Jon Vik - Academia.edu (original) (raw)

Papers by Jon Vik

Science, 2006

Several bird species have advanced the timing of their spring migration in response to recent cli... more Several bird species have advanced the timing of their spring migration in response to recent climate change. European short-distance migrants, wintering in temperate areas, have been assumed to be more affected by change in the European climate than long-distance migrants wintering in the tropics. However, we show that long-distance migrants have advanced their spring arrival in Scandinavia more than short-distance migrants. By analyzing a long-term data set from southern Italy, we show that long-distance migrants also pass through the Mediterranean region earlier. We argue that this may reflect a climate-driven evolutionary change in the timing of spring migration.

Dynamic models of biological systems often possess complex and multivariate mappings between inpu... more Dynamic models of biological systems often possess complex and multivariate mappings between input parameters and output state variables, posing challenges for comprehensive sensitivity analysis across the biologically relevant parameter space. In particular, more efficient and robust ways to obtain a solid understanding of how the sensitivity to each parameter depends on the values of the other parameters are sorely needed. We report a new methodology for global sensitivity analysis based on Hierarchical Cluster-based Partial Least Squares Regression (HC-PLSR)-based approximations (metamodelling) of the input-output mappings of dynamic models, which we expect to be generic, efficient and robust, even for systems with highly nonlinear input-output relationships. The two-step HC-PLSR metamodelling automatically separates the observations (here corresponding to different combinations of input parameter values) into groups based on the dynamic model behaviour, then analyses each group separately with Partial Least Squares Regression (PLSR). This produces one global regression model comprising all observations, as well as regional regression models within each group, where the regression coefficients can be used as sensitivity measures. Thereby a more accurate description of complex interactions between inputs to the dynamic model can be revealed through analysis of how a certain level of one input parameter affects the model sensitivity to other inputs. We illustrate the usefulness of the HC-PLSR approach on a dynamic model of a mouse heart muscle cell, and demonstrate how it reveals interaction patterns of probable biological significance not easily identifiable by a global regression-based sensitivity analysis alone. Applied for sensitivity analysis of a complex, high-dimensional dynamic model of the mouse heart muscle cell, several interactions between input parameters were identified by the two-step HC-PLSR analysis that could not be detected in the single-step global analysis. Hence, our approach has the potential to reveal new biological insight through the identification of complex parameter interaction patterns. The HC-PLSR metamodel complexity can be adjusted according to the nonlinear complexity of the input-output mapping of the analysed dynamic model through adjustment of the number of regional regression models included. This facilitates sensitivity analysis of dynamic models of varying complexities.

... 0811, Japan T. Takanishi Á S. Hayakashi Á M. Ohmori Á T. Morita Uryu Experimental Forest, Fie... more ... 0811, Japan T. Takanishi Á S. Hayakashi Á M. Ohmori Á T. Morita Uryu Experimental Forest, Field Science Center, Hokkaido University, Moshiri, Horokanai 074-0741, Japan S. Uemura ... et al. 1996; Elias et al. 2004, 2006). The aim ...

Wavelet analysis is a powerful tool that is already in use throughout science and engineering. Th... more Wavelet analysis is a powerful tool that is already in use throughout science and engineering. The versatility and attractiveness of the wavelet approach lie in its decomposition properties, principally its time-scale localization. It is especially relevant to the analysis of nonstationary systems, i.e., systems with short-lived transient components, like those observed in ecological systems. Here, we review the basic properties of the wavelet approach for time-series analysis from an ecological perspective. Wavelet decomposition offers several advantages that are discussed in this paper and illustrated by appropriate synthetic and ecological examples. Wavelet analysis is notably free from the assumption of stationarity that makes most methods unsuitable for many ecological time series. Wavelet analysis also permits analysis of the relationships between two signals, and it is especially appropriate for following gradual change in forcing by exogenous variables.

