On the relation between genetic and environmental variability in animals

Summary If a phenotypic character is under stabilizing selection, the selective disadvantage of a nonoptimal genotype will decrease exponentially to zero as the proportion of phenotypic variation that is environmental in origin -V _e /V _p - increases. Under the modified mutation-drift hypothesis of genetic polymorphism, the proportion of mutations that are effectively neutral and average heterozygosity should increase with this ratio. Invertebrates, because of their small size, fast development, and low degree of homeostasis (relative to vertebrates), are expected to show a larger environmental component of phenotypic variation than vertebrates. This may help explain why invertebrates are in general more genetically variable than vertebrates and why, when laboratory populations ofDrosophila are maintained in heterogeneous environments, genetic variability is lost less rapidly than when they are kept in constant conditions.     

How to separate genetic and environmental causes of similarity between relatives

Related individuals often have similar phenotypes, but this similarity may be due to the effects of shared environments as much as to the effects of shared genes. We consider here alternative approaches to separating the relative contributions of these two sources to phenotypic covariances, comparing experimental approaches such as cross-fostering, traditional statistical techniques and more complex statistical models, specifically the 'animal model'. Using both simulation studies and empirical data from wild populations, we demonstrate the ability of the animal model to reduce bias due to shared environment effects such as maternal or brood effects, especially where pedigrees contain multiple generations and immigration rates are low. However, where common environment effects are strong, a combination of both cross-fostering and an animal model provides the best way to avoid bias. We illustrate ways of partitioning phenotypic variance into components of additive genetic, maternal genetic, maternal environment, common environment, permanent environment and temporal effects, but also show how substantial confounding between these different effects may occur. Whilst the flexibility of the mixed model approach is extremely useful for incorporating the spatial, temporal and social heterogeneity typical of natural populations, the advantages will inevitably be restricted by the quality of pedigree information and care needs to be taken in specifying models that are appropriate to the data.     

Statistical limits to the identification of ion channel domains by sequence similarity

The study of ion channel function is constrained by the availability of structures for only a small number of channels. A commonly used bioinformatics technique is to assert, based on sequence similarity, that a domain within a channel of interest has the same structure as a reference domain for which the structure is known. This technique, while useful, is often employed when there is only a slight similarity between the channel of interest and the domain of known structure. In this study, we exploit recent advances in structural genomics to calculate the sequence-based probability of the presence of putative domains in a number of ion channels. We find strong support for the presence of many domains that have been proposed in the literature. For example, eukaryotic and prokaryotic CLC proteins almost certainly share a common structure. A number of proposed domains, however, are not as well supported. In particular, for the COOH terminus of the BK channel we find a number of literature proposed domains for which the assertion of common structure based on common sequence has a nontrivial probability of error.     

On limits to perception and pattern recognition

We propose certain general conditions that we believe are reasonable for any pattern recognition algorithm. We find that these conditions give rise to paradoxical identification. The algorithms are incapable of distinguishing composite patterns and must be able to distinguish patterns at an atomistic level.     

Spreading recruitment over time to cope with environmental variability

Seedling establishment is one of the most vulnerable life cycle stages, and a key component for the population dynamics in short-lived plants. In unpredictable environments, timing of emergence is critical for the success of plant performance, and different adaptive bet-hedging strategies have evolved to reduce the risk of failure in recruitment. In this study we describe the spatio-temporal pattern of seedling emergence (overall rate and timing) and survival in four contrasting Mediterranean habitats for Plantago coronopus, a small herb with dimorphic seeds. We then explore the importance of spreading germination within years, as well as the role of the two types of seeds from a broader temporal perspective. Populations strongly differed for all recruitment components analyzed in a given year, but this spatial differentiation diluted when a longer period was considered. Apical (smaller) seeds germinated later and in a significantly lower proportion than basal (larger) seeds. Both late emergents and seedlings from apical seeds had lower survival probability in a rainy year. However, our results suggest that in a population having the lowest production of apical seeds, late emergents coming from apical seeds may constitute a large fraction of yearly recruitment and that their performance was non-significantly different from that of early emergents over the 4-year study period. This study provides evidence of the importance of two related traits (spreading seedling emergence through time by producing dimorphic seeds) as bet-hedging strategies to cope with environmental unpredictability. This is at least partly accomplished by increasing the potential of recruitment in favourable years, instead of buffering such important process in extremely bad years.     

