No abstract

The 22,000-year-old cave painting of an Atlantic salmon (Salmo salar) near the Vézère River in France is a reminder of our fascination with, and dependence on, Atlantic salmon throughout human history. Atlantic salmon belongs to the salmonid lineage which comprises 11 genera, with at least 70 species that exhibit a wide range of ecological adaptations and use a variety of marine and freshwater life history strategies 1 . Salmonids hold important positions as socially iconic species and economic resources within aquaculture, wild fisheries and recreational sport fisheries. Moreover, they serve as key indicator species of the health of North Atlantic and Pacific coastal and river ecosystems.All teleosts share at least three rounds of whole-genome duplication (WGD), 1R and 2R before the divergence of lamprey from the jawed vertebrates 2 , and a third teleost-specific WGD (Ts3R) at the base of the teleosts ~320 million years ago (Mya) [3][4][5] . Very little is known about the mechanisms of genomic and chromosomal reorganization after WGD in vertebrates because the 1R, 2R and Ts3R occurred so long ago that few clear signatures of post-WGD reorganization events remain. In contrast, a fourth WGD (the Ss4R salmonid-specific autotetraploidization event) occurred in the common ancestor of salmonids ~80 Mya after their divergence from Esociformes ~125 Mya 6-8 (Fig. 1), and the continued presence of multivalent pairing at meiosis and evidence of tetrasomic inheritance in salmonid species suggests that diploidy is not yet fully re-established 6,9,10 . Salmonids thus appear to provide an unprecedented opportunity for studying vertebrate genome evolution after an autotetraploid WGD 11,12 over a time period that is long enough to reveal long-term evolutionary patterns, but short enough to give a high-resolution picture of the process. In addition, they provide an excellent setting for contextualizing genome evolution with a dramatic post-WGD species radiation and intricate adaptations to a whole range of life history regimes.Here we present a high-quality reference genome assembly of the Atlantic salmon, and use it to describe major patterns characterizing the post-Ss4R salmonid genome evolution over the past 80 million years (Myr). Our results challenge the recent claim that rediploidization in salmonids has been a gradual process unlinked to significant genome rearrangements 13 . They also challenge current views about the relative importance of sub-and neofunctionalization in vertebrate genomes (reviewed in ref. 14), and the importance of dosage balance as a gene duplicate retention mechanism 15 . Genome characterizationThe Atlantic salmon reference genome assembly (GenBank: GCA_000233375.4) adds up to 2.97 gigabases (Gb) with aThe whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high...

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 non-stationary 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.

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.

The population cycles of rodents at northern latitudes have puzzled people for centuries, and their impact is manifest throughout the alpine ecosystem. Climate change is known to be able to drive animal population dynamics between stable and cyclic phases, and has been suggested to cause the recent changes in cyclic dynamics of rodents and their predators. But although predator-rodent interactions are commonly argued to be the cause of the Fennoscandian rodent cycles, the role of the environment in the modulation of such dynamics is often poorly understood in natural systems. Hence, quantitative links between climate-driven processes and rodent dynamics have so far been lacking. Here we show that winter weather and snow conditions, together with density dependence in the net population growth rate, account for the observed population dynamics of the rodent community dominated by lemmings (Lemmus lemmus) in an alpine Norwegian core habitat between 1970 and 1997, and predict the observed absence of rodent peak years after 1994. These local rodent dynamics are coherent with alpine bird dynamics both locally and over all of southern Norway, consistent with the influence of large-scale fluctuations in winter conditions. The relationship between commonly available meteorological data and snow conditions indicates that changes in temperature and humidity, and thus conditions in the subnivean space, seem to markedly affect the dynamics of alpine rodents and their linked groups. The pattern of less regular rodent peaks, and corresponding changes in the overall dynamics of the alpine ecosystem, thus seems likely to prevail over a growing area under projected climate change.

Animals selecting habitats often have to consider many factors, e.g., food and cover for safety. However, each habitat type often lacks an adequate mixture of these factors. Analyses of habitat selection using resource selection functions (RSFs) for animal radiotelemetry data typically ignore trade-offs, and the fact that these may change during an animal's daily foraging and resting rhythm on a short-term basis. This may lead to changes in the relative use of habitat types if availability differs among individual home ranges, called functional responses in habitat selection. Here, we identify such functional responses and their underlying behavioral mechanisms by estimating RSFs through mixed-effects logistic regression of telemetry data on 62 female red deer (Cervus elaphus) in Norway. Habitat selection changed with time of day and activity, suggesting a trade-off in habitat selection related to forage quantity or quality vs. shelter. Red deer frequently used pastures offering abundant forage and little canopy cover during nighttime when actively foraging, while spending much of their time in forested habitats with less forage but more cover during daytime when they are more often inactive. Selection for pastures was higher when availability was low and decreased with increasing availability. Moreover, we show for the first time that in the real world with forest habitats also containing some forage, there was both increasing selection of pastures (i.e., not proportional use) and reduced time spent in pastures (i.e., not constant time use) with lowered availability of pastures within the home range. Our study demonstrates that landscape-level habitat composition modifies the trade-off between food and cover for large herbivorous mammals. Consequently, landscapes are likely to differ in their vulnerability to crop damage and threat to biodiversity from grazing.

No abstract

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.phenology ͉ global warming ͉ herbarium data ͉ fungi ͉ agarics P henological changes are among the most sensitive ecological responses to changing climate (1-3). The observed extension of the average annual growing season in Europe by nearly 11 days since the early 1960s (4) has been followed by rapid and recent changes in plant flowering time (5-8) and earlier spring migration in several bird species (9). In a recent study from the United Kingdom, it was reported for a set of mushroom species that fruiting on average started earlier and ended later in the season in recent years than 20 years ago, i.e., that the fruiting period has been greatly extended (10). These changes were linked to increased temperature and rainfall in August and October, respectively (10).Most fungi produce ephemeral fruiting bodies that can be observed only for a few days each year, which makes phenological data difficult and time-consuming to obtain. However, because of the short endurance of the fruiting bodies, collection time is a good estimate of fruiting time. A potential source of phenological information for this group of organisms is therefore herbarium collections, which, although sampled in a nonsystematic manner, share properties with random sampling processes. Herbarium data can enable us to understand and predict climate-induced ecological changes in the future by understanding how climate has affected ecological processes in the past. Several studies have already documented that herbarium collections may represent a valuable source of long-term and reliable phenological information (e.g., refs. 7 and 8).Our study of temporal trends in fruiting phenology is based on Ͼ34,500 herbarium records collected in Norway during the period 1940-2006 and representin...