Nature, Jan 19, 2004

Theory indicates that correlated weather may synchronize populations, but the extent to which thi... more Theory indicates that correlated weather may synchronize populations, but the extent to which this holds for non-identical, nonlinear systems is uncertain. Post and Forchhammer claim to have shown climate-induced synchrony for musk oxen and caribou that are separated by the Greenland ice sheet. However, logical and mathematical errors undermine their finding. Whether or not large-scale weather can be a major synchronizing factor across species remains an open question.

Population Ecology, 2008

The classic fur trade records on Canadian lynx (Lynx canadensis) have rarely been analysed in dir... more The classic fur trade records on Canadian lynx (Lynx canadensis) have rarely been analysed in direct conjunction with data on its principal prey, the snowshoe hare (Lepus americanus). Comparable long-term data for hare exist only for a region south of Hudson Bay. We fitted a bivariate log-linear time-series model to this hare and lynx data to disentangle the within-and between-population interactions of these species. To reduce problems with fur returns being non-normal and non-linearly related to abundance, we transformed the fur returns to a normal distribution based on sample quantiles. The estimated effect on next year's lynx abundance of a 1% increase in current hare abundance was a 0.23% (SE = 0.05) increase in lynx. Conversely, a 1% increase in current lynx abundance corresponded to a 0.46% (SE = 0.12) decrease in next year's hare abundance. This contrasts with some earlier studies. However, these studies mixed hare data from south of Hudson Bay with lynx totals for all of Canada. Despite this asymmetry of interaction strengths, coefficients of determination were similar for hare versus lynx and lynx versus hare, because hare abundance varies more than lynx. Both species showed clear intraspecific density-dependence of about equal strength. A 1% increase in current abundance increased next year's abundance by about 0.75%.

Nonlinear Analysis: Real World Applications, 2011

We review and complement the study of the mathematical properties of the predator-prey dynamical ... more We review and complement the study of the mathematical properties of the predator-prey dynamical system for spruce-budworm interactions studied in Ludwig et al. [D. Ludwig, D. Jones, C.S. Holling, Qualitative analysis of insect outbreak systems: the spruce budworm and forest, Journal of Animal Ecology 47 (1978), 315-332]. We use the singular perturbation method to identify parameter regimes which permit relaxation oscillations. The leading order contribution to the period of these oscillations is computed by means of this method and compared with the outcome of direct numerical simulations.

During the 1900s, the number of red foxes Vulpes vulpes increased in northern Europe. At higher a... more During the 1900s, the number of red foxes Vulpes vulpes increased in northern Europe. At higher altitudes and latitudes, red fox populations are likely to be limited by thick snow cover, which makes small rodents less available. The negative effects of snow could, however, be compensated for by high ungulate numbers, because of increased availability of carcasses in snow-rich winters. In the period 1897-1932, the number of foxes (mainly red foxes) killed was negatively related to snow depth indices in 13 of the 17 Norwegian counties. During 1947-1976, after a strong increase in ungulate and red fox numbers, the number of red foxes killed was negatively related to snow in only one county. The counties where ungulate density increased the most also had higher increases in the number of red fox bounties paid. The absence of large predators may at least partly be responsible for the strong increase in red fox populations, because eradication of large predators such as wolf Canis lupus in the late 1800s and early 1900s probably was a necessary condition for the strong increase in ungulate numbers, especially roe deer Capreolus capreolus.

Although lake-dwelling trout frequently eat smaller conspecifics in the absence of other fish pre... more Although lake-dwelling trout frequently eat smaller conspecifics in the absence of other fish prey, there are fewer reports of cannibalism in stream populations. However, a coarse riverbed structure and low discharge may facilitate cannibalism by providing pools for large fish whilst limiting refuges for small ones.

