Biological traits interact with human threats to drive extinctions: A modelling study

How a particular threat influences extinction risk may depend on biological traits. Empirical studies relating threats and traits are needed, but data are scarce, making simulations useful. We implemented an eco-evolutionary model to analyse how five threat types influence the extinction risk of virtual organisms differing in body size, maturity age, fecundity, and dispersal ability. The model consisted of observing the evolutionary shift in the mean trait values of an assemblage of organisms when a threat was added into the virtual world where they lived. If a positive shift was found in trait values, we considered that the threat negatively influenced organisms with lower values for that trait. Direct killing mostly affected organisms with slow life cycles (slower-living) and poorly dispersive organisms. Habitat loss caused a reduction in the average dispersal ability of organisms. Habitat fragmentation caused an increase of average dispersal ability, and had a negative effect on larger, less fecund organisms. Habitat degradation and the introduction of invasive competitors had similar effects, mostly affecting large and fast-living organisms, with habitat degradation also affecting highly fecund and poorly dispersive organisms. These results agree with previous empirical studies in which larger, slower-lived, and less fecund organisms are more vulnerable to a greater range of threats. On the other hand, our results challenge two commonly seen hypotheses in the literature: that organisms with high dispersal ability fare well under any high habitat loss scenarios, and that fast-living, highly fecund organisms always do well during environmental change. Our study shows that highly dispersive organisms may be the losers when habitat loss removes large continuous areas of habitat, and fast-living and highly reproductive organisms may be the losers when resources or energy availability dwindle to very low levels. Most importantly, our study underpins the importance of considering the type of threat when analysing the relation between traits and extinction. Even in simple scenarios such as the ones modelled here, different threats lead to different, sometimes opposite, extinction probabilities according to the biological traits of organisms.     

Repressor of phage 16-3 with altered binding specificity indicates spatial differences in repressor-operator complexes

The C repressor protein of phage 16-3, which is required for establishing and maintaining lysogeny, recognizes structurally different operators which differ by 2 bp in the length of the spacer between the conserved palindromic sequences. A "rotationally flexible protein homodimers" model has been proposed in order to explain the conformational adaptivity of the 16-3 repressor. In this paper, we report on the isolation of a repressor mutant with altered binding specificity which was used to identify a residue-base pair contact and to monitor the spatial relationship of the recognition helix of C repressor to the contacting major groove of DNA within the two kinds of repressor-operator complexes. Our results indicate spatial differences at the interface which may reflect different docking arrangements in recognition of the structurally different operators by the 16-3 repressor.     

Use of the abundance spectrum and relative-abundance distributions to analyze assemblage change in massively altered landscapes

Fragmentation of natural landscapes is a pervasive process in the world. Common models predict coherent change in assemblages, with less numerous species becoming locally extinct first, then species of intermediate abundance, and so forth. Relative-abundance distributions should change systematically in landscapes characterized by greater change. Such a predictable sequence of change is not evident in the avifaunas of landscapes of central Victoria, Australia, where relative-abundance patterns in more affected landscapes bear little resemblance to reference distributions. I provide two sets of analyses of relative-abundance distributions: (1) analyses that do not depend on the identity of individual species and (2) abundance spectra, which use ordered lists of species ranked by species' commonness in reference systems. While abundance spectra change dramatically in smaller remnants, relative-abundance distributions change little, suggesting that the "reorganization" of abundances occurs over ecological time frames. The dispersal-limited multinomial is a flexible distribution that may fit many data sets yet be unrelated to assumptions (species neutrality) and processes (fixed total numbers of individuals) of the unified neutral theory. A more complete understanding of human impacts at landscape scales must include capacities to predict those species that will be advantaged by change, as well as those that will be disadvantaged.     

Ways of collagen separation in pathologically altered tissue

A system of chromatographic methods using two successive DEAE-cellulose chromatographic steps and two successive separations on Bio-Gel A-1.5 m has been worked out for the separation of individual collagen types. The success of the procedure is based on the preliminary removal of proteoglycans during the first DEAE-cellulose run. Alternatively it is possible to replace chromatographic steps, following the removal of proteoglycans, with fraction precipitation.     

