculture and pasture amount at the landscape scale. Conversely, the effect of these predictors on species occurrence and ecological traits was highly variable and presented a weak phylogenetic signal. Furthermore, land-use homogenization (i.e., the conversion of forest to pasture or agriculture) led to pervasive consequences for forest-dependent bird species, whereas several generalist species thrived in deforested areas, replacing those sensitive to habitat disturbances.

Effects of human disturbances on wildlife behaviour and consequences for predator-prey overlap in Southeast Asia

Some animal species shift their activity towards increased nocturnality in disturbed habitats to avoid predominantly diurnal humans. This may alter diel overlap among species, a precondition to most predation and competition interactions that structure food webs. Here, using camera trap data from 10 tropical forest landscapes, we find that hyperdiverse Southeast Asian wildlife communities shift their peak activity from early mornings in intact habitats towards dawn and dusk in disturbed habitats (increased crepuscularity). Our results indicate that anthropogenic disturbances drive opposing behavioural adaptations based on rarity, size and feeding guild, with more nocturnality among the 59 rarer specialists' species, more diurnality for medium-sized generalists, and less diurnality for larger hunted species. Species turnover also played a role in underpinning community- and guild-level responses, with disturbances associated with markedly more detections of diurnal generalists and their medium-sized diurnal predators. However, overlap among predator-prey or competitor guilds does not vary with disturbance, suggesting that net species interactions may be conserved.

MC, Mandujano S, Martínez-Camilo R, Martínez-Ávalos JG, Martínez-Meléndez N, Monroy-Ojeda A, Mora F, Mora-Olivo A, Muench C, Peña-Mondragón JL, Percino-Daniel R, Ramírez-Marcial N, Reyna-Hurtado R, Rodríguez-Ruíz ER, Sánchez-Cordero V, Suazo-Ortuño I, Terán-Juárez SA, Valdivieso-Pérez IA, Valencia V, Valenzuela-Galván D, Vargas-Contreras JA, Vázquez-Pérez JR, Vega-Rivera JH, Venegas-Barrera CS, Martínez-Ramos M. Underlying and proximate drivers of biodiversity changes in Mesoamerican biosphere reserves

Protected areas are of paramount relevance to conserving wildlife and ecosystem contributions to people. Yet, their conservation success is increasingly threatened by human activities including habitat loss, climate change, pollution, and species overexploitation. Thus, understanding the underlying and proximate drivers of anthropogenic threats is urgently needed to improve protected areas' effectiveness, especially in the biodiversity-rich tropics. We addressed this issue by analyzing expert-provided data on long-term biodiversity change (last three decades) over 14 biosphere reserves from the Mesoamerican Biodiversity Hotspot. Using multivariate analyses and structural equation modeling, we tested the influence of major socioeconomic drivers (demographic, economic, and political factors), spatial indicators of human activities (agriculture expansion and road extension), and forest landscape modifications (forest loss and isolation) as drivers of biodiversity change. We uncovered a significant proliferation of disturbance-tolerant guilds and the loss or decline of disturbance-sensitive guilds within reserves causing a "winner and loser" species replacement over time. Guild change was directly related to forest spatial changes promoted by the expansion of agriculture and roads within reserves. High human population density and low nonfarming occupation were identified as the main underlying drivers of biodiversity change. Our findings suggest that to mitigate anthropogenic threats to biodiversity within biosphere reserves, fostering human population well-being via sustainable, nonfarming livelihood opportunities around reserves is imperative.

Effects of landscape metrics on scorpion (Arachnida: Scorpiones) assemblage in a tropical urban ecosystem

Urban landscapes restrain the distribution of forest-dwelling species, which may be related to challenging conditions that impair body condition. The dynamics in urban areas lead to the simplification of communities that inhabit forest patches in cities with the turnover of sensitive species for opportunistic ones. In this study, we investigated the effect of urbanization on the body condition and diversity of scorpions at the landscape scale. Sampling was carried out in 10 forest patches in an urban matrix in Brazil, originally covered by a tropical rainforest. The surroundings of the landscape of each forest patch were characterized through the amount of forest, agriculture, and urban land cover. Individual body length, dry, lipid, and muscular masses were used as proxies of Tityus pusillus body condition. In total, 147 scorpions were collected, belonging to the species Ananteris mauryi, T. pusillus, T. stigmurus, and T. neglectus. Forest cover explained 28% of species variation. There was a positive relationship between forest cover and T. pusillus and A. mauryi abundances, while T. stigmurus was negatively affected by forest cover. Species richness and total scorpion abundance were not influenced by landscape metrics. In terms of body condition, only females of T. pusillus were affected by landscape variables, with individuals showing higher body mass with an increase in forest cover. Our results suggest that urban forests can support scorpion assemblages. However, there is a turnover in specialist forest species for opportunistic species. Forest cover is a crucial factor in maintaining healthy scorpion populations in urban areas.

