Selecting for extinction: nonrandom disease-associated extinction homogenizes amphibian biotas

Studying the patterns in which local extinctions occur is critical to understanding how extinctions affect biodiversity at local, regional and global spatial scales. To understand the importance of patterns of extinction at a regional spatial scale, we use data from extirpations associated with a widespread pathogenic agent of amphibian decline, Batrachochytrium dendrobatidis ( Bd ) as a model system. We apply novel null model analyses to these data to determine whether recent extirpations associated with Bd have resulted in selective extinction and homogenization of diverse tropical American amphibian biotas. We find that Bd -associated extinctions in this region were nonrandom and disproportionately, but not exclusively, affected low-occupancy and endemic species, resulting in homogenization of the remnant amphibian fauna. The pattern of extirpations also resulted in phylogenetic homogenization at the family level and ecological homogenization of reproductive mode and habitat association. Additionally, many more species were extirpated from the region than would be expected if extirpations occurred randomly. Our results indicate that amphibian declines in this region are an extinction filter, reducing regional amphibian biodiversity to highly similar relict assemblages and ultimately causing amplified biodiversity loss at regional and global scales.     

Reductions in connectivity and habitat quality drive local extinctions in a plant diversity hotspot

It is well documented that habitat loss is a major cause of biodiversity decline. However, the roles of the different aspects of habitat loss in local extinctions are less understood. Anthropogenic destruction of an area of habitat causes immediate local extinction but subsequently three additional gradual drivers influence the likelihood of delayed extinction: decreased habitat patch size, lower connectivity and habitat deterioration. We investigated the role of these drivers in local extinctions of 82 declining species in a UK biodiversity hotspot. We combined a unique set of ≈ 7000 vegetation surveys and habitat maps from the 1930s with contemporary species’ occurrences. We extrapolated from these surveys to the whole 2500‐km² study area using habitat suitability surfaces. The strengths of drivers in explaining local extinctions over this 70 yr period were determined by contrasting connectivity, patch size and habitat quality loss for locations at which a species went extinct and those with persisting occurrences. Species’ occurrences declined on average by 60%, with half of local extinctions attributable to immediate habitat loss and half to the gradual processes causing delayed extinctions. On average, locations where a species persisted had a 73% higher contemporary connectivity than those suffering extinctions, but showed no differences in historical connectivity. Furthermore, locations with extinctions experienced a 37% greater decline in suitability associated with changes in habitat type. The strength of the drivers and the proportion of extinctions depended on the species’ habitat specialism, but were affected only minimally by life‐history characteristics. In conclusion, we identified a hierarchy of drivers influencing local extinction: with connectivity loss being the strongest, suitability change being moderately important, but changes in habitat patch size having only weak effects. We suggest conservation efforts could be most effective by strengthening connectivity along with reducing habitat deterioration, which would benefit a wide range of species.     

Scenarios of freshwater fish extinctions from climate change and water withdrawal

Reductions in river discharge (water availability) like those from climate change or increased water withdrawal, reduce freshwater biodiversity. We combined two scenarios from the Intergovernmental Panel for Climate Change with a global hydrological model to build global scenarios of future losses in river discharge from climate change and increased water withdrawal. Applying these results to known relationships between fish species and discharge, we build scenarios of losses (at equilibrium) of riverine fish richness. In rivers with reduced discharge, up to 75% (quartile range 4–22%) of local fish biodiversity would be headed toward extinction by 2070 because of combined changes in climate and water consumption. Fish loss in the scenarios fell disproportionately on poor countries. Reductions in water consumption could prevent many of the extinctions in these scenarios.     

Local extinctions and recolonisations of passerine bird populations in small woods

This paper considers, for eight species of woodland bird, the factors that influenced both local extinctions and recolonisations in 145 woods over 3 years. In all species, probability of local extinction was inversely related to population size; most local extinctions occurred in woods containing one to three breeding pairs. However, considerable variation in extinction probabilities occurred between species and between years. In addition, the suitability of habitat within a wood (more extinctions in less suitable woods) was important for wren Troglodytes troglodytes, song thrush Turdus philomelos and blue tit Parus caeruleus; also, the structure of the surrounding landscape was important for blue tit, great tit Parus major, and chaffinch Fringilla coelebs (more extinctions in localities with less woodland). In only two species was the probability of recolonisation related to any of the measured variables. Wrens were more likely to recolonise larger woods, whereas song thrushes were more likely to recolonise woods with a high habitat suitability rating and those which are more isolated from other woodland     

