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.

     

Towards realistic benchmarks for multiple alignments of non-coding sequences

Background  

With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the most effective tools. Simulation-based benchmarks have been proposed to meet this necessity, especially for non-coding sequences. However, it is not clear if such benchmarks truly represent real sequence data from any given group of species, in terms of the difficulty of alignment tasks.     

Diversity–productivity relationships in two ecologically realistic rarity–extinction scenarios

To develop a better understanding of how biodiversity loss and productivity are related, we need to consider ecologically realistic rarity (i.e. reduced evenness and increased dominance) and extinction (i.e. reduced richness) scenarios. Furthermore, we need to identify and better understand the factors that influence species and community yielding behaviors because the general conditions for overyielding are the same as those for coexistence. We established experimental tallgrass prairie plots in Iowa to determine how two ecologically realistic rarity–extinction scenarios influenced aboveground net primary productivity (ANPP) and disassembly. Equal‐mass seedlings of six tallgrass prairie species were transplanted into field plots to establish realistic declining species evenness (high, medium, low) and richness (4, 1) treatments. Across declining evenness treatments, the relative abundance of the ubiquitous tall species Andropogon gerardii increased, the relative abundance of the tall species Salvia azurea was constant, and the relative abundance of two short (dissimilar height scenario) or two tall species (tall scenario) decreased. Monocultures of Andropogon represented a continuation of this trend until there was complete dominance by Andropogon and extinction of all other species. Our treatments also allowed us to test if variation in plant height contributes to the complementarity effect. Niche partitioning in plant height was not positively related to complementarity. The effects of declining species evenness and richness on the diversity–productivity relationship were different for these two ecologically realistic rarity–extinction scenarios. Specifically, as diversity declined across treatments, ANPP and the selection effects decreased in tall communities, but not in dissimilar communities. Additionally, differences between these two scenarios revealed that decreased species yielding behavior is associated with two tallgrass prairie extinction risk factors, rarity and short height. The differences between these scenarios demonstrate the importance of incorporating the known patterns of diversity declines into future studies.     

Alignment-free sequence comparison for biologically realistic sequences of moderate length

The D(2) statistic, defined as the number of matches of words of some pre-specified length k, is a computationally fast alignment-free measure of biological sequence similarity. However there is some debate about its suitability for this purpose as the variability in D(2) may be dominated by the terms that reflect the noise in each of the single sequences only. We examine the extent of the problem and the effectiveness of overcoming it by using two mean-centred variants of this statistic, D(2)* and D(2c). We conclude that all three statistics are potentially useful measures of sequence similarity, for which reasonably accurate p-values can be estimated under a null hypothesis of sequences composed of identically and independently distributed letters. We show that D(2) and D(2)c, and to a somewhat lesser extent D(2)*, perform well in tests to classify moderate length query sequences as putative cis-regulatory modules.     

Metapopulation extinction in fragmented landscapes: using bacteria and protozoa communities as model ecosystems

Extinction is notoriously difficult to study because of the long timescales involved and the difficulty in ascertaining that extinction has actually occurred. The effect of habitat subdivision, or fragmentation, on extinction risk is even harder to study, as it requires copious replication of habitat patches on large spatial scales and control of area effects between treatments. I used simple small-scale communities of bacteria and protozoa to study extinction in response to habitat loss and habitat fragmentation. I studied several different community configurations, each with three trophic levels. Unlike most metapopulation studies (experimental as well as theoretical), which have tended to deal with inherently unstable species interactions, I deliberately used community configurations that were persistent in large stock cultures. I recorded the time to extinction of the top predator in single habitat patches of different sizes and in fragmented systems with different degrees of subdivision but the same amount of available habitat. Habitat loss reduced the time to extinction of isolated populations. Fragmented systems went extinct sooner than corresponding unfragmented (continuous) systems of the same overall size. Unfragmented populations persisted longer than fragmented systems (metapopulations) with or without dispersal corridors between subpopulations. In fact, fragmented systems where the fragments were linked by dispersal corridors went extinctly significantly sooner than those where subpopulations were completely isolated from each other. If these results extend to more "natural" systems, it suggests a need for caution in management programs that emphasize widespread establishment of wildlife corridors in fragmented landscapes.     