Climate change should drive mammal defaunation in tropical dry forests

Human-induced climate change has intensified negative impacts on socioeconomic factors, the environment, and biodiversity, including changes in rainfall patterns and an increase in global average temperatures. Drylands are particularly at risk, with projections suggesting they will become hotter, drier, and less suitable for a significant portion of their species, potentially leading to mammal defaunation. We use ecological niche modelling and community ecology biodiversity metrics to examine potential geographical range shifts of non-volant mammal species in the largest Neotropical dryland, the Caatinga, and evaluate impacts of climate change on mammal assemblages. According to projections, 85% of the mammal species will lose suitable habitats, with one quarter of species projected to completely lose suitable habitats by 2060. This will result in a decrease in species richness for more than 90% of assemblages and an increase in compositional similarity to nearby assemblages (i.e., reduction in spatial beta diversity) for 70% of the assemblages. Small-sized mammals will be the most impacted and lose most of their suitable habitats, especially in highlands. The scenario is even worse in the eastern half of Caatinga where habitat destruction already prevails, compounding the threats faced by species there. While species-specific responses can vary with respect to dispersal, behavior, and energy requirements, our findings indicate that climate change can drive mammal assemblages to biotic homogenization and species loss, with drastic changes in assemblage trophic structure. For successful long-term socioenvironmental policy and conservation planning, it is critical that findings from biodiversity forecasts are considered.

The rise of hyperabundant native generalists threatens both humans and nature

In many disturbed terrestrial landscapes, a subset of native generalist vertebrates thrives. The population trends of these disturbance-tolerant species may be driven by multiple factors, including habitat preferences, foraging opportunities (including crop raiding or human refuse), lower mortality when their predators are persecuted (the 'human shield' effect) and reduced competition due to declines of disturbance-sensitive species. A pronounced elevation in the abundance of disturbance-tolerant wildlife can drive numerous cascading impacts on food webs, biodiversity, vegetation structure and people in coupled human-natural systems. There is also concern for increased risk of zoonotic disease transfer to humans and domestic animals from wildlife species with high pathogen loads as their abundance and proximity to humans increases. Here we use field data from 58 landscapes to document a supra-regional phenomenon of the hyperabundance and community dominance of Southeast Asian wild pigs and macaques. These two groups were chosen as prime candidates capable of reaching hyperabundance as they are edge adapted, with gregarious social structure, omnivorous diets, rapid reproduction and high tolerance to human proximity. Compared to intact interior forests, population densities in degraded forests were 148% and 87% higher for wild boar and macaques, respectively. In landscapes with >60% oil palm coverage, wild boar and pig-tailed macaque estimated abundances were 337% and 447% higher than landscapes with <1% oil palm coverage, respectively, suggesting marked demographic benefits accrued by crop raiding on calorie-rich food subsidies. There was extreme community dominance in forest landscapes with >20% oil palm cover where two pig and two macaque species accounted for >80% of independent camera trap detections, leaving <20% for the other 85 mammal species >1 kg considered. Establishing the population trends of pigs and macaques is imperative since they are linked to cascading impacts on the fauna and flora of local forest ecosystems, disease and human health, and economics (i.e., crop losses). The severity of potential negative cascading effects may motivate control efforts to achieve ecosystem integrity, human health and conservation objectives. Our review concludes that the rise of native generalists can be mediated by specific types of degradation, which influences the ecology and conservation of natural areas, creating both positive and detrimental impacts on intact ecosystems and human society.