CLIMATE PREDICTORS OF LATE QUATERNARY EXTINCTIONS

Between 50,000 and 3,000 years before present (BP) 65% of mammal genera weighing over 44 kg went extinct, together with a lower proportion of small mammals. Why species went extinct in such large numbers is hotly debated. One of the arguments proposes that climate changes underlie Late Quaternary extinctions, but global quantitative evidence for this hypothesis is still lacking. We test the potential role of global climate change on the extinction of mammals during the Late Quaternary. Our results suggest that continents with the highest climate footprint values, in other words, with climate changes of greater magnitudes during the Late Quaternary, witnessed more extinctions than continents with lower climate footprint values, with the exception of South America. Our results are consistent across species with different body masses, reinforcing the view that past climate changes contributed to global extinctions. Our model outputs, the climate change footprint dataset, provide a new research venue to test hypotheses about biodiversity dynamics during the Late Quaternary from the genetic to the species richness level.     

Global versus local extinction in a network model of plant–pollinator communities

The loss of a species from an ecological community can trigger a cascade of additional extinctions; the complex interactions that comprise ecological communities make the dynamics and impacts of such a cascade challenging to predict. Previous studies have typically considered global extinctions, where a species cannot re-enter a community once it is lost. However, in some cases a species only becomes locally extinct, and may be able to reinvade from surrounding communities. Here, we use a dynamic, Boolean network model of plant–pollinator community assembly to analyze the differences between global and local extinction events in mutualistic communities. As expected, we find that compared to global extinctions, communities respond to local extinctions with lower biodiversity loss, and less variation in topological network properties. We demonstrate that in the face of global extinctions, larger communities suffer greater biodiversity loss than smaller communities when similar proportions of species are lost. Conversely, smaller communities suffer greater loss in the face of local extinctions. We show that targeting species with the most interacting partners causes more biodiversity loss than random extinctions in the case of global, but not local, extinctions. These results extend our understanding of how mutualistic communities respond to species loss, with implications for community management and conservation efforts.     

The role of infectious diseases in biological conservation

Recent increases in the magnitude and rate of environmental change, including habitat loss, climate change and overexploitation, have been directly linked to the global loss of biodiversity. Wildlife extinction rates are estimated to be 100–1000 times greater than the historical norm, and up to 50% of higher taxonomic groups are critically endangered. While many types of environmental changes threaten the survival of species all over the planet, infectious disease has rarely been cited as the primary cause of global species extinctions. There is substantial evidence, however, that diseases can greatly impact local species populations by causing temporary or permanent declines in abundance. More importantly, pathogens can interact with other driving factors, such as habitat loss, climate change, overexploitation, invasive species and environmental pollution to contribute to local and global extinctions. Regrettably, our current lack of knowledge about the diversity and abundance of pathogens in natural systems has made it difficult to establish the relative importance of disease as a significant driver of species extinction, and the context when this is most likely to occur. Here, we review the role of infectious diseases in biological conservation. We summarize existing knowledge of disease-induced extinction at global and local scales and review the ecological and evolutionary forces that may facilitate disease-mediated extinction risk. We suggest that while disease alone may currently threaten few species, pathogens may be a significant threat to already-endangered species, especially when disease interacts with other drivers. We identify control strategies that may help reduce the negative effects of disease on wildlife and discuss the most critical challenges and future directions for the study of infectious diseases in the conservation sciences.     

An empirical test of the relative and combined effects of land‐cover and climate change on local colonization and extinction

Land‐cover and climate change are two main drivers of changes in species ranges. Yet, the majority of studies investigating the impacts of global change on biodiversity focus on one global change driver and usually use simulations to project biodiversity responses to future conditions. We conduct an empirical test of the relative and combined effects of land‐cover and climate change on species occurrence changes. Specifically, we examine whether observed local colonization and extinctions of North American birds between 1981–1985 and 2001–2005 are correlated with land‐cover and climate change and whether bird life history and ecological traits explain interspecific variation in observed occurrence changes. We fit logistic regression models to test the impact of physical land‐cover change, changes in net primary productivity, winter precipitation, mean summer temperature, and mean winter temperature on the probability of Ontario breeding bird local colonization and extinction. Models with climate change, land‐cover change, and the combination of these two drivers were the top ranked models of local colonization for 30%, 27%, and 29% of species, respectively. Conversely, models with climate change, land‐cover change, and the combination of these two drivers were the top ranked models of local extinction for 61%, 7%, and 9% of species, respectively. The quantitative impacts of land‐cover and climate change variables also vary among bird species. We then fit linear regression models to test whether the variation in regional colonization and extinction rate could be explained by mean body mass, migratory strategy, and habitat preference of birds. Overall, species traits were weakly correlated with heterogeneity in species occurrence changes. We provide empirical evidence showing that land‐cover change, climate change, and the combination of multiple global change drivers can differentially explain observed species local colonization and extinction.     