Compensation limits of fish muscle myofibrillar ATPase enzyme to environmental temperature

1. 1.|Goldfish acclimated to a range of temperatures between 5 and 35°C were found to only compensate the specific activity of their myofibrillar ATPase enzyme between 10 and 30°C.

2. 2.|The preferred temperatures of goldfish acclimated to 5°C and to 30°C were determined to be about 10 and 26°C respectively.

3. 3.|It is conlcuded that goldfish are only able to acclimate their myofibrillar ATPase system to temperatures between 10 and 30°C, but acclimation to these temperatures enables them to tolerate extremes.

Demographic response of plant populations to habitat fragmentation and temporal environmental variability

Many plant species currently exist in fragmented populations of different sizes, while they also experience unpredictable climatic fluctuation over time. However, we still understand little about how plant demography responds to such spatial and temporal environmental variability. We studied population dynamics of an understory perennial herb Trillium camschatcense in the Tokachi plain of Hokkaido, Japan, where a significant effect of forest fragmentation on seedling recruitment was previously reported. Four populations across a range of fragment sizes were studied for 6 years, and the data were analyzed using matrix population models. Per capita fecundity (the number of recruits per plant) varied greatly among populations, but the variation in population growth rates (λ) was mainly driven by the variation in stasis and growth rates, suggesting that the general trend of reduced fecundity in fragmented populations may not be readily translated into subsequent dynamics. Temporal variation in λ among years was more than 2 times larger than spatial variation among populations, and this result was likely attributable to the contrasting response of correlation structures among demographic rates. The among-population variation in λ was dampened by negative covariation between matrix elements possibly due to density-dependent regulation as well as an inherent constraint that some elements are not independent, whereas positive covariation between matrix elements resulted in large temporal variation in λ. Our results show that population dynamics responded differently to habitat fragmentation and temporal variability of the environment, emphasizing the need to discriminate these spatial and temporal variations in demographic models. Although no populations were projected to be declining in stochastic simulations, correlation between current habitat size and plant density implies historical λ is positively related to habitat size.     

Developmental variability and the limits of adaptation: Interactions with stress

1. Little evolutionary change may occur at species borders since the cost of accommodating environmental stresses is high. Extreme examples of such stasis include cave animals in stable stressed environments and ‘living fossils’ in widely fluctuating stressed environments. 2. Variability from the molecular to the organismic level tends to be high under extreme stress. At the developmental level, the fitness of such variants may be low. This means that much developmental variability in natural populations may have little evolutionary significance. 3. Rapid evolutionary change of morphological traits is most likely to be based upon genes acting late in a developmental pathway under conditions which are ecologically and energetically permissive. 4. Although some increases in resistance to temperature extremes have been recorded in laboratory selection experiments, major extensions of extremes in natural populations appear difficult to achieve. The energetic costs of surviving extremes at species borders implies that the evolution of major developmental and morphological shifts is more likely to be a feature of populations of more equable habitats.     

Size variability of juvenile Atlantic salmon: links to environmental conditions

Climate change models predict a 2 to 6° C increase in air temperature within the next 100 years in the Maritime Provinces of eastern Canada. Higher air temperatures are expected to contribute to increased water temperatures, alterations in stream flow conditions, and ultimately reductions in fish growth. Mean annual size-at-age of juvenile Atlantic salmon Salmo salar decreased in the Northwest Miramichi and Southwest Miramichi Rivers between 1971–1999. Lengths-at-age of juveniles were significantly correlated between the two rivers. For Atlantic salmon parr, stronger associations between inter-cohort fork length ( L _F) than intra-cohort L _F were observed, suggesting that environmental conditions in the current year of growth have the more significant effects on size of age 2 year parr than conditions encountered the previous year by age 1 year parr of the same cohort. Fork lengths of parr were significantly and negatively associated with spring air and water temperatures. In the Miramichi River, increases in air and water temperature as predicted from climate change models may adversely affect growth of juvenile Atlantic salmon parr, reducing the overall productivity of the Atlantic salmon populations in this region.     