Anthropogenic land-use legacies underpin climate change-related risks to forest ecosystems

Forest ecosystems with long-lasting human imprints can emerge worldwide as outcomes of land-use cessation. However, the interaction of these anthropogenic legacies with climate change impacts on forests is not well understood. Here, we set out how anthropogenic land-use legacies that persist in forest properties, following alterations in forest distribution, structure, and composition, can interact with climate change stressors. We propose a risk-based framework to identify anthropogenic legacies of land uses in forest ecosystems and quantify the impact of their interaction with climate-related stress on forest responses. Considering anthropogenic land-use legacies alongside environmental drivers of forest ecosystem dynamics will improve our predictive capacity of climate-related risks to forests and our ability to promote ecosystem resilience to climate change.

Beyond species loss: How anthropogenic disturbances drive functional and phylogenetic homogenization of Neotropical dung beetles

Anthropogenic activities drive tropical forest loss and biodiversity decay. However, few studies have addressed how the biodiversity response varies between disturbance-adapted species (i.e., winners) and those highly susceptible to disturbance (i.e., losers), or whether such responses differ between the taxonomic, functional, or phylogenetic dimensions of diversity. Understanding these dynamics can help prevent or buffer biotic homogenization processes. Using a meta-analytical approach with dung beetles as model organisms, we evaluated how anthropogenic habitat disturbances influence the multiple diversity dimensions of winner and loser species relative to conserved forest sites in the Neotropics. Habitats were organized according to a disturbance gradient ranging from second-growth forests, shaded agroforestry, lowly-shaded agroforestry, living fences, and pastures. Our database included 30 studies, from which we calculated nine metrics divided into three alfa diversity aspects: richness, evenness, and divergence. We also evaluated the beta-diversity response to disturbance and forest protection. All dimensions of dung beetle diversity decreased significantly with increasing disturbance levels, with phylogenetic diversity showing the highest losses, whereas evenness metrics increased in second-growth forests and agroforestry systems. Loser dung beetles showed high diversity loss as well as functional and phylogenetic clustering, reflecting a pervasive biotic homogenization in the most severely disturbed habitats, whereas winner species were insensitive to anthropogenic disturbances. Beta diversity increased significantly with disturbance and forest protection. Our study showed that heavy disturbances erode and homogenized all diversity dimensions of loser dung beetles. However, second-growth forests and agroforestry systems mitigated diversity loss and homogenization processes by favoring the coexistence between functional and phylogenetically distant species and maintaining assemblages compositionally similar to those in conserved forests, highlighting their importance for conservation. We encourage natural resource managers to consider protection of disturbed off-reserve forests in management schemes as these are essential for maintaining biodiversity in an increasingly anthropized world.

Future-proofing ecosystem restoration through enhancing adaptive capacity

Social-ecological ecosystem restoration involves interacting challenges, including climate change, resource overexploitation and political instability. To prepare for these and other emerging threats, we synthesized key restoration and social-ecological systems literature and derived three guiding themes that can help to enhance the adaptive capacity of restoration sites: (i) work with the existing system, (ii) create self-sustaining, adaptive systems, and (iii) foster diversity and participation. We propose a two-step approach and provide an example from Rwanda detailing the application of these principles. While site-specific activities have to be designed and implemented by local practitioners, our synthesis can guide forward-thinking restoration practice.

Regional occupancy increases for widespread species but decreases for narrowly distributed species in metacommunity time series

While human activities are known to elicit rapid turnover in species composition through time, the properties of the species that increase or decrease their spatial occupancy underlying this turnover are less clear. Here, we used an extensive dataset of 238 metacommunity time series of multiple taxa spread across the globe to evaluate whether species that are more widespread (large-ranged species) differed in how they changed their site occupancy over the 10-90 years the metacommunities were monitored relative to species that are more narrowly distributed (small-ranged species). We found that on average, large-ranged species tended to increase in occupancy through time, whereas small-ranged species tended to decrease. These relationships were stronger in marine than in terrestrial and freshwater realms. However, in terrestrial regions, the directional changes in occupancy were less extreme in protected areas. Our findings provide evidence for systematic decreases in occupancy of small-ranged species, and that habitat protection could mitigate these losses in the face of environmental change.

