Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations?

Lethal mutagenesis is a promising new antiviral therapy that kills a virus by raising its mutation rate. One potential shortcoming of lethal mutagenesis is that viruses may resist the treatment by evolving genomes with increased robustness to mutations. Here, we investigate to what extent mutational robustness can inhibit extinction by lethal mutagenesis in viruses, using both simple toy models and more biophysically realistic models based on RNA secondary-structure folding. We show that although the evolution of greater robustness may be promoted by increasing the mutation rate of a viral population, such evolution is unlikely to greatly increase the mutation rate required for certain extinction. Using an analytic multi-type branching process model, we investigate whether the evolution of robustness can be relevant on the time scales on which extinction takes place. We find that the evolution of robustness matters only when initial viral population sizes are small and deleterious mutation rates are only slightly above the level at which extinction can occur. The stochastic calculations are in good agreement with simulations of self-replicating RNA sequences that have to fold into a specific secondary structure to reproduce. We conclude that the evolution of mutational robustness is in most cases unlikely to prevent the extinction of viruses by lethal mutagenesis.     

Are algal communities driven toward maximum biomass?

In this continental-scale study, we show that in major benthic and planktonic stream habitats, algal biovolume--a proxy measure of biomass--is a unimodal function of species richness (SR). The biovolume peak is observed at intermediate to high SR in the benthos but at low richness in the phytoplankton. The unimodal nature of the biomass-diversity relationship implies that a decline in algal biomass with potential harmful effects on all higher trophic levels, from invertebrates to fish, can result from either excessive species gain or species loss, both being common consequences of human-induced habitat alterations. SR frequency distributions indicate that the most frequent richness is habitat-specific and significantly higher in the benthos than in the plankton. In all studied stream environments, the most frequent SR is lower than the SR that yields the highest biovolume, probably as a result of anthropogenic influences, but always within one standard deviation from it, i.e. they are statistically indistinguishable. This suggests that algal communities may be driven toward maximum biomass.     

Are Glaciers ‘Good to Think With’? Recognising Indigenous Environmental Knowledge 1

Lively debates in arctic and subarctic communities centre on potential contributions of indigenous knowledge to environmental sciences. Some scientists are now attempting to integrate traditional ecological knowledge (TEK) into existing knowledge frameworks as data. Anthropologists working with oral tradition propose an alternative approach. They reason that greater knowledge value, especially the possibility of surprises, may come from unfamiliar oral accounts that do not seem to fit easily within conventional frameworks. This paper builds on accounts I first heard from senior indigenous women in north-western North America about unorthodox behaviour of glaciers. These glaciers were depicted as sentient, wilful beings that responded directly and sometimes dramatically to human behaviour, often with devastating results. Similar themes are documented in colonial records where such ideas were discounted as ‘superstition’. Oral traditions, though, do not provide straightforward data for contemporary sciences. As practices such as oral storytelling now become recognised as knowledge and translated in new contexts, concepts like indigenous knowledge travel and accumulate meanings. Surging glaciers disrupt conceptual fields. Stories about them may prove good to ‘think with’ as we consider challenges of gathering diverse practices into the ubiquitous but narrowly framed category, knowledge.     

Are Defenses of Wild Radish Populations Well Matched with Variability and Predictablity of Herbivory?

Theory predicts that plants should employ constitutive (fixed) defenses when herbivory is consistently strong among years and induced (plastic) defenses when herbivory varies among years but is predictable within a season. We tested this theory by examining the herbivore species and damage censused over three seasons for 20 populations of wild radish in northern California. We conducted assays of constitutive resistance by challenging undamaged plants from these 20 populations with their common herbivores in the greenhouse. We assayed induced resistance by comparing the performance of herbivores on plants that had been experimentally damaged to undamaged plants from the same populations. Following damage, plants generally became more resistant to chewing herbivores (caterpillars) but more susceptible to sucking herbivores (aphids). Constitutive resistance to caterpillars was not stronger for populations that had high levels of herbivory that varied little among years, contrary to theory. Induced resistance may be stronger for plants from populations where herbivory varied more among years, consistent with expectations, although low power makes this conclusion equivocal. Induced resistance was not stronger for populations where early herbivory was a good predictor of late season herbivory. This lack of support for theory could have been caused by inadequacies with the experimental tests or with the theory and its assumptions. The theory assumes a coevolutionary equilibrium; however, high gene flow that has been reported for wild radish could disrupt matches between risk of herbivory and plant defense. The theory also assumes that resistance traits evolved as defenses against herbivory although these traits also serve other functions. Finally, the correlation we measured between early and late season herbivory may be at a temporal scale that is irrelevant since wild radish appears to adjust its defenses very rapidly.     

High Turnover Rates in Remnant Populations of the Harlequin Frog Atelopus cruciger (Bufonidae): Low Risk of Extinction?