Persistence of selected Spartina alterniflora rhizoplane diazotrophs exposed to natural and manipulated environmental variability

Rhizoplane-rhizosphere nitrogen-fixing microorganisms (diazotrophs) are thought to provide a major source of biologically available nitrogen in salt marshes dominated by Spartina alterniflora. Compositional and functional stability has been demonstrated for this important functional group; however, the quantitative responses of specific diazotroph populations to environmental variability have not been assessed. Changes in the relative abundances of selected rhizoplane diazotrophs in response to long-term fertilization were monitored quantitatively by reverse sample genome probing. Fertilization stimulated Spartina, with plant height nearly tripling after 1 year. Fertilization also resulted in significant changes in interstitial porewater parameters. Diazotrophic activity (acetylene reduction assay) was sensitive to the fertilization treatments and was inhibited in some plots on several sampling dates. However, inhibition was never consistent across all of the replicates within a treatment and activity always recovered. The rhizoplane diazotrophs were quite responsive to environmental variability and to experimental treatments, but none were displaced by either environmental variability or experimental treatments. All strains were detected consistently throughout this study, and extensive spatial heterogeneity in the distribution patterns of these organisms was observed. The physiological traits that differentiate the diazotroph populations presumably support competitiveness and niche specialization, resulting in the observed resilience of the diazotroph populations in the rhizosphere.     

Climate change shifts environmental space and limits transferability of treeline models

Our study aims at gaining insights into the processes determining the current treeline dynamics in Finnish Lapland. Using forest surveys conducted in 1978 and 2003 we modelled the occurrence and abundance of three dominant tree species in Finnish Lapland, i.e. Pinus sylvestris, Picea abies and Betula pubescens, with boosted regression trees. We assessed the importance of climatic, biotic and topographic variables in predicting tree occurrence and abundance based on their relative importance and response curves. We compared temporal and spatial transferability by using an extended transferability index. Site fertility, the abundance of co‐occurring species and growing degree days were generally the most important predictors for both occurrence and abundance across all species and datasets. Climatic predictors were more important for modelling occurrences than for modelling abundances. Occurrence models were able to reproduce the observed treeline pattern within one time period or region. Abundance models underestimated basal area but captured the general pattern of low and high values. Model performance as well as transferability differed considerably between species and datasets. Pinus sylvestris was modelled more successfully than P. abies and B. pubescens. Generally, spatial transferability was greater than temporal transferability. Comparing the environmental space between datasets revealed that transferring models means extrapolating to novel environments, providing a plausible explanation for limited transferability. Our study illustrates how climate change can shift the environmental space and lead to limited model transferability. We identified non‐climatic factors to be important in predicting the distribution of dominant tree species, contesting the widespread assumption of climatically induced range expansion.     

On the similarity of dendrograms

A metric on binary trees is defined to give the similarity of two dendrograms. One of the major desirable properties of the proposed tree similarity measure is to clarify the decision ordering nature of biological trees. This metric is applied to evolutionary tree reconstructions and comparative embryogenesis. The mathematical properties of this metric are discussed, and an algorithm is proposed to compute the metric.“ …. our essential task lies in the comparison of related forms rather than in the precise definition of each; and the deformation of a complicated figure may be a phenomenon easy of comprehension, though the figure itself have to be left unanalysed ….”     