In quantitative genetics, the degree of resemblance between parents and offspring is described in... more In quantitative genetics, the degree of resemblance between parents and offspring is described in terms of the additive variance (V A ) relative to genetic (V G ) and phenotypic (V P ) variance. For populations with extreme allele frequencies, high V A ⁄ V G can be explained without considering properties of the genotype-phenotype (GP) map. We show that randomly generated GP maps in populations with intermediate allele frequencies generate far lower V A ⁄ V G values than empirically observed. The main reason is that orderbreaking behaviour is ubiquitous in random GP maps. Rearrangement of genotypic values to introduce order-preservation for one or more loci causes a dramatic increase in V A ⁄ V G . This suggests the existence of order-preserving design principles in the regulatory machinery underlying GP maps. We illustrate this feature by showing how the ubiquitously observed monotonicity of dose-response relationships gives much higher V A ⁄ V G values than a unimodal dose-response relationship in simple gene network models.

Many species of fungi produce ephemeral autumnal fruiting bodies to spread and multiply. Despite ... more Many species of fungi produce ephemeral autumnal fruiting bodies to spread and multiply. Despite their attraction for mushroom pickers and their economic importance, little is known about the phenology of fruiting bodies. Using Ϸ34,500 dated herbarium records we analyzed changes in the autumnal fruiting date of mushrooms in Norway over the period 1940 -2006. We show that the time of fruiting has changed considerably over this time period, with an average delay in fruiting since 1980 of 12.9 days. The changes differ strongly between species and groups of species. Early-fruiting species have experienced a stronger delay than late fruiters, resulting in a more compressed fruiting season. There is also a geographic trend of earlier fruiting in the northern and more continental parts of Norway than in more southern and oceanic parts. Incorporating monthly precipitation and temperature variables into the analyses provides indications that increasing temperatures during autumn and winter months bring about significant delay of fruiting both in the same year and in the subsequent year. The recent changes in autumnal mushroom phenology coincide with the extension of the growing season caused by global climate change and are likely to continue under the current climate change scenario.

Trends in Ecology & …, 2005

Understanding the causal chain from genotypic to phenotypic variation is a tremendous challenge w... more Understanding the causal chain from genotypic to phenotypic variation is a tremendous challenge with huge implications for personalized medicine. Here we argue that linking computational physiology to genetic concepts, methodology, and data provides a new framework for this endeavor. We exemplify this causally cohesive genotype-phenotype (cGP) modeling approach using a detailed mathematical model of a heart cell. In silico genetic variation is mapped to parametric variation, which propagates through the physiological model to generate multivariate phenotypes for the action potential and calcium transient under regular pacing, and ion currents under voltage clamping. The resulting genotype-to-phenotype map is characterized using standard quantitative genetic methods and novel applications of high-dimensional data analysis. These analyses reveal many well-known genetic phenomena like intralocus dominance, interlocus epistasis, and varying degrees of phenotypic correlation. In particular, we observe penetrance features such as the masking/release of genetic variation, so that without any change in the regulatory anatomy of the model, traits may appear monogenic, oligogenic, or polygenic depending on which genotypic variation is actually present in the data. The results suggest that a cGP modeling approach may pave the way for a computational physiological genomics capable of generating biological insight about the genotype-phenotype relation in ways that statistical-genetic approaches cannot.

PLOS Computational Biology, 2012

Polymorphisms identified in genome-wide association studies of human traits rarely explain more t... more Polymorphisms identified in genome-wide association studies of human traits rarely explain more than a small proportion of the heritable variation, and improving this situation within the current paradigm appears daunting. Given a well-validated dynamic model of a complex physiological trait, a substantial part of the underlying genetic variation must manifest as variation in model parameters. These parameters are themselves phenotypic traits. By linking whole-cell phenotypic variation to genetic variation in a computational model of a single heart cell, incorporating genotype-to-parameter maps, we show that genome-wide association studies on parameters reveal much more genetic variation than when using higherlevel cellular phenotypes. The results suggest that letting such studies be guided by computational physiology may facilitate a causal understanding of the genotype-to-phenotype map of complex traits, with strong implications for the development of phenomics technology.

Science, 2006

Nature, Jan 19, 2004

Population Ecology, 2008

Nonlinear Analysis: Real World Applications, 2011

Trends in Ecology & …, 2005

PLOS Computational Biology, 2012