Atelopus is among the most threatened of all amphibian genera. Most species of harlequin frogs disappeared more than two decades ago and only a few still exist. From ten critically endangered Atelopus species endemic to Venezuela, Atelopus cruciger is the only one that can be located at present. To assess the status of remnant populations of A. cruciger and to provide the demographic data for designing in situ management programs, we estimated: (1) the population size; (2) the apparent survival; and (3) the recruitment rates of one remnant population using mark‐recapture data. The adult population size varied (69–117), and this variation was not related to that of abundance indices based on visual counts at the river margins. Thus, caution is recommended when using visual counts as an index of abundance in Atelopus, because capture rates differ significantly among months and between seasons. Despite the observed variations, this population appears to be stable. Previous reports suggest that species of Atelopus are long‐lived. For populations of long‐lived species to remain approximately constant, recruitment must be low. Our mark‐recapture study, however, showed that adults tend to remain in the population for approximately 15 mo, but an average of 165 new frogs are recruited every year. Although immigration and emigration are possibilities, the site fidelity and the absence of nearby streams suggests that movement in and out of the study area is less important than births and deaths. Under the proposed hypothesis of a short life expectancy/high recruitment, the risk of extinction must be lower than previously thought.     

Are Baby Animals Less Appetizing? Tenderness toward Baby Animals and Appetite for Meat

Three studies investigated whether thoughts and feelings generated by baby animals might oppose appetite for meat. A prestudy established babyness as an important factor predicting moral concern for farmed animals. Study 1 showed that presenting images of baby animals, versus adult animals, as the source of meat reduced appetite for meat, but this effect was weak and found exclusively among women. Study 2 replicated and extended study 1 using a larger sample and two new animal sources. Study 3 included a no animal comparison condition, and found greatest levels of reduced appetite for meat when the meat source was presented as a baby animal, as opposed to an adult animal or with no visual indication of the animal source. A meta-analysis of the results using Bayes factors revealed considerable cumulative evidence in favor of the hypothesis that images of baby animals temporarily reduce women’s appetite for meat. In contrast, the evidence for men was less strong. Our results highlight a tension within some omnivores between caring for baby animals and appetite for meat.     

Genetic Structure of Chum Salmon (Oncorhynchus keta) Populations in the Lower Columbia River: Are Chum Salmon in Cascade Tributaries Remnant Populations?

The lower Columbia River drainage once supported a run of over a million chum salmon. By the late 1950s, the run had decreased to often a few hundred fish. With the exception of Grays River near the coast and an aggregation of chum salmon spawning in creeks and the main stem near Bonneville Dam in the Columbia Gorge, most populations were thought to be extinct. However, chum salmon consistently return in low numbers to tributaries originating in the Cascade Range: the Cowlitz, Lewis, and Washougal rivers. To assess whether Cascade spawners were strays or remnants of former populations, chum salmon from the Coastal, Cascade and Gorge ecoregional zones were characterized at 17 microsatellite loci. Significant heterogeneity in genotype distributions was detected between zones and collections formed regional groups in a neighbor-joining tree. Cascade collections had higher allelic richness and private alleles, and the Cowlitz River supported genetically divergent fall and summer runs, the only summer chum salmon run extant in the Columbia River drainage. We propose that chum salmon in the Cascade zone are remnants of original populations. We attribute the divergence between zonal groups to diverse ecological conditions in each zone, which promoted regional genetic adaptation, and to genetic drift experienced in small populations.     

Should I Stay or Should I Go? Dispersal and Population Structure in Small,Isolated Desert Populations of West African Crocodiles

The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (F _ST range: 0.12–0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.     

Is Chytridiomycosis Driving Darwin’s Frogs to Extinction?

Darwin’s frogs (Rhinoderma darwinii and R. rufum) are two species of mouth brooding frogs from Chile and Argentina that have experienced marked population declines. Rhinoderma rufum has not been found in the wild since 1980. We investigated historical and current evidence of Batrachochytrium dendrobatidis (Bd) infection in Rhinoderma spp. to determine whether chytridiomycosis is implicated in the population declines of these species. Archived and live specimens of Rhinoderma spp., sympatric amphibians and amphibians at sites where Rhinoderma sp. had recently gone extinct were examined for Bd infection using quantitative real-time PCR. Six (0.9%) of 662 archived anurans tested positive for Bd (4/289 R. darwinii; 1/266 R. rufum and 1/107 other anurans), all of which had been collected between 1970 and 1978. An overall Bd-infection prevalence of 12.5% was obtained from 797 swabs taken from 369 extant individuals of R. darwinii and 428 individuals representing 18 other species of anurans found at sites with current and recent presence of the two Rhinoderma species. In extant R. darwinii, Bd-infection prevalence (1.9%) was significantly lower than that found in other anurans (7.3%). The prevalence of infection (30%) in other amphibian species was significantly higher in sites where either Rhinoderma spp. had become extinct or was experiencing severe population declines than in sites where there had been no apparent decline (3.0%; x ² = 106.407, P<0.001). This is the first report of widespread Bd presence in Chile and our results are consistent with Rhinoderma spp. declines being due to Bd infection, although additional field and laboratory investigations are required to investigate this further.     

