Patterns Of Species Loss Research Articles

NetworkExtinction: An R package to simulate extinction propagation and rewiring potential in ecological networks

Abstract Earth's biosphere is undergoing drastic reorganization due to the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, leading to secondary extinctions and exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for directly simulating and quantifying extinction cascades and creating novel interactions (i.e. rewiring) remains absent. Here, we present NetworkExtinction—a novel R package which we have developed to explore the propagation of species extinction sequences through ecological networks and quantify the effects of rewiring potential in response to primary species extinctions. With NetworkExtinction, we integrate ecological theory and computational simulations to develop functionality with which users may analyse and visualize the structure and robustness of ecological networks. The core functions introduced with NetworkExtinction focus on simulations of sequential primary extinctions and associated secondary extinctions, allowing user‐specified secondary extinction thresholds and realization of rewiring potential. With the package NetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In‐built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can estimate the network's degree distribution by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analysing a Chilean coastal marine food web. NetworkExtinction is a compact and easy‐to‐use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds and rewiring potential. Therefore, this package is particularly useful for evaluating ecosystem responses to anthropogenic and environmental perturbations that produce nonrandom and sometimes targeted, species extinctions.

Predicting diversity changes in subalpine moorland ecosystems based on geometry of species distributions and realistic area loss

AbstractQuestionHow does plant species richness respond to simulated area loss based on the realistic geometry of area loss in subalpine moorland ecosystems?LocationHakkoda mountain range, Aomori, Japan.MethodsWe constructed species distribution models based on relationships between species distributions and environmental conditions in subalpine moorland ecosystems. We then simulated moorland area loss based on the realistic geometry of area loss from the past (1967) to the present (2019) to predict future changes in plant diversity. Here, we defined the realistic geometry of area loss as the plausible spatial pattern of future habitat loss. Finally, we analyzed how the rate of species loss in response to the realistic area loss can be explained by a range of factors including spatial patterns in species distributions, total number of species present, and environmental variables for the focal moorland.ResultsWithin each moorland site, areas prone or those less prone to be lost were distributed non‐randomly at a local scale. In general, the patterns of species loss caused by the realistic area loss differed from those caused by random area loss. At most sites, realistic area loss caused a relatively small decline in species richness up to a certain threshold of area loss, and accelerating decline thereafter. None of the factors can explain the rate of decrease in species richness caused by the realistic area loss. At the species level, however, species with lower occurrence rates at a given site can be lost earlier than those with higher occurrence rates by the realistic area loss.ConclusionsPatterns of habitat loss and species distributions are not spatially random, and the classical approach based on the species–area relationship assuming random area loss can thus either under‐ or overestimate the risk of species loss.

Metabarcoding of canopy arthropods reveals negative impacts of forestry insecticides on community structure across multiple taxa

Abstract Insecticides used to combat outbreaks of forest defoliators can adversely affect non‐target arthropods. Forestry insecticides typically suppress Lepidoptera larvae which are the cornerstone of the canopy community of deciduous oak forests. The abrupt removal of this dominant component of the food web could have far‐reaching implications for forest ecosystems, yet it is rarely investigated in practice owing to several methodological shortcomings. The taxonomic impediment and the biased nature of arthropod sampling techniques particularly impede the assessment of insecticide impacts on diverse communities. To tackle this issue, we propose an experimental approach combining sampling by pyrethrum knockdown and species determination via DNA metabarcoding, using community subsampling to derive estimates of species abundances. We applied this protocol to investigate the short‐term effects of the insecticides diflubenzuron (DFB) and Bacillus thuringiensis var. kurstaki (BTK) on canopy‐dwelling arthropod communities in German oak woodlands. Our approach allowed us to detect most of the diversity and integrate species abundances in our analyses. By classifying arthropod species into assemblages based on their expected sensitivity rather than coarse taxonomic groupings, we could unveil substantial effects of DFB across multiple taxa 5 weeks after application. Although strong effects on single species appear related to direct toxicity, substantial impacts of DFB on parasitoids and xylophagous beetles suggest that anti‐defoliator treatments can have previously unsuspected indirect effects on some components of forest arthropod communities. The impacts of BTK on community structure were consistent with that of DFB though much weaker. Synthesis and applications. Comparing diversity patterns in the arthropod communities of sprayed and unsprayed oak canopies, our results show that selective insecticides can alter species diversity in presumably non‐sensitive taxa. Even though the ecological significance of these impacts has yet to be assessed in an operational setting, their existence calls for increased regulatory scrutiny on indirect effects. As community approaches become more attainable with the rapid development of DNA metabarcoding, we suggest the inclusion of community‐level end points as regulatory requirements for the approval of forest‐use insecticides.