Modelling the unpredictability of future biodiversity in ecological networks

We consider the question of how accurately we can hope to predict future biodiversity in a world in which many interacting species are at risk of extinction. Simple models assuming that species’ extinctions occur independently are easily analysed, but do not account for the fact that many species depend on or otherwise interact with each other. In this paper we evaluate the effect of explicitly incorporating ecological dependencies on the predictive ability of models of extinction. In particular, we compare a model in which species’ extinction rates increase because of the extinction of their prey to a model in which the same average rate increase takes place, but in which extinctions occur independently from species to species. One might expect that including this ecological information would make the prediction of future biodiversity more accurate, but instead we find that accounting for food web dependencies reveals greater uncertainty. The expected loss of biodiversity over time is similar between the two models, but the variance in future biodiversity is considerably higher in the model that includes species interactions. This increased uncertainty is because of the non-independence of species—the tendency of two species to respond similarly to the loss of a species on which both depend. We use simulations to show that this increase in variance is robust to many variations of the model, and that its magnitude should be largest in food webs that are highly dependent on a few basal species. Our results should hold whenever ecological dependencies cause most species’ extinction risks to covary positively, and illustrate how more information does not necessarily improve our ability to predict future biodiversity loss.     

Non‐random patterns of invasion and extinction reduce phylogenetic diversity in island bird assemblages

Anthropogenically driven changes in bird communities on oceanic islands exemplify the biotic upheaval experienced by island floras and faunas. While the influence of invasions and extinctions on species richness and beta‐diversity of island bird assemblages has been explored, little is known about the impact of these invasions and extinctions on phylogenetic diversity. Here we quantify phylogenetic diversity of island bird assemblages resulting from extinctions alone, invasions alone, and the combination of extinctions and invasions in the historic time period (1500 CE to the current), and compare it to the expected phylogenetic diversity that would result if these processes involved randomly selected island bird species. We assessed phylogenetic diversity and structure at the scale of the island (n = 152), the archipelago containing the islands (n = 22), and the four oceans containing the archipelagos using three measures. We found that extinction, invasion, and the combination of invasion and extinction generally resulted in lower phylogenetic diversity than expected, regardless of the spatial scale examined. We conclude that extinction and invasion of birds on islands are non‐random with respect to phylogeny and that these processes generally leave bird assemblages with lower phylogenetic diversity than we would expect under random invasion or extinction.     

Dynamics of extinction and the selection of nature reserves

Familiar quantitative reserve-selection techniques are tailored to simple decision problems, where the representation of species is sought at minimum cost. However, conservationists have begun to ask whether representing species in reserve networks is sufficient to avoid local extinctions within selected areas. An attractive, but previously untested idea is to model current species' probabilities of occurrence as an estimate of local persistence in the near future. Using distribution data for passerine birds in Great Britain, we show that (i) species' probabilities of occurrence are negatively related to local probabilities of extinction, at least when a particular 20-year period is considered, and (ii) local extinctions can be reduced if areas are selected to maximize current species' probabilities of occurrence We suggest that more extinctions could be avoided if even a simple treatment of persistence were to be incorporated within reserve selection methods.     

Selective extinction and rapid loss of evolutionary history in the bird fauna

The extinction of species results in a permanent loss of evolutionary history. Recent theoretical studies show that this loss may be proportionally much smaller than the loss of species, but under some conditions can exceed it. Such conditions occur when the phylogenetic tree that describes the evolutionary relationships among species is highly imbalanced due to differences between lineages in past speciation and/or extinction rates. I used the taxonomy by C. G. Sibley and B. L. Monroe Jr to estimate the global loss of bird evolutionary history from historical and predicted extinctions, and to quantify the ensuing changes in balance of the bird phylogenetic tree. In the global bird fauna, evolutionary history is being lost at a high rate, similar to the rate of species extinction. The bird phylogenetic tree is highly imbalanced, and the imbalance is increased significantly by anthropogenic extinction. Historically, the elevated loss of bird evolutionary history has been fuelled mostly by phylogenetic non-randomness in the extinction of species, but the direct effect of tree imbalance is substantial and could dominate in the future.     

Anthropogenic stressors and riverine fish extinctions

Human activities are often implicated in the contemporary extinction of contemporary species. Concerning riverine fishes, the major biotic and abiotic threats widely cited include introduction of non-native species, habitat fragmentation and homogenization in stream flow dynamics due to the damming of rivers, dumping of organic loadings, degradation of the riverine habitat by agricultural practices and water abstraction for human and agricultural consumption. However, few studies have evaluated the role of each of these threats on fish extinction at large spatial scales. Focusing on Western Europe and the USA, two of the most heavily impacted regions on Earth, we quantify fish species loss per river basin and evaluate for the first time to what extent, if any, these threats have been promoting fish extinctions. We show that mean fish extinction rates during the last 110 years in both continents is ∼112 times higher than calculated natural extinction rates. However, we identified only weak effects of our selected anthropogenic stressors on fish extinctions. Only river fragmentation by dams and percentage of non-native species seem to be significant, although weak, drivers of fish species extinction. In our opinion, the most probable explanation for the weak effects found here comes from limitations of both biological and threats datasets currently available. Obtaining realistic estimates on both extinctions and anthropogenic threats in individual river basins is thus urgently needed.     

Characterising extinction debt following habitat fragmentation using neutral theory

Habitat loss leads to species extinctions, both immediately and over the long term as ‘extinction debt’ is repaid. The same quantity of habitat can be lost in different spatial patterns with varying habitat fragmentation. How this translates to species loss remains an open problem requiring an understanding of the interplay between community dynamics and habitat structure across temporal and spatial scales. Here we develop formulas that characterise extinction debt in a spatial neutral model after habitat loss and fragmentation. Central to our formulas are two new metrics, which depend on properties of the taxa and landscape: ‘effective area’, measuring the remaining number of individuals and ‘effective connectivity’, measuring individuals’ ability to disperse through fragmented habitat. This formalises the conventional wisdom that habitat area and habitat connectivity are the two critical requirements for long‐term preservation of biodiversity. Our approach suggests that mechanistic fragmentation metrics help resolve debates about fragmentation and species loss.     

Potential extinction debt due to habitat loss and fragmentation in subalpine moorland ecosystems

Habitat loss and fragmentation would often induce delayed extinction, referred to as extinction debt. Understanding potential extinction debts would allow us to reduce future extinction risk by restoring habitats or implementing conservation actions. Although growing empirical evidence has predicted extinction debts in various ecosystems exposed to direct human disturbances, potential extinction debts in natural ecosystems with minimal direct human disturbance are little studied. Ongoing climate change may cause habitat loss and fragmentation, particularly in natural ecosystems vulnerable to environmental change, potentially leading to future local extinctions. Recent climate change would lead to extended growing season caused by earlier snowmelt in spring, resulting in expansion of shrubby species and thereby habitat loss and fragmentation of mountainous moorlands. We examined the potential extinction debts of species diversity and functional diversity (FD; trait variation or multivariate trait differences within a community) in subalpine moorland ecosystems subjected to few direct human disturbances. Plant species richness for all species and for moorland specialists were primarily explained by the past kernel density of focal moorlands (a proxy for spatial clustering of moorlands around them) but not the past area of the focal moorlands, suggesting potential extinction debt in subalpine moorland ecosystems. The higher kernel density of the focal moorland in the past indicates that it was originally surrounded by more neighborhood moorlands and/or had been locally highly fragmented. Patterns in current plant species richness have been shaped by the historical spatial configuration of moorlands, which have disappeared over time. In contrast, we found no significant relationships between the FD and historical and current landscape variables depicting each moorland. The prevalence of trait convergence might result in a less sensitive response of FD to habitat loss and fragmentation compared to that of species richness. Our finding has an important implication that climate change induced by human activities may threaten biodiversity in natural ecosystems through habitat loss and fragmentation.

     

Potential net primary production footprint of agriculture: A global trade analysis

Agriculture is one of the most important sources of biomass for human society but increasingly contributes to anthropogenic degradation of ecosystems through negative impacts on biodiversity, ecosystem integrity, climate change, and ecosystem services. Here we estimate NPP_pot agricultural footprint, that is, the level of appropriation of potential net primary production (NPP_pot) by global cropland and human‐made pastures from the consumer responsibility (footprint) perspective and reveal the role of international trade. To quantify the NPP_pot agricultural footprint, we utilize environmentally extended multi‐regional input–output analysis to attribute the terrestrial potential NPP altered by global cropland and human‐made pastures to the final consumers responsible for pulling the supply chains. We identify the NPP_pot of geographically specific cropland area of 186 agricultural crops in 236 countries and we track each of those crops through the global web of international trade and supply chains to the point of final consumption. We show that human society appropriates 20% (13 petagrams of carbon per year) of global potential net primary production by the transformation of natural ecosystems into cropland and human‐made pastures. International trade accounts for 23% of global NPP_pot footprint of agriculture. While the two and half billion people living in China and India (the two countries with lowest NPP_pot agricultural footprint per capita) appropriate about 16% of the global NPP_pot agricultural footprint of cropland and human‐made pastures, the same share is appropriated by only 360 million people living in countries with the highest per capita footprint.     