Are Dogs Children,Companions, or Just Animals? Understanding Variations in People's Orientations toward Animals

ABSTRACT

This paper examines the variations in dog owners' attitudes toward, treatment of, and interactions with, animals. Based on 28 in-depth interviews with dog owners from a county in the Midwestern United States, I demonstrate that pets are an important part of many people's lives, often providing companionship, entertainment, and meaningful interactions; however, there are notable, distinct variations in how people relate to them. Pet owners typically exhibit one of three orientations toward pets: “dominionistic,” “humanistic,” or “protectionistic.” The dominionistic have relatively low regard for their pets, valuing them primarily for the uses they provide, such as protection. Those employing the humanistic orientation elevate their pets to the status of surrogate humans and value their pets primarily for the affective benefits they enjoy from their close attachments. The protectionistic have high regard for both pets and animals more generally. They view pets as valuable companions and as creatures with their own interests. This typology offers insights for understanding the source and variety of the often ambiguous and contradictory relations between people and pets. I argue that individual characteristics and experiences impact how people understand and relate to animals, in large part, because they represent exposure to different cultural messages. I suggest that these orientations represent three sets of distinct cultural logics, each with distinct histories and contemporary sources.     

Extinction debt in fragmented grasslands: paid or not?

Fragmentation of grasslands and forests is considered a major threat to biodiversity. In the case of plants, the effect of fragmentation or landscape context is still unclear and published results are divergent. One explanation for this divergence is the slow response of long‐lived plants, creating an extinction debt. However, this has not been empirically confirmed. In this study, data were compiled from broad‐scale studies of grasslands from throughout the world that relate plant diversity to fragmentation effects. Only seven studies from northern Europe, out of a total 61, gave any information on actual habitat fragmentation in time and space. In landscapes with >10% grassland remaining, present‐day species richness was related to past landscape or habitat pattern. In landscapes with <10% grassland remaining, in contrast, plant species richness was more related to contemporary landscape or habitat pattern. Studies from landscapes with >10% grassland remaining supported the concept of an extinction debt, while studies from more fragmented landscapes did not provide any evidence of an extinction debt. In order to make generalisations about historical legacies on species diversity in grasslands it is important to consider a range of highly transformed landscapes, and not only landscapes with a high amount of grassland remaining.     

The Decline of the Endangered Populations of the Native Freshwater Crayfish (Austropotamobius pallipes) in Southern Spain: It is Possible to Avoid Extinction?

The southeastern mountains of Spain represent the southernmost limit of the genus Austropotamobius and the species A. pallipes (Lereboullet). The taxonomic position of this isolated crayfish in southern Spain is not clear, being genetically close to A. italicus, but morphologically distinct. A severe decline occurred during the 1980s, especially due to expansion of the alien species Procambarus clarkii, a North American freshwater crayfish and a vector of the aphanomycosis disease. In order to design a strategy for native crayfish conservation, recent trends in native crayfish populations, influence of isolation and habitat variables on their survival and possibilities for their recovery through restocking were studied. A decline in populations was observed between 1991 and 2002 (from 26 to 14 populations), and a total extinction could be predicted within the next 13 years. Two well-defined periods of rapid extinction rates were detected, 1991–1994 (1.25 populations/year) and 1999–2002 (1.50 populations/year). Main causes of extinction for these two periods were invasion by P. clarkii and mortality by unknown causes, respectively. The isolation variables had some positive effects on survival of populations but these cannot offer a sufficient guarantee, since several cases of extinction can be affected by a large component of stochastic factors, including random catastrophes. On the other hand, survival trials and restocking experiments showed that it was possible to recover lost habitats, when P. clarkii was absent and environmental conditions were good. It is concluded that it is possible to avoid extinction of the native crayfish populations; however, the conservation strategies must be based on an urgent stocking/restocking program.     

Does Haplodiploidy Purge Inbreeding Depression in Rotifer Populations?

Background

Inbreeding depression is an important evolutionary factor, particularly when new habitats are colonized by few individuals. Then, inbreeding depression by drift could favour the establishment of later immigrants because their hybrid offspring would enjoy higher fitness. Rotifers are the only major zooplanktonic group where information on inbreeding depression is still critically scarce, despite the fact that in cyclical parthenogenetic rotifers males are haploid and could purge deleterious recessive alleles, thereby decreasing inbreeding depression.

Methodology/Principal Findings

We studied the effects of inbreeding in two populations of the cyclical parthenogenetic rotifer Brachionus plicatilis. For each population, we compared both the parental fertilization proportion and F1 fitness components from intraclonal (selfed) and interclonal (outcrossed) crosses. The parental fertilization proportion was similar for both types of crosses, suggesting that there is no mechanism to avoid selfing. In the F1 generation of both populations, we found evidence of inbreeding depression for the fitness components associated with asexual reproduction; whereas inbreeding depression was only found for one of the two sexual reproduction fitness components measured.

Conclusions/Significance

Our results show that rotifers, like other major zooplanktonic groups, can be affected by inbreeding depression in different stages of their life cycle. These results suggest that haplodiploidy does not purge efficiently deleterious recessive alleles. The inbreeding depression detected here has important implications when a rotifer population is founded and intraclonal crossing is likely to occur. Thus, during the foundation of new populations inbreeding depression may provide opportunities for new immigrants, increasing gene flow between populations, and affecting genetic differentiation.