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Finding more efficient ways to monitor and estimate the diversity of mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. Here, we first focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding two rivers in southeastern England. Community diversity and composition was then assessed based on species richness and β-diversity, with differences between communities partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling. eDNA metabarcoding detected 25 wild mammal species from five orders, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorphs) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers. eDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.

Reviewing the past, present and potential lizard faunas of New Zealand cities

Cities and urban processes typically have a negative impact on biodiversity via land cover change, high rates of disturbance and high densities of pest species. Increasingly, however, people are being encouraged and empowered to reduce these impacts through urban restoration and backyard conservation initiatives. Internationally, lizards are a common feature of urban biodiversity, but in New Zealand where many species are threatened, little is known about populations of native skinks and geckos in cities. Yet cities may offer unique opportunities for lizard conservation compared with alternatively modified habitats. To explore the potential of cities for the conservation of lizards, we collated knowledge about the current lizard faunas of six New Zealand cities and developed a list of species that would likely have been present in the locations of these cities prior to human settlement. Comparing the two, we found that, although each of the cities has at least one currently urban-dwelling species, the diversity of lizards in all of the cities has declined dramatically since human colonisation. Patterns of species loss in cities reflect those observed across New Zealand more generally; that is, the loss of large-bodied skinks and geckos, probably resulting from predation by introduced mammalian predators, as well as the loss of regionally endemic species. The high diversity of species that are currently, or were historically, present in the locations of New Zealand cities means that urban restoration involving recovery or reintroduction of populations could have significant benefits for lizard conservation and advocacy.

Forest-bird Species Assemblages in the Lowland Rainforest of Madagascar: The Effects of Forest Fragmentation Revisited

Although the eastern lowland rainforest of Madagascar houses a high proportion of endemic birds, little is known about how fragmentation effects and habitat loss specifically impact them. We analyzed published lists of forest birds across several eastern lowland rainforest fragments of three size classes (large: ~ 6,000 ha, medium: ~ 2,000 ha, small: ~ 600 ha) and varying distance (0.45-20 km) from a nearby continuous forest block. Several key species traits were incorporated to elucidate 1) patterns of species loss across forest fragments and the characteristics of lost species; 2) rela- tionships of species richness and composition with fragment size and distance, and the factors that potentially drive these associations; and 3) pattern of nestedness in the resulting species assemblages. At the scale of our study, we found that species' vulnerability to loss was a function of degree of rarity and ecological specialization, such as insectivorous diet and habitat restriction. Fragment size was associated with species richness and composition. However, distance from the remaining continuous forest block and human disturbance, such as selective logging, may also influence their patterns of association. Both ecological factors and sampling effects (passive sampling of the regional species pool) appeared to in- fluence species distribution across our fragments. Although no significant pattern of nested subset was detected among in- dividual fragments, such a pattern is apparent among fragments from the three size classes. We briefly address conserva- tion implications of these findings.

Fragmentation, grazing and the species–area relationship

Habitat loss is one of the greatest threats to species persistence. Gauging the scale of this problem requires quantitative methods that can predict the number of extinctions resulting from habitat loss. For the past three decades, the species–area relationship, an empirical relationship between the number of species present in an area and the size of that area, has been this tool. However, it fails to incorporate threats to species aside from habitat loss and the heterogeneous distribution of these threats across habitats. Recent studies have improved species–area predictions by incorporating not only direct effects of area on richness, but also indirect effects of area (through area‐mediated predator abundance), on prey species richness. We extend this work to test the hypotheses that the indirect effects of the multiple threats of grazing and trampling in addition to fragmentation will amplify the effect of area on species richness and that this effect will be greatest in zones closest to the fragment edge. Further, we test for species and population level effects of fragmentation and grazing, including the non‐random pattern of species loss and the decline in population sizes. We test our hypotheses with a field study of land snail richness in fragments with and without the additional threats of grazing and trampling. Our study supports the hypotheses that fragments with multiple threats in addition to habitat loss harbour fewer species than fragments without these threats, and that this effect is non‐uniform across fragments, populations and species.

Mechanisms of avian population decline and species loss in tropical forest fragments

Even large fragments of tropical forest lose bird species over time. The speed of disappearance and permanence of these losses depend on a variety of factors, but the pattern of species loss appears more universal. We still do not understand the degree to which different mechanisms lead to population declines and local extinction in fragmented tropical landscapes. We review data currently available to evaluate three of the leading hypotheses, which include altered community dynamics producing mesopredator release and indirect effects of elevated herbivore populations; sensitivity of forest birds to altered microclimatic conditions in fragments, and the constraint of poor dispersal ability that reduces connectivity in fragmented landscapes. We find that all three mechanisms require additional study and suggest steps to be taken in future studies.

Patterns of species impoverishment in managed forests of Catalonia (NE Spain)

AbstractQuestion: In managed forests, woody plant richness shows great variations in pattern. Herein we try to elucidate the role of major factors, such as successional status, to explain this variation. Assuming that less competitive or disturbance‐sensitive species will be systematically more prone to disappear, we investigate the existence of non‐random patterns of species impoverishment – i.e., the number of species unable to attain maximal richness – and the ecological and successional status of species associated with impoverishment in relation to a regional climatic gradient.Methods: We explored species composition in approximately 7500 forest plots in Catalonia (NE Spain). We evaluated non‐random patterns of species impoverishment by analyzing their nestedness. Multivariate analysis was used to relate environmental variables and impoverishment to species occurrence. Plot successional status and ecological range were also estimated from species composition, and species impoverishment was then correlated to these estimators.Results: Most forests show a non‐random pattern of species loss: poor stands tend to retain the same species, and the species determining high richness tend to be the same. Late successional species tend to be more common in impoverished plots of drier and warmer forests, while species typical of open or disturbed habitats are more common in impoverished plots of moister and colder forests. Communities dominated by early or late successional species are mostly impoverished, while the richest stands are constituted by species of intermediate stages. Forests dominated by species with a narrow or wide ecological range showed high impoverishment levels, while the richest stands had species with an intermediate ecological range.Discussion: In warmer Mediterranean forests, impoverishment tends to be associated with late successional stages, while in moister and colder forests, species loss is more closely related to disturbance and exploitation. This study reveals the difficulties involved in using species richness as a simple descriptor of the degree of forest conservation. Identification of dominant species and species indicative of ecological processes would constitute an easily applicable practice that would consolidate assessment of forests status.

Habitat reduction and patterns of species loss

Abstract This paper uses data of The Distribution Atlas of Polish Butterflies to simulate the effect of four different types of area loss (aggregated, fractal, random, and nested) on species diversity and species–area relationships (SARs). We found that power function and logarithmic SAR models overestimated species loss in the case of aggregated, fractal, and random patterns of area reduction. Instead, the modification of the power function by Plotkin et al. (Proc. Natl. Acad. Sci. USA 97 (2000b) 10850) ( S = S 0 A z e − kA ) with k being a shape-adjusting parameter worked better and gave sufficient predictions of species loss. The net effects of the aggregated, fractal, and random types of area loss on species diversity were very similar with an aggregated pattern of area loss leading to slightly higher rates of species loss than both other processes. We conclude that SARs might be useful tools for biodiversity forecasting if they are constructed in a case-specific manner. The use of standard models instead might be misleading.

Dominant species maintain ecosystem function with non‐random species loss

AbstractLoss of species caused by widespread stressors, such as drought and fragmentation, is likely to be non‐random depending on species abundance in the community. We experimentally reduced the number of rare and uncommon plant species while independently reducing only the abundance of dominant grass species in intact, native grassland. This allowed us to simulate a non‐random pattern of species loss, based on species abundances, from communities shaped by natural ecological interactions and characterized by uneven species abundance distributions. Over two growing seasons, total above‐ground net primary productivity (ANPP) declined with reductions in abundance of the dominant species but was unaffected by a threefold decline in richness of less common species. In contrast, productivity of the remaining rare and uncommon species decreased with declining richness, in part due to loss of complementary interactions among these species. However, increased production of the dominant grasses offset the negative effects of species loss. We conclude that the dominant species, as controllers of ecosystem function, can provide short‐term resistance to reductions in ecosystem function when species loss is nonrandom. However, the concurrent loss of complementary interactions among rare and uncommon species, the most diverse component of communities, may contribute to additional species loss and portends erosion of ecosystem function in the long term.