Assessing extinction risk in the absence of species-level data: quantitative criteria for terrestrial ecosystems

The conservation of individual plant and animal species has been advanced greatly by the World Conservation Union’s (IUCN) development of objective, repeatable, and transparent criteria for assessing extinction risk, which explicitly separate the process of risk assessment from priority-setting. Here we present an analogous procedure for assessing the extinction risk of terrestrial ecosystems, which may complement traditional species-specific risk assessments, or may provide an alternative when only landscape-level data are available. We developed four quantitative risk criteria, derived primarily from remotely sensed spatial data, information on one of which must be available to permit classification. Using a naming system analogous to the present IUCN species-specific system, our four criteria were: (A) reduction of land cover and continuing threat, (B) rapid rate of land cover change, (C) increased fragmentation, and (D) highly restricted geographical distribution. We applied these criteria to five ecosystems covering a range of spatial and temporal scales, regions of the world, and ecosystem types, and found that Indonesian Borneo’s lowland tropical forests and the Brazilian Atlantic rainforest were Critically Endangered, while South Africa’s grasslands and Brazil’s Mato Grosso were Vulnerable. Furthermore, at a finer grain of analysis, one region of Venezuela’s coastal dry forests (Margarita Island) qualified as Vulnerable, while another (the Guasare River watershed) was Critically Endangered. In northern Venezuela, deciduous forests were classified as Endangered, semi-deciduous forests Vulnerable, and evergreen forests of Least Concern. We conclude that adoption of such a standardized system will facilitate globally comparable, repeatable geographic analyses that clearly separate risk assessment (a fundamentally scientific process), from the definition of conservation priorities, which should take into account additional factors, such as ecological distinctiveness, costs, logistics, likelihood of success, and societal preferences. Jon Paul Rodríguez and Jennifer K. Balch are contributed equally to this work     

Genetic diversity of bacteria adapted to cyanide-bearing compounds in the technogenic ecosystems as detected by 16S rDNA sequences

The genetic diversity of microbial communities that developed naturally within the system of ore heap–solution of heap leaching process has been studied. The difference in the microbial community structure is identified. It is found that phylotypes Serratia and Achromobacter dominated within the ore heap and Hydrogenophaga and Acinetobacter dominated in the solution. Phylogenetic analyses revealed that there are microorganisms among the closest homologues that are able to destruct toxic compounds and/or exhibit their enzyme activity at low temperature. It is shown that aerobic organoheterotrophs are the most promising for the isolation from autochthonous microbial communities of technogenic complexes in East Siberia, as well for studying their destructive potential and use in bioremediation.     

Risks of pesticides to groundwater ecosystems

The current standard for pesticides in groundwater in the Netherlands is the same as that for drinking water: a maximum of 0.1 μg per liter for each individual pesticide and a maximum of 0.5 μg per liter for all agents collectively. This standard applies to water located at least ten meters below ground level. It is based on an old detection limit, which is out of date by now, and on the view that drinking water should be entirely free of pesticides. Recently, however, there are increasing calls for a system of standards underpinned by toxicological data. A committee of the Health Council of the Netherlands (please see note at the end of this article) has dealt with the question whether, apart from human health criteria, ecotoxicological criteria should be taken into consideration when evaluating the risks posed by pesticides in groundwater. This paper closely follows the executive summary of her report     