Behavioural strategies towards human disturbances explain individual performance in woodland caribou

Behavioural strategies may have important fitness, ecological and evolutionary consequences. In woodland caribou, human disturbances are associated with higher predation risk. Between 2004 and 2011, we investigated if habitat selection strategies of female caribou towards disturbances influenced their calf’s survival in managed boreal forest with varying intensities of human disturbances. Calf survival was 53 % and 43 % after 30 and 90 days following birth, respectively, and 52 % of calves that died were killed by black bear. The probability that a female lose its calf to predation was not influenced by habitat composition of her annual home range, but decreased with an increase in proportion of open lichen woodland within her calving home range. At the local scale, females that did not lose their calf displayed stronger avoidance of high road density areas than females that lost their calf to predation. Further, females that lost their calf to predation and that had a low proportion of ≤5-year-old cutovers within their calving home range were mostly observed in areas where these young cutovers were locally absent. Also, females that lost their calf to predation and that had a high proportion of ≤5-year-old cutovers within their calving home range were mostly observed in areas with a high local density of ≤5-year-old cutovers. Our study demonstrates that we have to account for human-induced disturbances at both local and regional scales in order to further enhance effective caribou management plans. We demonstrate that disturbances not only impact spatial distribution of individuals, but also their reproductive success.     

Population genetic structure of orchid bees (Euglossini) in anthropogenically altered landscapes

Habitat degradation and fragmentation are widespread phenomena in tropical regions. Negative effects on the biota are numerous, ranging from interruption of gene flow among populations, to the loss of genetic diversity within populations, to a decline in species richness over time. Orchid bees (Hymenoptera: Apidae: Euglossini) are of major conservation interest due to their function as pollinators of numerous orchid species and other tropical plants. Here, we used microsatellite markers to investigate the effects of geographic distance and habitat fragmentation on gene flow among populations. Populations of Euglossa dilemma in three geographic regions??the Yucat??n peninsula (Mexico), Veracruz (Mexico), and Florida (USA)??were genetically structured predominantly across the regions, with the strength of differentiation among populations being positively correlated with geographic distance. Within geographic regions only little substructure was found, suggesting that dispersal is substantial in the absence of geographic or ecological barriers. In a second study, patterns of genetic differentiation among eight species of Euglossa were not related to habitat fragmentation following deforestation in southern Mexico (Veracruz). Specifically, most bee populations in the 9,800?ha forest remnant of Los Tuxtlas (Volcano San Martin) were neither differentiated from, nor had less genetic diversity than, populations in near-continuous forest separated from Los Tuxtlas by 130?km of agricultural land. Either occasional long distance dispersal across open areas has buffered the expected genetic effects of fragmentation, or the history of fragmentation in southern Mexico is too recent to have caused measurable shifts in allelic composition.     

Nesting ecology of stingless bees and potential threats to their survival within selected landscapes in the northern Volta region of Ghana

Stingless bees are key insects in the tropics, both as pollinators of crops and as contributors to the maintenance of floral diversity through pollination of wild plants. This study investigated the nesting ecology and threats to three stingless bee species: Meliponula bocandei (Spinola), Meliponula ferruginea (Lepeletier) and Dactylurina staudingeri (Gribodo) in three landscapes characterized as forest with logging and wild honey hunting; farmlands that experience annual wild fires and a national park. The study was carried out in July 2011 and February 2012. A total of 93 stingless bee nests were found in 48 ha (density 1.9 nests per ha), 81% in tree cavities and 19% in deserted termite mounds and in the ground. M. ferruginea was the only species using deserted termite mounds (seventeen nests) and in the ground (1 nest). Although tree size (diameter at breast height, DBH >15 cm) and density of large tree were important for nest site selection, there was no influence of tree species. M. bocandei may be restricted in choice of nest site in farmland areas by the absence of trees. Reduced availability of trees in agricultural landscape together with bush burning and wild honey collecting is the main threats to stingless bees survival and abundance which need to be addressed for their successful conservation in Ghana.     

An isotopic approach to measuring nitrogen balance in caribou

Nutritional restrictions in winter may reduce the availability of protein for reproduction and survival in northern ungulates. We refined a technique that uses recently voided excreta on snow to assess protein status in wild caribou (Rangifer tarandus) in late winter. Our study was the first application of this non-invasive, isotopic approach to assess protein status of wild caribou by determining dietary and endogenous contributions of nitrogen (N) to urinary urea. We used isotopic ratios of N (δ¹⁵N) in urine and fecal samples to estimate the proportion of urea N derived from body N (p-UN) in pregnant, adult females of the Chisana Herd, a small population that ranged across the Alaska-Yukon border. We took advantage of a predator-exclosure project to examine N status of penned caribou in April 2006. Lichens were the primary forage (>40%) consumed by caribou in the pen and δ¹⁵N of fiber tracked the major forages in their diets. The δ¹⁵N of urinary urea for females in the pen was depleted relative (−1.3 ± 1.0 parts per thousand [‰], ) to the δ¹⁵N of body N (2.7 ± 0.7‰). A similar proportion of animals in the exclosure lost core body mass (excluding estimates of fetal and uterine tissues; 55%) and body protein (estimated by isotope ratios; 54%). This non-invasive technique could be applied at various spatial and temporal scales to assess trends in protein status of free-ranging populations of northern ungulates. Intra- and inter-annual estimates of protein status could help managers monitor effects of foraging conditions on nutritional constraints in ungulates, increase the efficiency and efficacy of management actions, and help prepare stakeholders for potential changes in population trends. © 2010 The Wildlife Society.     

Multiple spatial-scale resource selection function models in relation to human disturbance for moose in northeastern China

The moose (Alces alces cameloides) population in northeastern China is on the southernmost edge of its distribution in Asia. A survey was conducted to determine moose resource selection and the effects of human disturbance on moose in a study area of 20,661 ha located on the northwestern slope of the Lesser Khingan Mountains, located in northeastern China. Predictive models of resource selection were developed using logistic and autologistic regression. All models considered resource variable selection at two spatial scales, patch and landscape. At the patch scale, moose preferred larger birch (Betula platyphylla) patches, but avoided larger tamarack (Larix gmelinii) patches. At the landscape scale, moose preferred higher densities of tamarack patches, i.e., heterogeneity of tamarack stands, selected areas with more abundant annual shoots, terrain conducive to better concealment, higher altitudes and areas saturated with soil moisture. Roads and forest harvest intervals were identified as important human disturbance factors. This is the first time that moose have been reported to avoid roads, and the avoidance distance was nearly 3 km. We believe that in this region moose under the influence of roads are behaviorally plastic, compared with the indifference of moose to the presence of roads in other regions. Moose avoided forest areas logged more than 3 years previously and preferred areas logged 1–2 years previously. In addition, it may be necessary to monitor the effect of the dynamic of density of roe deer on the spatial distribution of the moose population.     

Conglutinin, immunoconglutinins and heterophile antibodies in the sera of apparently healthy moose (Alces alces) and caribou (Rangifer tarandus) in Quebec

Serum samples from apparently healthy wild populations of moose and caribou in the province of Quebec, Canada were screened for the presence of conglutinin (K), immunoconglutinins (IKS) and heterophile antibodies. The conglutinating factor in moose and caribou sera was characterized utilizing the necessity of calcium ions for its reaction with sensitized sheep erythrocytes which had been alexinated with horse complement. The conglutinating substance in these animals did not require calcium ions for its activity. The conglutinating activity in both moose and caribou sera was characterized due to IKS as those present in sheep, dog and rabbit sera. Both moose and caribou had non-agglutinating type of heterophile antibodies. Their titres varied from 0 to 80. None of the animals tested had K in their blood. The titre of IKS varied from 0 to 640 with a mean value of 41 in moose, whereas it varied from 0 to 80 with a mean value of 18 in caribou. About 75% of all the animals in both the groups were positive for IKS. The specificity of IKS was demonstrated by the total removal of its activity on absorption with alexinated cells. Presence of IKS in these animals is suggestive of latent infection(s) possibly of bacterial, viral or parasitic origin.     

Efficient targeting to storage granules of human proinsulins with altered propeptide domain

In neuronal and endocrine cells, peptide hormones are selectively segregated into storage granules, while other proteins are exported continuously without storage. Sorting of hormones by cellular machinery involves the recognition of specific structural domains on prohormone molecules. Since the propeptide of insulin is known to play an important role in its three-dimensional structure, it is reasonable to speculate that targeting of proinsulin to storage granules would require a functional connecting peptide. To test this hypothesis, we constructed two mutations in human proinsulin with different predicted structures. In one mutation, Ins delta C, the entire C peptide was deleted, resulting in an altered insulin in which the B and the A chains are joined contiguously. In the other mutation, Ins/IGF, the C peptide of proinsulin was replaced with the unrelated 12-amino acid connecting peptide of human insulin-like growth factor-I; this substitution should permit correct folding of the B and A chains to form a tertiary structure similar to that of proinsulin. By several biochemical and morphological criteria, we found that Ins/IGF is efficiently targeted to storage granules, suggesting that the C peptide of proinsulin does not contain necessary sorting information. Unexpectedly, Ins delta C, which presumably cannot fold properly, is also targeted to granules at a high efficiency. These results imply that either the targeting machinery can tolerate changes in the tertiary structure of transported proteins, or that the B and A chains of insulin can form a relatively intact three-dimensional structure even in the absence of C peptide.     

Increased abdominal-to-peripheral fat distribution contributes to altered autonomic-circulatory control with human aging

Autonomic nervous system (ANS) control of the circulation is altered with aging in adult humans. Similar changes are observed in obesity, particularly abdominal obesity. To determine whether age-associated differences in ANS-circulatory function can be partially explained by increased body fatness, we examined ANS function and three expressions of adiposity (total body fat, abdominal body fat, and abdominal-to-peripheral body fat distribution; dual-energy X-ray absorptiometry) in 43 healthy men: 27 young (25 +/- 1 yr) and 16 older (65 +/- 1). ANS functions assessed included 1) autonomic support of arterial blood pressure (BP; radial artery catheter), i.e., the reduction in BP during versus before acute ganglionic blockade (GB; intravenous trimethaphan); 2) baroreflex buffering, i.e., the increase in systolic BP with continuous incremental and bolus infusions of phenylephrine during versus before GB; 3) cardiovagal baroreflex sensitivity (Oxford technique); and 4) heart rate variability (time- and frequency-domain analyses). Covarying for abdominal-to-peripheral fat distribution reduced or abolished age-related differences in ANS support of BP, cardiovagal baroreflex sensitivity, and heart rate variability but did not affect age-related differences in baroreflex buffering. Covarying for abdominal and total fat had small selective or no effects on age-associated differences in autonomic-circulatory control. Abdominal-to-peripheral fat distribution explains a significant portion of the variance in a number of autonomic-circulatory functions attributable to aging. Therefore, the development of this fat pattern may contribute to several changes in ANS-cardiovascular function observed with aging. These results may help explain how changes in body fat distribution with advancing age are linked to impairments in circulatory control.     

Allocating protein to reproduction in arctic reindeer and caribou

Reindeer (Rangifer tarandus tarandus) and caribou (Rangifer tarandus granti) use body stores (capital) and food intake (income) for survival and reproduction. Intakes of low-nitrogen (N) food declined in winter and increased in spring (51-83 g dry matter kg(-0.75) d(-1)). Reindeer calved before regaining food intake, whereas caribou calved 28 d later. Body N was conserved by minimizing oxidation of amino acid N to urea. Maternal protein stored from early winter was used for 96% of fetal growth in reindeer but only 84% of fetal growth in later-birthing caribou. Both subspecies rely on maternal body protein for 91% of the protein deposited in the neonate via milk over the first 4 wk. All females lost body protein over winter, but lactating females continued to lose protein while nonreproductive females regained protein. Net costs of lactation above maintenance were greater for N (110%-130%) than for energy (40%-59%). Large fat stores in reindeer spare body protein from oxidation in winter, whereas in caribou, less fat with the same body protein favors migration when food is inadequate. The resilience of Rangifer populations to variable patterns of food supply and metabolic demand may be related to their ability to alter the timing and allocation of body protein to reproduction.     

Integrating human behavior and snake ecology with agent-based models to predict snakebite in high risk landscapes

Snakebite causes more than 1.8 million envenoming cases annually and is a major cause of death in the tropics especially for poor farmers. While both social and ecological factors influence the chance encounter between snakes and people, the spatio-temporal processes underlying snakebites remain poorly explored. Previous research has focused on statistical correlates between snakebites and ecological, sociological, or environmental factors, but the human and snake behavioral patterns that drive the spatio-temporal process have not yet been integrated into a single model. Here we use a bottom-up simulation approach using agent-based modelling (ABM) parameterized with datasets from Sri Lanka, a snakebite hotspot, to characterise the mechanisms of snakebite and identify risk factors. Spatio-temporal dynamics of snakebite risks are examined through the model incorporating six snake species and three farmer types (rice, tea, and rubber). We find that snakebites are mainly climatically driven, but the risks also depend on farmer types due to working schedules as well as species present in landscapes. Snake species are differentiated by both distribution and by habitat preference, and farmers are differentiated by working patterns that are climatically driven, and the combination of these factors leads to unique encounter rates for different landcover types as well as locations. Validation using epidemiological studies demonstrated that our model can explain observed patterns, including temporal patterns of snakebite incidence, and relative contribution of bites by each snake species. Our predictions can be used to generate hypotheses and inform future studies and decision makers. Additionally, our model is transferable to other locations with high snakebite burden as well.     

Proteasome response to interferon-gamma is altered in senescent human fibroblasts

We have investigated immunoproteasomes in human fibroblasts during replicative senescence. Unlike levels of constitutive proteasome catalytic subunits and 26S proteasome regulatory subunits, levels of immunosubunits did not decrease dramatically in senescent cells. However, the induction of immunosubunits by interferon-gamma (IFN-gamma) was lost in senescent cells. In contrast, levels of the 11S proteasome regulator, PA28, were increased by IFN-gamma even in senescent cells, and both immunosubunits and PA28 increased with the reversible growth arrest in confluent cell cultures. The results highlight differences in the mechanisms of regulation of immunoproteasomes compared to constitutive proteasomes and in the irreversible growth arrest of senescent cells compared to reversible contact-induced growth arrest.