Land‐use change is a significant cause of anthropogenic extinctions, which are likely to continue and accelerate as habitat conversion proceeds in most biomes. One way to understand the effects of habitat loss on biodiversity is through improved tools for predicting the number and identity of species losses in response to habitat loss. There are relatively few methods for predicting extinctions and even fewer opportunities for rigorously assessing the quality of these predictions. In this paper, we address these issues by applying a new method based on rarefaction to predict species losses after random, but aggregated, habitat loss. We compare predictions from three rarefaction models, individual‐based, sample‐based, and spatially clustered, to those derived from a commonly used extinction estimation method, the species–area relationship (SAR). We apply each method to a mesocosm experiment, in which we aim to predict species richness and extinctions of arthropods immediately following 50% habitat loss. While each model produced strikingly accurate predictions of species richness immediately after the habitat loss disturbance, each model significantly underestimated the number of extinctions occurring at both the local (within‐mesocosm) and regional (treatment‐wide) scales. Despite the stochastic nature of our small‐scale, short‐term, and randomly applied habitat loss experiment, we found surprisingly clear evidence for extinction selectivity, for example, when abundant species with low extinction probabilities were extirpated following habitat loss. The important role played by selective extinction even in this contrived experimental system suggests that ecologically driven, trait‐based extinctions play an equally important role to stochastic extinction, even when the disturbance itself has no clear selectivity. As a result, neutrally stochastic null models such as the SAR and rarefaction are likely to underestimate extinctions caused by habitat loss. Nevertheless, given the difficulty of predicting extinctions, null models provide useful benchmarks for conservation planning by providing minimum estimates and probabilities of species extinctions.
Habitat loss disrupts species interactions through local extinctions, potentially orphaning species that depend on interacting partners, via mutualisms or commensalisms, and increasing secondary extinction risk. Orphaned species may become functionally or secondarily extinct, increasing the severity of the current biodiversity crisis. While habitat destruction is a major cause of biodiversity loss, the number of secondary extinctions is largely unknown. We investigate the relationship between habitat loss, orphaned species, and bipartite network properties. Using a real seed dispersal network, we simulate habitat loss to estimate the rate at which species are orphaned. To be able to draw general conclusions, we also simulate habitat loss in synthetic networks to quantify how changes in network properties affect orphan rates across broader parameter space. Both real and synthetic network simulations show that even small amounts of habitat loss can cause up to 10% of species to be orphaned. More area loss, less connected networks, and a greater disparity in the species richness of the network's trophic levels generally result in more orphaned species. As habitat is lost to land‐use conversion and climate change, more orphaned species increase the loss of community‐level and ecosystem functions. However, the potential severity of repercussions ranges from minimal (no species orphaned) to catastrophic (up to 60% of species within a network orphaned). Severity of repercussions also depends on how much the interaction richness and intactness of the community affects the degree of redundancy within networks. Orphaned species could add substantially to the loss of ecosystem function and secondary extinction worldwide.
more » « less- Award ID(s):
- 1701858
- NSF-PAR ID:
- 10397037
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Ecological Applications
- Volume:
- 32
- Issue:
- 6
- ISSN:
- 1051-0761
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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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. WithNetworkExtinction , 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 withNetworkExtinction 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. -
BACKGROUND The Republic of Madagascar is home to a unique assemblage of taxa and a diverse set of ecosystems. These high levels of diversity have arisen over millions of years through complex processes of speciation and extinction. Understanding this extraordinary diversity is crucial for highlighting its global importance and guiding urgent conservation efforts. However, despite the detailed knowledge that exists on some taxonomic groups, there are large knowledge gaps that remain to be filled. ADVANCES Our comprehensive analysis of major taxonomic groups in Madagascar summarizes information on the origin and evolution of terrestrial and freshwater biota, current species richness and endemism, and the utilization of this biodiversity by humans. The depth and breadth of Madagascar’s biodiversity—the product of millions of years of evolution in relative isolation —is still being uncovered. We report a recent acceleration in the scientific description of species but many remain relatively unknown, particularly fungi and most invertebrates. DIGITIZATION Digitization efforts are already increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge in Madagascar. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. Among the new data presented, our update on plant numbers estimates 11,516 described vascular plant species native to Madagascar, of which 82% are endemic, in addition to 1215 bryophyte species, of which 28% are endemic. Humid forests are highlighted as centers of diversity because of their role as refugia and centers of recent and rapid radiations, but the distinct endemism of other areas such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest is also important despite lower species richness. Endemism in Malagasy fungi remains poorly known given the lack of data on the total diversity and global distribution of species. However, our analysis has shown that ~75% of the fungal species detected by environmental sequencing have not been reported as occurring outside of Madagascar. Among the 1314 species of native terrestrial and freshwater vertebrates, levels of endemism are extremely high (90% overall)—all native nonflying terrestrial mammals and native amphibians are found nowhere else on Earth; further, 56% of the island’s birds, 81% of freshwater fishes, 95% of mammals, and 98% of reptile species are endemic. Little is known about endemism in insects, but data from the few well-studied groups on the island suggest that it is similarly high. The uses of Malagasy species are many, with