On distance and similarity in fold space

Metric information on similarities and distances in fold space is essential for quantitative work in structural bioinformatics and structural biology. Here we derive a suitable metric for protein structures from the fundamental axioms of similarity. Derivation of the metric also clarifies the relationship between the interrelated concepts of distance and similarity.     

Action potential waveform variability limits multi-unit separation in freely behaving rats

Extracellular multi-unit recording is a widely used technique to study spontaneous and evoked neuronal activity in awake behaving animals. These recordings are done using either single-wire or multiwire electrodes such as tetrodes. In this study we have tested the ability of single-wire electrodes to discriminate activity from multiple neurons under conditions of varying noise and neuronal cell density. Using extracellular single-unit recording, coupled with iontophoresis to drive cell activity across a wide dynamic range, we studied spike waveform variability, and explored systematic differences in single-unit spike waveform within and between brain regions as well as the influence of signal-to-noise ratio (SNR) on the similarity of spike waveforms. We also modelled spike misclassification for a range of cell densities based on neuronal recordings obtained at different SNRs. Modelling predictions were confirmed by classifying spike waveforms from multiple cells with various SNRs using a leading commercial spike-sorting system. Our results show that for single-wire recordings, multiple units can only be reliably distinguished under conditions of high recording SNR (≥ 4) and low neuronal density (≈ 20,000/ mm(3)). Physiological and behavioural changes, as well as technical limitations typical of awake animal preparations, reduce the accuracy of single-channel spike classification, resulting in serious classification errors. For SNR <4, the probability of misclassifying spikes approaches 100% in many cases. Our results suggest that in studies where the SNR is low or neuronal density is high, separation of distinct units needs to be evaluated with great caution.     

Network variability limits stimulus-evoked spike timing precision in retinal ganglion cells

Visual, auditory, somatosensory, and olfactory stimuli generate temporally precise patterns of action potentials (spikes). It is unclear, however, how the precision of spike generation relates to the pattern and variability of synaptic input elicited by physiological stimuli. We determined how synaptic conductances evoked by light stimuli that activate the rod bipolar pathway control spike generation in three identified types of mouse retinal ganglion cells (RGCs). The relative amplitude, timing, and impact of excitatory and inhibitory input differed dramatically between On and Off RGCs. Spikes evoked by repeated somatic injection of identical light-evoked synaptic conductances were more temporally precise than those evoked by light. However, the precision of spikes evoked by conductances that varied from trial to trial was similar to that of light-evoked spikes. Thus, the rod bipolar pathway modulates different RGCs via unique combinations of synaptic input, and RGC temporal variability reflects variability in the input this circuit provides.     

Anthropogenic subsidies mitigate environmental variability for insular rodents

The exogenous input of nutrients and energy into island systems fuels a large array of consumers and drives bottom-up trophic cascades in island communities. The input of anthropogenic resources has increased on islands and particularly supplemented non-native consumers with extra resources. We test the hypothesis that the anthropogenic establishments of super-abundant gulls and invasive iceplants Carpobrotus spp. have both altered the dynamics of an introduced black rat Rattus rattus population. On Bagaud Island, two habitats have been substantially modified by the anthropogenic subsidies of gulls and iceplants, in contrast to the native Mediterranean scrubland with no anthropogenic inputs. Rats were trapped in all three habitats over two contrasting years of rainfall patterns to investigate: (1) the effect of anthropogenic subsidies on rat density, age-ratio and growth rates, and (2) the role of rainfall variability in modulating the effects of subsidies between years. We found that the growth rates of rats dwelling in the non-subsidized habitat varied with environmental fluctuation, whereas rats dwelling in the gull colony maintained high growth rates during both dry and rainy years. The presence of anthropogenic subsidies apparently mitigated environmental stress. Age ratio and rat density varied significantly and predictably among years, seasons, and habitats. While rat densities always peaked higher in the gull colony, especially after rat breeding in spring, higher captures of immature rats were recorded during the second year in all habitats, associated with higher rainfall. The potential for non-native rats to benefit from anthropogenic resources has important implications for the management of similar species on islands.