Subnational greenhouse gas and land‐based biodiversity footprints in the European Union

Insights into subnational environmental impacts and the underlying drivers are scarce, especially from a consumption‐based perspective. Here, we quantified greenhouse gas (GHG) emissions and land‐based biodiversity losses associated with final consumption in 162 regions in the European Union in 2010. For this purpose, we developed an environmentally extended multi‐regional input–output (MRIO) model with subnational European information on demand, production, and trade structures subdivided into 18 major economic sectors, while accounting for trade outside Europe. We employed subnational data on land use and national data on GHG emissions. Our results revealed within‐country differences in per capita GHG and land‐based biodiversity footprints up to factors of 3.0 and 3.5, respectively, indicating that national footprints may mask considerable subnational variability. The per capita GHG footprint increased with per capita income and income equality, whereas we did not find such responses for the per capita land‐based biodiversity footprint, reflecting that extra income is primarily spent on energy‐intensive activities. Yet, we found a shift from the domestic to the foreign part of the biodiversity footprints with rising population density and income. Because our analysis showed that most regions are already net importers of GHG emissions and biodiversity losses, we conclude that it is increasingly important to address the role of trade in national and regional policies on mitigating GHG emissions and averting further biodiversity losses, both within and outside the region itself. To further increase the policy relevance of subnational footprint analyses, we also recommend the compilation of more detailed subnational MRIO databases including harmonized environmental data.     

How do habitat amount and habitat fragmentation drive time-delayed responses of biodiversity to land-use change?

Land-use change is a root cause of the extinction crisis, but links between habitat change and biodiversity loss are not fully understood. While there is evidence that habitat loss is an important extinction driver, the relevance of habitat fragmentation remains debated. Moreover, while time delays of biodiversity responses to habitat transformation are well-documented, time-delayed effects have been ignored in the habitat loss versus fragmentation debate. Here, using a hierarchical Bayesian multi-species occupancy framework, we systematically tested for time-delayed responses of bird and mammal communities to habitat loss and to habitat fragmentation. We focused on the Argentine Chaco, where deforestation has been widespread recently. We used an extensive field dataset on birds and mammals, along with a time series of annual woodland maps from 1985 to 2016 covering recent and historical habitat transformations. Contemporary habitat amount explained bird and mammal occupancy better than past habitat amount. However, occupancy was affected more by the past rather than recent fragmentation, indicating a time-delayed response to fragmentation. Considering past landscape patterns is therefore crucial for understanding current biodiversity patterns. Not accounting for land-use history ignores the possibility of extinction debt and can thus obscure impacts of fragmentation, potentially explaining contrasting findings of habitat loss versus fragmentation studies.     

How humans drive speciation as well as extinction

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.     

Evidence for a possible extinction debt in Swiss wetland specialist plants

1. Habitat loss leading to smaller patch sizes and decreasing connectivity is a major threat to global biodiversity. While some species vanish immediately after a change in habitat conditions, others show delayed extinction, that is, an extinction debt. In case of an extinction debt, the current species richness is higher than expected under present habitat conditions.
2. We investigated wetlands of the canton of Zürich in the lowlands of Eastern Switzerland where a wetland loss of 90% over the last 150 years occurred. We related current species richness to current and past patch area and connectivity (in 1850, 1900, 1950, and 2000). We compared current with predicted species richness in wetlands with a substantial loss in patch area based on the species‐area relationship of wetlands without substantial loss in patch area and studied relationships between the richness of different species groups and current and historical area and connectivity of wetland patches.
3. We found evidence of a possible extinction debt for long‐lived wetland specialist vascular plants: in wetlands, which substantially lost patch area, current species richness of long‐lived specialist vascular plants was higher than would have been expected based on current patch area. Additionally and besides current wetland area, historical area also explained current species richness of these species in a substantial and significant way. No evidence for an extinction debt in bryophytes was found.
4. The possible unpaid extinction debt in the wetlands of the canton of Zürich is an appeal to nature conservation, which has the possibility to prevent likely future extinctions of species through specific conservation measures. In particular, a further reduction in wetlands must be prevented and restoration measures must be taken to increase the number of wetlands.