Bird species occupancy trends in Southeast Mexico over 1900-2020: Accounting for sighting record absences

Long-term land-use change impacts tropical bird communities through population-level and functional diversity effects from habitat loss, degradation and fragmentation, leading to land management and conservation challenges. Assessing the temporal impacts of land-use change on occupancy patterns, population change and functional traits of bird species in tropical areas is limited by the treatment of nondetections as true absences or artefacts of low sampling effort during and throughout years. With this in mind, we developed a novel Bayesian species occupancy framework to account for species absences to evaluate bird community changes in Palenque, Chiapas, Mexico, where there is opportunity for study given exceptional records of change across habitats from rainforest to urban centres. We created a novel dataset of population trends for 244 bird species over the years 1900 to 2020 from published short-term field studies, expert field notes and community science pages. Our results show that open area species had higher population increases than forest specialists over time, represented most evidently by the turnover of rainforest specialists for urban species. Modelled influence of functional traits displayed the importance of main habitat types, body mass and habitat and dietary breadth as factors that associated with bird population trends. On average, species with body masses <6.6 and > 948.4 g showed decreasing trends, while all other species showed increasing or stable trends. Our findings illuminate the value of accounting for species absences from several data sources to discover long-term species population trends and affiliated functional traits whose preservation requires conservation and land management action to protect bird ecosystem services. Primary forest conservation is key to maintaining populations of habitat and dietary specialists, such as small understorey insectivorous and large frugivorous species. Protecting rare natural savanna patches from conversion to cattle pasture is vital to prevent further extirpation of native granivores and to slow colonization by exotic and invasive species.

Biotic homogenization and differentiation of plant communities in tropical and subtropical forests

Anthropogenic impacts on biodiversity can lead to biotic homogenization (BH) and biotic differentiation (BD). BH is a process of increasing similarity in community composition (including taxonomic, functional, and phylogenetic components), whereas BD is a process of decreasing similarity over space and time. Here, we conducted a systematic review of BH and BD in plant communities in tropical and subtropical forests to identify trends and knowledge gaps. Our bibliometric search in the Web of Science returned 1989 papers, of which 151 matched our criteria and were included in the analysis. The Neotropical region had the largest number of articles, and Brazil was the most represented country with 92 studies. Regarding the type of change, homogenization was more frequent than differentiation (noted in 69.6% of publications). The taxonomic diversity component was measured more often than functional and phylogenetic diversity components. Most studies (75.6%) assessed homogenization and differentiation based on a single observation in time; as opposed to few studies that monitored plant community over multiple years. Forest fragmentation was cited as the main determinant of homogenization and differentiation processes (57.2% of articles). Our results highlight the importance of evaluating community composition over time and more than taxonomic components (i.e., functional and phylogenetic) to advance understanding of homogenization and differentiation. Both processes were scale dependent and not mutually exclusive. As such, future research should consider differentiation as a potential transition phase to homogenization and that potential differences in both processes may depend on the spatial and temporal scale adopted. Understanding the complexity and causes of homogenization and differentiation is essential for biodiversity conservation in a world increasingly affected by anthropogenic disturbances.

Seasonal flooding decreases fruit-feeding butterfly species dominance and increases spatial turnover in floodplain forests of central Amazonia

The seasonal flood pulse in Amazonia can be considered a primary driver of community structure in floodplain environments. Although this natural periodic disturbance is part of the landscape dynamics, the seasonal inundation presents a considerable challenge to organisms that inhabit floodplain forests. The present study investigated the effect of seasonal flooding on fruit-feeding butterfly assemblages in different forest types and strata in central Amazonia. We sampled fruit-feeding butterflies in the canopy and the understory using baited traps in adjacent upland (unflooded forests-terra firme), white and blackwater floodplain forests (várzea and igapó, respectively) during the low- and high-water seasons. Butterfly abundance decreased in the high-water season, especially of dominant species in várzea, but the number of species was similar between seasons in the three forest types. Species composition differed between strata in all forest types. However, the flood pulse only affected butterfly assemblages in várzea forest. The β-diversity components also differed only in várzea. Species replacement (turnover) dominated the spatial β-diversity in igapó and terra firme in both seasons and várzea in the high-water season. Nonetheless, nestedness was relatively higher in várzea forests during the low-water season, mainly due to the effect of dominant species. These results emphasize the importance of seasonal flooding to structure butterfly assemblages in floodplain forests and reveal the idiosyncrasy of butterfly community responses to flooding in different forest types. Our results also suggest that any major and rapid changes to the hydrological regime could severely affect floodplain communities adapted to this natural seasonal hydrological cycle, threatening the existence of these unique environments.