Biodiversity and ecosystem function: the consumer connection

Proposed links between biodiversity and ecosystem processes have generated intense interest and controversy in recent years. With few exceptions, however, empirical studies have focused on grassland plants and laboratory aquatic microbial systems, whereas there has been little attention to how changing animal diversity may influence ecosystem processes. Meanwhile, a separate research tradition has demonstrated strong top‐down forcing in many systems, but has considered the role of diversity in these processes only tangentially. Integration of these research directions is necessary for more complete understanding in both areas. Several considerations suggest that changing diversity in multi‐level food webs can have important ecosystem effects that can be qualitatively different than those mediated by plants. First, extinctions tend to be biased by trophic level: higher‐level consumers are less diverse, less abundant, and under stronger anthropogenic pressure on average than wild plants, and thus face greater risk of extinction. Second, unlike plants, consumers often have impacts on ecosystems disproportionate to their abundance. Thus, an early consequence of declining diversity will often be skewed trophic structure, potentially reducing top‐down influence. Third, where predators remain abundant, declining diversity at lower trophic levels may change effectiveness of predation and penetrance of trophic cascades by reducing trait diversity and the potential for compensation among species within a level. The mostly indirect evidence available provides some support for this prediction. Yet effects of changing animal diversity on functional processes have rarely been tested experimentally. Evaluating impacts of biodiversity loss on ecosystem function requires expanding the scope of current experimental research to multi‐level food webs. A central challenge to doing so, and to evaluating the importance of trophic cascades specifically, is understanding the distribution of interaction strengths within natural communities and how they change with community composition. Although topology of most real food webs is extremely complex, it is not at all clear how much of this complexity translates to strong dynamic linkages that influence aggregate biomass and community composition. Finally, there is a need for more detailed data on patterns of species loss from real ecosystems (community “disassembly” rules).

Insular biogeography of mammals in Canadian parks: a re‐analysis

Summary Aim Glenn & Nudds (1989) compared mammal species richness in Canadian parks to estimated species‐area relationships prior to European settlement to test if parks presently contain their historical compliment of species. However, the data they used to estimate the presettlement species‐area relationships were not commensurate with the scale of the parks and were not independent. This uncertainty reduces the utility of Glenn and Nudds analysis to detect which, if any, parks are experiencing mammal extirpations and ultimately to direct conservation efforts to enhance mammal conservation in Canada. We improved Glenn and Nudds methods and re‐assesed the conservation status of mammals in Canadian parks. Location Canada. Methods We constructed species‐area curves for disturbance tolerant and intolerant species in five mammal regions of Canada by sampling historical range maps using plots of 10– 10,000 km2. We compared these estimates of expected species richness to current species richness in thirty‐six parks and contrast our results with those of Glenn and Nudds. Results All ten re‐estimated species‐area regressions had higher intercepts than those reported by Glenn and Nudds; four had lower slopes. Of seventy‐two cases analysed, we found twenty in which parks had fewer species than expected and four in which parks had more species than expected, compared to fourteen and thirty‐three, respectively, reported by Glenn and Nudds. Changes in both the regression parameters and increases in the prediction intervals accounted for the disparity between these results. Park residuals were not significantly different from zero in eight of ten analyses. Residuals for parks in the Alleghenian‐Illinoian mammal province were negative and decreased with increasing park size. Main conclusions Improvement of Glenn and Nudds methods had an effect on both the parameter estimates and precison of the presettlement species‐area curves. As a result, mammal conservation in some Canadian parks is worse than Glenn and Nudds reported. Six additional parks contained fewer disturbance intolerant species than predicted. However, Glenn and Nudds finding of systematic differences between expected and observed species richness in parks in the densely populated region of southern Ontario, southern Quebec and the maritime provinces was not an artefact of their methods. In this region, seven of ten parks appear to have lost disturbance‐sensitive species of mammals. The pattern of species loss in this region was consistent with the idea that these parks have become isolated from mammal dispersal by surrounding habitat change and have experienced local species extirpations.

Species loss in a forest bird community near Lagoa Santa in southeastern Brazil

Patterns of species loss and decline in a forest bird community following deforestation near Lagoa Santa, Brazil, were examined in three forest fragments during 1987. Records of 107 species were compared with those collected by Lund and Reinhardt [Reinhardt, J. (1870). Vidensk. medd. Dansk Nat.-hist. Foren., 22, 1–124, 315–457]. Thirteen forest species recorded in the last century were not found in the same area in 1987. Some of these species were previously common. Species loss was related to fragment size; thus, in fragments of 24, 63 and 198 ha, we found 20, 29 and 34 forest species, respectively. The more diverse community of the original forest has been replaced by a community strongly dominated by a few species, at least four of which apparently were uncommon in the last century. Species that had increased in the area were small forest birds that feed on small insects in the understorey. Those that declined included species with specialized food requirements or feeding behaviour and species at the limit of their distributional range.

Ecological Determinants of Species Loss in Remnant Prairies

Recensuses of 54 Wisconsin prairie remnants showed that 8 to 60 percent of the original plant species were lost from individual remnants over a 32- to 52-year period. The pattern of species loss was consistent with the proposed effects of fire suppression caused by landscape fragmentation. Short, small-seeded, or nitrogen-fixing plants showed the heaviest losses, as did species growing in the wettest, most productive environments. The interruption of landscape-scale processes (such as wildfire) by fragmentation is an often overlooked mechanism that may be eroding biodiversity in many habitats around the world.