Predicting how populations decline to extinction

Global species extinction typically represents the endpoint in a long sequence of population declines and local extinctions. In comparative studies of extinction risk of contemporary mammalian species, there appear to be some universal traits that may predispose taxa to an elevated risk of extinction. In local population-level studies, there are limited insights into the process of population decline and extinction. Moreover, there is still little appreciation of how local processes scale up to global patterns. Advancing the understanding of factors which predispose populations to rapid declines will benefit proactive conservation and may allow us to target at-risk populations as well as at-risk species. Here, we take mammalian population trend data from the largest repository of population abundance trends, and combine it with the PanTHERIA database on mammal traits to answer the question: what factors can be used to predict decline in mammalian abundance? We find in general that environmental variables are better determinants of cross-species population-level decline than intrinsic biological traits. For effective conservation, we must not only describe which species are at risk and why, but also prescribe ways to counteract this.     

Resistance to extinction and behavioral momentum

In the metaphor of behavioral momentum, reinforcement is assumed to strengthen discriminated operant behavior in the sense of increasing its resistance to disruption, and extinction is viewed as disruption by contingency termination and reinforcer omission. In multiple schedules of intermittent reinforcement, resistance to extinction is an increasing function of reinforcer rate, consistent with a model based on the momentum metaphor. The partial-reinforcement extinction effect, which opposes the effects of reinforcer rate, can be explained by the large disruptive effect of terminating continuous reinforcement despite its strengthening effect during training. Inclusion of a term for the context of reinforcement during training allows the model to account for a wide range of multiple-schedule extinction data and makes contact with other formulations. The relation between resistance to extinction and reinforcer rate on single schedules of intermittent reinforcement is exactly opposite to that for multiple schedules over the same range of reinforcer rates; however, the momentum model can give an account of resistance to extinction in single as well as multiple schedules. An alternative analysis based on the number of reinforcers omitted to an extinction criterion supports the conclusion that response strength is an increasing function of reinforcer rate during training.     

Time to extinction in deteriorating environments

Habitat degradation and destruction are the predominant drivers of population extinction, but there is little theory to guide the analysis of population viability in deteriorating environments. To address this gap, we investigated extinction times in time-varying, demographically stochastic versions of the logistic model for population dynamics. A property of these models is the “extinction delay,” a quantitative measure of the time lag in extinction created by species-specific extinction debt. For completeness, three models were constructed to represent the different demographic routes by which deterioration may affect population dynamics. Numerical analysis for two notional life histories indicated that the demographic response to environmental deterioration had a large effect on extinction delay, but a third analysis showed that the trajectory of the decline in carrying capacity ultimately characterized its magnitude. A concave decline in carrying capacity produced a large extinction delay while a small delay occurred with a convex decline. Furthermore, our results explore the non-monotonicity of extinction debt with respect to the speed of deterioration. A peak is present at low levels of deterioration, and the height of the peak and the asymptote of delay are affected by both life history parameterizations and the rate of change of the carrying capacity. The results suggest that population viability analyses must consider not only environmental deterioration, but also the effects of deterioration on the trajectory of the decline in carrying capacity.     

The ecosystems approach to water management. The main features of the ecosystems concept

This paper summarizes the conceptual basis for ecosystemic water management, principally as it is discernible through a series of discussion papers contributed to the UN/ECE Seminar held in Oslo in May, 1991. The ecosystems approach seeks the objective management of water quality in lakes and river catchments, the sustainable exploitation of water resources (sensu lato) and the maintenance of biodiversity within aquatic catchments. It also seeks an attitude founded upon the sharing of habitat with other ecosystem components and the minimization of human impact. Moreover, there is no final condition: rather, there is an ethos always to improve performance. Emphasis is nevertheless placed on the unevolved, subclimactic state in which many ecosystems find themselves and the elasticity of structure which this imparts and which may, within limits, be exploited. Methods for assessing environmental quality and for measuring the performance of corrective management are briefly discussed. Future progress is suggested to be less than easy but proper ecosystemic attitudes and approaches are seen to be essential ingredients if past mistakes are to be overcome.     

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximum-likelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass.