Searching for the fundamental niche using individual‐based habitat selection modelling across populations

Strictly speaking, fundamental niches are inestimable. Nevertheless, ecologists attempt approximating them to understand species’ distribution and plasticity to environmental changes, with invaluable repercussions on both theoretical and applied ecology. So far, individual‐based habitat selection models only characterized realized niches of populations delimited by physical (e.g. fences), historical (colonization) and biotic (competition) barriers constraining access to a subset of resources available to the species. As populations with different realized niches share the same fundamental niche, we developed a novel framework to scale‐up response curves from population‐scale habitat selection models to approximate the species’ optimal habitat choices, unbiased by barriers constraining accessibility. We used GPS‐locations from 147 wild mountain reindeer Rangifer t. tarandus, belonging to 7 of the remaining populations scattered throughout the subspecies’ range. We linked individual choices to accessible habitat features using conditional‐logistic regression with log‐link function in a use‐available design. Focal variables were modeled using 2nd degree polynomials on log‐scale, which correspond to a Gaussian curve used to approximate the fundamental niche optimum (curve mean) and breadth (variance). Using both real and simulated data we demonstrate that robust approximations of a fundamental niche optimum and breadth can be estimated using a relatively small number of representative populations with relatively few individuals. While each classical realized niche model had strong predictive power for the focal population but poorly predicted across populations, the approximation of the fundamental niche allowed for robust inter‐population comparisons in habitat quality. The proposed approach brings individual‐based habitat selection models forward along the continuum from investigating the realized niche of a population towards investigating a species’ fundamental niche, and allows us to quantify empirically the relationship between realized and fundamental niches. This allows improving the understanding of differences in fitness among populations, the prediction of species’ distributions and plasticity to environmental changes, and suggestions for mitigation priorities.     

THE SIGNIFICANCE OF INTRACELLULAR SELF-SHADING ON THE BIOOPTICAL PROPERTIES OF BROWN,RED, AND GREEN MACROALGAE1

The spectral light absorption and fluorescence excitation spectra from thalli (in vivo) and thylakoid micelles (no intracellular self-shading) from the macroalgae Laminaria digitata (L.) Edmonson, Palmaria palmata (L.) Kuntze, and Ulva sp. were examined. In all the examined species, the intracellular self-shading (i.e. the package effect) was highly significant to the extent that absorption peaks related to individual pigments were significantly suppressed. Thus, for studies related to taxonomy and physiology, “unpacked”spectra may be more informative. Thylakoid micelle preparations offer opportunities to examine more closely species-specific differences in the packaging effect, light harvesting and utilization, and pigmentation. As well, the thylakoid micelles, when analyzed with biochemical assays or fluoromtry, may provide insight into components of the photosynthetic machinery that are specific to different classes of mncroalgne. We present the Chl a-specific absorption coefficients and the corresponding fluorescence excitation spectra of macroalgal thylakoid micelles for the three species.     

An Unaccounted Fraction of Marine Biogenic CaCO3 Particles

Biogenic production and sedimentation of calcium carbonate in the ocean, referred to as the carbonate pump, has profound implications for the ocean carbon cycle, and relate both to global climate, ocean acidification and the geological past. In marine pelagic environments coccolithophores, foraminifera and pteropods have been considered the main calcifying organisms. Here, we document the presence of an abundant, previously unaccounted fraction of marine calcium carbonate particles in seawater, presumably formed by bacteria or in relation to extracellular polymeric substances. The particles occur in a variety of different morphologies, in a size range from <1 to >100 µm, and in a typical concentration of 10⁴–10⁵ particles L⁻¹ (size range counted 1–100 µm). Quantitative estimates of annual averages suggests that the pure calcium particles we counted in the 1–100 µm size range account for 2–4 times more CaCO₃ than the dominating coccolithophoride Emiliania huxleyi and for 21% of the total concentration of particulate calcium. Due to their high density, we hypothesize that the particles sediment rapidly, and therefore contribute significantly to the export of carbon and alkalinity from surface waters. The biological and environmental factors affecting the formation of these particles and possible impact of this process on global atmospheric CO₂ remains to be investigated.     

CYP2C9 genotype does not affect risk of tobacco-related cancer in the general population

Background: CYP2C9 enzymes are important in the metabolism of procarcinogenic chemicals such as polycyclic aromatic hydrocarbons (PAHs) found in tobacco smoke. Two functional variants in the CYP2C9 gene (CYP2C9*2 and CYP2C9*3) are known to be associated with decreased enzyme activity towards tolbutamide and warfarin, while this has not been investigated for PAHs. We hypothesised that these two variants in the CYP2C9 gene influence risk of tobacco-related cancer. Methods: In a prospective study of the general population (n = 10 392) with 60 years of follow-up, the Copenhagen City Heart Study, we associated two variants of CYP2C9 (CYP2C9*2 and CYP2C9*3) with risk of tobacco-related cancer and all cancer. All results were re-tested in a cross-sectional study of the general population (n = 36 856), the Copenhagen General Population Study. Results: We found no association between any of the CYP2C9 genotypes and risk of tobacco-related cancer, individual tobacco-related cancers, or all cancer. For the combined carriers (any CYP2C9*2 or CYP2C9*3 heterozygotes or homozygotes) vs. non-carriers we had 90% statistical power to exclude measures of relative risks below/above 0.8/1.2 and 0.9/1.1 in the Copenhagen City Heart Study and below/above 0.8/1.3 and 0.9/1.1 in the Copenhagen General Population Study for tobacco-related cancer and all cancer, respectively. Conclusion: Genetic variations in CYP2C9 do not affect risk of tobacco-related cancers.     

Long-term trends and variation in <Superscript>137</Superscript>Cs activity concentrations in brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) from Øvre Heimdalsvatn,a Norwegian subalpine lake

The Norwegian mountain lake, Øvre Heimdalsvatn, received major fallout from the Chernobyl accident in the spring of 1986. Activity concentrations of ¹³⁷Cs have been monitored annually in the brown trout (Salmo trutta) population of the lake over a 22-year period since 1986. The activity concentrations of ¹³⁷Cs in brown trout have declined over the period, although in recent years there has been little or no reduction in activity concentrations. Throughout the period, there has been considerable individual variation in ¹³⁷Cs activity concentrations. Within a single year, fish weight was the most significant factor affecting activity concentrations of ¹³⁷Cs in individual fish, although sex and age·weight were significant explanatory variables. The “size effect” was not significant during the initial period after fallout and in some recent years. During the first years after fallout, the ecological half-life of ¹³⁷Cs in brown trout was 3–4 years, but during the last decade this has increased significantly and has approached the physical half-life of 30 years for ¹³⁷Cs, suggesting a dynamic equilibrium between catchments inputs, possible remobilisation from lake sediments and lake outputs of ¹³⁷Cs.     

Evaluation of the ‘maximum price paid’ as an index of motivational strength for farmed silver foxes (Vulpes vulpes)

To measure farmed foxes’ motivations for full, naturalistic social contact, we constructed an apparatus where they could perform an operant to access stimuli, but then leave freely and thence determine their own bout lengths. Motivational measures based on demand curves can be invalid in such set-ups, and we therefore sought to validate the measure ‘maximum price paid’. This was achieved by measuring six silver fox males’ maximum operant responding for access or proximity to three resources differing in biological significance: food, vixens in oestrus and males. We predicted that if valid, maximum price paid would be highest for food and vixens. Maximum price were 970 ± 399 (S.E.) for food, 677 ± 173 (S.E.) for vixens and 389 ± 101 (S.E.) for other males (P < 0.05). In contrast, our complementary measures of motivation – price elasticity, expenditure and consumer surplus – did not differentiate between the resources, and ranked them in different orders (albeit not significantly). This was because the foxes rescheduled their behaviour with increasing costs, decreasing bout number while increasing bout length, to different extents with the three resources. Additional findings showed that all subjects ‘overpaid’, performing the operant response more than was required. This increased as the costs increased, perhaps due to increasing ‘time outs’ on the time-restricted schedule (DRH) as the task got harder. However, the overpayment was also highest when males were the resource, suggesting that operant responding was slowest and least efficient when working for less-valued resources. The resources present also affected how the foxes used the rest of the apparatus and influenced their behaviour; subjects staying more in the operant compartment when the resource was social (especially a female), but retreating to a distant compartment when it was food. While proximity to oestrous vixens elicited higher levels of tail wagging and only low levels of pacing, indicating a positive motivation, proximity to males elicited relatively high levels of pacing plus agonistic gaping, suggesting that the motives for seeking contact with males related to aggression. Thus, although our operant set-up reveals a drive to approach other males, the possible aggressive motives suggest that this sort of social contact would not necessarily improve their welfare in a traditional housing system. Overall, these results help improve the design and interpretation of preference tests, and confirm maximum price paid as a useful motivational measure for farmed foxes.     

Preferences of sheep for different types of pen flooring

In countries where the climate makes it practical with indoor housing during cold periods of the year and access to straw is limited, e.g. Iceland and Norway, housing of sheep on slats or expanded metal floors is common practice. However, European regulations for organic farming require that all animals should have access to a lying area with solid floor. The objective of this experiment was to investigate sheep preferences for different types of pen flooring.

In Experiment 1, a total number of 16 ewes, divided into four groups, were subjected to four different treatments. In each treatment, the ewes could choose between two lying areas with one of the following flooring materials: (1) solid wood versus rubber mats, (2) expanded metal versus solid wood, (3) solid wood versus straw, (4) expanded metal versus straw. In Experiment 2, a total number of eight ewes were individually subjected to the same treatments, first fully coated and then sheared. The ewes were video taped for 48 h in each treatment period.

In Experiment 1, the first animal that lay down after feeding preferred to lie down on straw or wood to expanded metal and straw to wooden floor (P < 0.05), but this first choice did not reflect the overall flooring preference for unsheared ewes. The groups of unsheared ewes showed no significant preferences for lying area.

In Experiment 2, single housed, unsheared ewes preferred wooden floor to rubber mats (P < 0.05), and tended to prefer expanded metal floor to straw (P = 0.08). There were no significant preferences in the two other treatments. After shearing, the ewes’ preferred wooden floor to expanded metal (P < 0.05), straw to wooden floor (P < 0.05), and straw to expanded metal floor (P< 0.0001). There were no significant preferences between rubber mats and wooden floor. Mean lying time (% of observations) for all treatments was 64.7% for unsheared ewes, and there were no significant differences between treatments. Mean lying time (% of observations) for all treatments the first 2–3 days after shearing was 43%. Significant differences in pre-shearing versus post-shearing lying times (% of observations) existed when the ewes were housed in pens with no straw (P < 0.05), this was not the case when the ewes had access to straw.

In conclusion, sheared but not unsheared ewes, preferred softer floors with low thermal conductivity (straw and wood). The less dramatically reduction in lying time (% of observations) after shearing when the ewes had access to straw, suggest that access to straw the first weeks after shearing may improve animal welfare.     

Francisella sp. (Family Francisellaceae) causing mortality in Norwegian cod (Gadus morhua) farming

In 2004, a new disease was detected in cod (Gadus morhua) in western Norway. Affected cod had white granulomas in the visceral organs and skin. A species of Francisella was isolated on blood agar plates from moribund cod. The bacterium could be grown at temperatures ranging from 6 to 22°C, but did not grow at 37°C. Challenge experiments showed that Francisella sp. was the cause for the new disease. The 16S rDNA gene sequence from Francisella sp. showed 99.17% similarity to F. philomiragia, and the 16S–23S ribosomal RNA intergenic spacer (249 nt), shows a similarity with that from Francisella isolated from tilapia and F. tularensis of 96.8 and 35.9%, respectively. The 23S sequence is more similar to F. tularensis, 97.7% (2,862 nt), compared to the tilapia isolate 96.8% (2,131 nt). The partial putative outer membrane protein (FopA) sequence (781 nt) from Francisella sp. shows a similarity with that from F. tularensis and F. philomiragia of 77.3 and 98.2%, respectively. Based on sequence data, culturing temperatures and pathogenicity for cod, it is suggested that this Francisella sp. from cod could be a new species of Francisella, Family Francisellaceae.     

Average attributable fractions: a coherent theory for apportioning excess risk to individual risk factors and subpopulations

The attributable fraction in a population and the attributable fraction in exposed are different epidemiologic measures for quantifying the contribution of a risk factor to the risk of disease. While the attributable fraction in a population depends on both the relative risk of disease and the risk of being exposed in the population, the attributable fraction in exposed depends only on the relative risk. Similar relationships apply to the combined attributable fraction in a population and in exposed, respectively, for quantifying the total contribution of a group of risk factors. Eide and Gefeller (1995) showed how the sequential and average attributable fractions could be applied to quantify the contributions of the individual risk factors to a combined attributable fraction in a population. The present paper shows how this methodology can be extended to the combined attributable fraction in exposed. The resulting average attributable fractions in exposed are compared to other proposed methods. The relationship between the average attributable fractions in a population and in exposed is outlined, thus establishing a coherent theory for apportioning attributable fractions in individuals, groups of individuals and populations, to single risk factors or groups of risk factors like modifiable versus nonmodifiable factors.