much potential for the uncovering of useful traits for food, medicine, and climate mitigation. OUTLOOK Considerable work remains to be done to fully characterize Madagascar’s biodiversity and evolutionary history. The multitudes of known and potential uses of Malagasy species reported here, in conjunction with the inherent value of this unique and biodiverse region, reinforce the importance of conserving this unique biota in the face of major threats such as habitat loss and overexploitation. The gathering and analysis of data on Madagascar’s remarkable biota must continue and accelerate if we are to safeguard this unique and highly threatened subset of Earth’s biodiversity. Emergence and composition of Madagascar’s extraordinary biodiversity. Madagascar’s biota is the result of over 160 million years of evolution, mostly in geographic isolation, combined with sporadic long distance immigration events and local extinctions. (Left) We show the age of the oldest endemic Malagasy clade for major groups (from bottom to top): arthropods, bony fishes, reptiles, flatworms, birds, amphibians, flowering plants, mammals, non-flowering vascular plants, and mollusks). Humans arrived recently, some 10,000 to 2000 years (top right) and have directly or indirectly caused multiple extinctions (including hippopotamus, elephant birds, giant tortoises, and giant lemurs) and introduced many new species (such as dogs, zebu, rats, African bushpigs, goats, sheep, rice). Endemism is extremely high and unevenly distributed across the island (the heat map depicts Malagasy palm diversity, a group characteristic of the diverse humid forest). Human use of biodiversity is widespread, including 1916 plant species with reported uses. The scientific description of Malagasy biodiversity has accelerated greatly in recent years (bottom right), yet the diversity and evolution of many groups remain practically unknown, and many discoveries await.more » « less
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Abstract Predicting the functional consequences of biodiversity loss in realistic, multitrophic communities remains a challenge. No existing biodiversity–ecosystem function study to date has simultaneously incorporated information on species traits, network topology, and extinction across multiple trophic levels, while all three factors are independently understood as critical drivers of post‐extinction network structure and function. We fill this gap by comparing the functional consequences of simulated species loss both within (monotrophic) and across (bitrophic) trophic levels, in an ecological interaction network estimated from spatially explicit field data on tropical fecal detritus producer and consumers (mammals and dung beetles). We simulated trait‐ordered beetle and mammal extinction separately (monotrophic extinction) and the coextinction of beetles following mammal loss (bitrophic extinction), according to network structure. We also compared the diversity effects of bitrophic extinction models using a standard monotrophic function (the daily production or consumption of fecal detritus) and a unique bitrophic functional metric (the proportion of daily detritus production that is consumed). We found similar mono‐ and bitrophic diversity effects, regardless of which species traits were used to drive extinctions, yet divergent predictions when different measures of function were used. The inclusion of information on network structure had little apparent effect on the qualitative relationship between diversity and function. These results contribute to our growing understanding of the functional consequences of biodiversity from real systems and underscore the importance of species traits and realistic functional metrics to assessments of the ecosystem impacts of network degradation through species loss.
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Abstract Climate change is increasing the frequency, severity, and extent of wildfires and drought in many parts of the world, with numerous repercussions for the physical, chemical, and biological characteristics of streams. However, information on how these perturbations affect top predators and their impacts on lower trophic levels in streams is limited.
The top aquatic predator in southern California streams is native
Oncorhynchus mykiss , the endangered southern California steelhead trout (trout). To examine relationships among the distribution of trout, environmental factors, and stream invertebrate resources and assemblages, we sampled pools in 25 stream reaches that differed in the presence (nine reaches) or absence (16 reaches) of trout over 12 years, including eight reaches where trout were extirpated during the study period by drought or post‐fire flood disturbances.Trout were present in deep pools with high water and habitat quality. Invertebrate communities in trout pools were dominated by a variety of medium‐sized collector–gatherer and shredder invertebrate taxa with non‐seasonal life cycles, whereas tadpoles and large, predatory invertebrates (Odonata, Coleoptera, Hemiptera [OCH]), often with atmospheric breather traits, were more abundant in troutless than trout pools.
Structural equation modelling of the algal‐based food web indicated a trophic cascade from trout to predatory invertebrates to collector–gatherer taxa and weaker direct negative trout effects on grazers; however, both grazers and collector–gatherers also were positively related to macroalgal biomass. Structural equation modelling also suggested that bottom‐up interactions and abiotic factors drove the detritus‐based food web, with shredder abundance being positively related to leaf litter (coarse particulate organic matter) levels, which, in turn, were positively related to canopy cover and negatively related to flow. These results emphasise the context dependency of trout effects on prey communities and of the relative importance of top‐down versus bottom‐up interactions on food webs, contingent on environmental conditions (flow, light, nutrients, disturbances) and the abundances and traits of component taxa.
Invertebrate assemblage structure changed from a trout to a troutless configuration within a year or two after trout were lost owing to post‐fire scouring flows or drought. Increases in OCH abundance after trout were lost were much more variable after drought than after fire. The reappearance of trout in one stream resulted in quick, severe reductions in OCH abundance.
These results indicate that climate‐change induced disturbances can result in the extirpation of a top predator, with cascading repercussions for stream communities and food webs. This study also emphasises the importance of preserving or restoring refuge habitats, such as deep, shaded, perennial, cool stream pools with high habitat and water quality, to prevent the extirpation of sensitive species and preserve native biodiversity during a time of climate change.