Climate change threatens the distribution of major woody species and ecosystem services provision in southern Africa

In southern Africa, woody vegetation provides essential ecological, regulation, and cultural ecosystem services (ES), yet many species and ecosystems are increasingly threatened by climate change and land-use transformations. We investigated the effect of climate change on the distribution of eight species in 18 countries in southern Africa, covering 36% of the continent. We proposed a loser/winner ranking of the species based on the changes in land climatic suitability within their historical distribution and future gains and losses of suitable areas. We interpreted these findings in terms of changes in key ES (timber, food, and energy) provision and identified hotspots of ES provision decline. We used species presence data from the Global Biodiversity Information Facility, climatic data from the AfriClim dataset, and the MaxEnt algorithm to project the changes in species-specific land climatic suitability. Among the eight investigated species, the baseline suitability range of Mopane (Colophosperm mopane) was least affected by climate change. At the same time, the area of its future distribution was projected to double, rendering it a regional winner. Another two species, manketti (Schinziophyton rautanenii) and leadwood (Combretum imberbe) showed high future gains too; however, the impact on their baseline suitability range differed between the climatic scenarios. The baseline range of African rosewood (Guibourtia coleosperma) declined entirely, and the future gains were negligible, rendering the species a regional loser. The effect of climate change was particularly severe on timber-producing species (four out of eight species), while species providing food (four species) and energy (four species) were affected less. Our projections portrayed distinct hotspot and coldspot areas, where climatic suitability for multiple species was concurrently projected to decline or persist. This assessment can inform spatially targeted adaptation and conservation actions and strategies, which are currently lacking in many African regions.

Native or Exotic: A Bibliographical Review of the Debate on Ecological Science Methodologies: Valuable Lessons for Urban Green Space Design

Knowledge from ecological sciences is an important reference for landscape design as Urban Green Spaces (UGS) play a critical role in the ecological protection of cities. There is an ongoing debate among ecologists on the value of exotic vegetation to ecosystem resilience and integrity, with authors arguing that in order for ecosystems to survive in future climates, exotic species with similar conditions in their current range must be considered. Others deem biodiversity vital for ecosystem functions and services, stating that most biodiversity losses are man-induced and should be addressed through the enhancement of native communities. Through a literature review, we confronted the arguments used in this debate, with the aim of conducting a comprehensive analysis of the potential of exotic and native vegetation in different aspects of the vegetation’s performance. The outcomes are important for the assessment of vegetation assemblages within UGS projects. Despite the strong arguments regarding their performative and adaptive capacity, we conclude that exotics pose significant ecological risks and have multiple negative impacts on ecosystem processes. Natives not only present high adaptive capacity, but also provide additional benefits for biodiversity, ecosystem integrity, and for people. In a broader framework, the literature demonstrates a preference for the use of native species in most situations.

Strong floristic distinctiveness across Neotropical successional forests

Forests that regrow naturally on abandoned fields are important for restoring biodiversity and ecosystem services, but can they also preserve the distinct regional tree floras? Using the floristic composition of 1215 early successional forests (≤20 years) in 75 human-modified landscapes across the Neotropic realm, we identified 14 distinct floristic groups, with a between-group dissimilarity of 0.97. Floristic groups were associated with location, bioregions, soil pH, temperature seasonality, and water availability. Hence, there is large continental-scale variation in the species composition of early successional forests, which is mainly associated with biogeographic and environmental factors but not with human disturbance indicators. This floristic distinctiveness is partially driven by regionally restricted species belonging to widespread genera. Early secondary forests contribute therefore to restoring and conserving the distinctiveness of bioregions across the Neotropical realm, and forest restoration initiatives should use local species to assure that these distinct floras are maintained.

Invasive rat drives complete collapse of native small mammal communities in insular forest fragments

As tropical forests are becoming increasingly fragmented, understanding the magnitude and time frame of biodiversity declines is vital for 21^st century sustainability goals. Over three decades, we monitored post-isolation changes in small mammal species richness and abundance within a forest landscape fragmented by the construction of a dam in Thailand.^1,2 We observed the near-complete collapse of species richness within 33 years, with no evidence of a recolonization effect across repeatedly sampled islands. Our results further revealed a decline in species richness as island size decreased and isolation time increased, accelerated by the increasing dominance of the ubiquitous Malayan field rat, Rattus tiomanicus. This species was already hyper-abundant on smaller islands in the initial surveys (1992-1994, 66% of individuals) but became monodominant on all islands, regardless of island size, by the most recent survey (2020, 97%). Our results suggest that insular forest fragments are highly susceptible to rapid species loss, particularly due to the competitive nature of Rattus accelerating the rate at which extinction debts are paid. To mitigate these impacts, reducing the extent of habitat degradation, as triggered by fragmentation and exacerbated by isolation time, can help to sustain native biodiversity while averting Rattus hyper-abundance.

Overcoming biotic homogenization in ecological restoration

Extensive evidence shows that regional (gamma) diversity is often lower across restored landscapes than in reference landscapes, in part due to common restoration practices that favor widespread species through selection of easily-grown species with high survival and propagation practices that reduce genetic diversity. We discuss approaches to counteract biotic homogenization, such as reintroducing species that are adapted to localized habitat conditions and are unlikely to colonize naturally; periodically reintroducing propagules from remnant populations to increase genetic diversity; and reintroducing higher trophic level fauna to restore interaction networks and processes that promote habitat heterogeneity. Several policy changes would also increase regional diversity; these include regional coordination amongst restoration groups, financial incentives to organizations producing conservation-valued species, and experimental designations for rare species introductions.

The ecology of the banded civet ( Hemigalus derbyanus ) in Southeast Asia with implications for mesopredator release, zoonotic diseases, and conservation

Habitat loss and degradation threaten forest specialist wildlife species, but some generalist mesopredators exploit disturbed areas and human‐derived food, which brings them into closer contact with humans. Mesopredator release is also important for human health for known zoonotic disease reservoirs, such as Asian civets (Viverridae family), since this group includes the intermediator species for the SARS‐CoV‐1 outbreak. Here we use camera trapping to evaluate the habitat associations of the widespread banded civet (Hemigalus derbyanus) across its range in Southeast Asia. At the regional scale, banded civet detections among published studies were positively associated with forest cover and negatively associated with human population. At the local scale (within a landscape), hierarchical modeling of new camera trapping showed that abundance was negatively associated with forest loss and positively associated with distance to rivers. These results do not support mesopredator release and suggest a low likelihood overlap with humans in degraded habitats and, therefore, a low risk of zoonotic disease transmission from this species in the wild. We also estimate that banded civet distribution has contracted to under 21% of its currently recognized IUCN Red List range, only 12% of which falls within protected areas, and a precipitous recent decline in population size. Accordingly, we suggest the banded civet's Red List status should be re‐evaluated in light of our findings.

Environmental variables drive plant species composition and distribution in the moist temperate forests of Northwestern Himalaya, Pakistan

By assessing plant species composition and distribution in biodiversity hotspots influenced by environmental gradients, we greatly advance our understanding of the local plant community and how environmental factors are affecting these communities. This is a proxy for determining how climate change influences plant communities in mountainous regions ("space-for-time" substitution). We evaluated plant species composition and distribution, and how and which environmental variables drive the plant communities in moist temperate zone of Manoor valley of Northwestern Himalaya, Pakistan. During four consecutive years (2015-2018), we sampled 30 sampling sites, measuring 21 environmental variables, and recording all plant species present in an altitudinal variable range of 1932-3168 m.a.s.l. We used different multivariate analyses to identify potential plant communities, and to evaluate the relative importance of each environmental variable in the species composition and distribution. Finally, we also evaluated diversity patterns, by comparing diversity indices and beta diversity processes. We found that (i) the moist temperate zone in this region can be divided in four different major plant communities; (ii) each plant community has a specific set of environmental drivers; (iii) there is a significant variation in plant species composition between communities, in which six species contributed most to the plant composition dissimilarity; (iv) there is a significant difference of the four diversity indices between communities; and (v) community structure is twice more influenced by the spatial turnover of species than by the species loss. Overall, we showed that altitudinal gradients offer an important range of different environmental variables, highlighting the existence of micro-climates that drive the structure and composition of plant species in each micro-region. Each plant community along the altitudinal gradient is influenced by a set of environmental variables, which lead to the presence of indicator species in each micro-region.

Common palm civets (Paradoxurus hermaphroditus) are positively associated with humans and forest degradation with implications for seed dispersal and zoonotic diseases

1. Habitat loss and degradation can undermine wildlife communities and ecosystem functioning. However, certain generalist wildlife species like mesopredators and omnivores can exploit these disturbed habitats, sometimes leading to population increases (e.g., "mesopredator release" in degraded areas). Although mesopredator release may cause negative effects on food webs and zoonotic disease management, some disturbance-tolerant species may help perpetuate important ecological interactions, such as seed dispersal. 2. We evaluated the habitat associations of common palm civets (Paradoxurus hermaphroditus), which are widespread generalist mesopredators in Southeast Asia. Common palm civets are also high-quality seed dispersers, and potential zoonotic disease hosts. 3. We used published and new camera trapping data to map their probability of presence across Southeast Asia and evaluate regional-scale associations between capture rates and habitat variables such as elevation, ecoregion intactness, and Human Footprint Index, among others. We also assessed the influence of habitat variables on their relative abundance at the local scale. 4. At the regional scale, we found that common palm civets showed significant positive associations with landscapes characterized by lower ecoregion intactness, higher Human Footprint Index, and lower elevations. At the local scale, their relative abundance showed a significant positive association with higher Human Footprint Index, but only to a certain point, after which it started decreasing. They also favored lower elevations at the local scale. 5. These multi-scale results indicate that common palm civets' abundance can increase under certain levels of human disturbances, consistent with the "mesopredator release" hypothesis. This suggests they may be crucial seed dispersers in degraded forest landscapes, especially where more sensitive seed dispersers have disappeared. Our results are also consistent with previous studies reporting that habitat degradation increases populations of potential zoonotic disease hosts, and thus risks of transmission to humans.

Land-use change and rodent-borne diseases: hazards on the shared socioeconomic pathways

Land-use change has a direct impact on species survival and reproduction, altering their spatio-temporal distributions. It acts as a selective force that favours the abundance and diversity of reservoir hosts and affects host-pathogen dynamics and prevalence. This has led to land-use change being a significant driver of infectious diseases emergence. Here, we predict the presence of rodent taxa and map the zoonotic hazard (potential sources of harm) from rodent-borne diseases in the short and long term (2025 and 2050). The study considers three different land-use scenarios based on the shared socioeconomic pathways narratives (SSPs): sustainable (SSP1-Representative Concentration Pathway (RCP) 2.6), fossil-fuelled development (SSP5-RCP 8.5) and deepening inequality (SSP4-RCP 6.0). We found that cropland expansion into forest and pasture may increase zoonotic hazards in areas with high rodent-species diversity. Nevertheless, a future sustainable scenario may not always reduce hazards. All scenarios presented high heterogeneity in zoonotic hazard, with high-income countries having the lowest hazard range. The SSPs narratives suggest that opening borders and reducing cropland expansion are critical to mitigate current and future zoonotic hazards globally, particularly in middle- and low-income economies. Our study advances previous efforts to anticipate the emergence of zoonotic diseases by integrating past, present and future information to guide surveillance and mitigation of zoonotic hazards at the regional and local scale. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one another. As a result, non-saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false-negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.

Avian extinctions induced by the oldest Amazonian hydropower mega dam: evidence from museum collections and sighting data spanning 172 years

Hydroelectric dams represent an emergent threat to lowland tropical forest biodiversity. Despite the large number of operational, under-construction, and planned hydroelectric dams, their long-term effects on biodiversity loss are still poorly documented. Here, we investigate avian extinctions resulting from the Tucuruí Hydroelectric Reservoir (THR), the oldest Amazonian mega dam, which impounded the Tocantins River in 1984. Our avian inventory-based on several sampling methods (mist-netting, point-counts, boat census and qualitative surveys) during 280 days of fieldwork from 2005 to 2007-was combined with an exhaustive search of museum vouchers and digital online databases of citizen science from the lower Tocantins River to identify long-term trends in species persistence and extinction in the THR influence area. The regional avifauna was comprised of 479 species, 404 of which were recorded during our fieldwork. Based on recent and historical records spanning 172 years, we found evidence for likely extinctions at THR influence area for 53 (11.06%) species that have remained entirely unreported since 1984. We were further able to estimate extinction probabilities for 20 species; 15 species were considered to be extinct, including Psophia interjecta and Pyrilia vulturina that are red-listed by IUCN. Our study serves as a baseline for avifaunal monitoring in the THR influence area and shows that degree of habitat specialization is a key factor in determining species extinctions caused by nonrandom habitat loss from either inundation or deforestation. Avian species extinctions will most likely continue across the area affected by the reservoir as a direct impact of alluvial forest loss and ongoing habitat degradation of upland forests.