Will genomics guide a greener forest biotech?

Forest biotechnology has been increasingly associated with wood production using plantation forestry, and has stressed applications that use pedigreed material and transgenic trees. Reasons for this emphasis include limitations of available technologies to conform to underlying genetic features of undomesticated forest tree populations. More recently, genomic technologies have rapidly begun to expand the scope of forest biotechnology. Genomic technologies are well suited to describe and make use of the abundant genetic variation present in undomesticated forest tree populations. Genomics thus enables new research and applications for conservation and management of natural forests, and is a primary technological driver for new research addressing the use of forests trees for carbon sequestration, biofuels feedstocks, and other 'green' applications.     

Climatic sensitivity of species’ vegetative and reproductive phenology in a Hawaiian montane wet forest

Understanding how tropical tree phenology (i.e., the timing and amount of seed and leaf production) responds to climate is vital for predicting how climate change may alter ecological functioning of tropical forests. We examined the effects of temperature, rainfall, and photosynthetically active radiation (PAR) on seed phenology of four dominant species and community-level leaf phenology in a montane wet forest on the island of Hawaiʻi using monthly data collected over ~ 6 years. We expected that species phenologies would be better explained by variation in temperature and PAR than rainfall because rainfall at this site is not limiting. The best-fit model for all four species included temperature, rainfall, and PAR. For three species, including two foundational species of Hawaiian forests (Acacia koa and Metrosideros polymorpha), seed production declined with increasing maximum temperatures and increased with rainfall. Relationships with PAR were the most variable across all four species. Community-level leaf litterfall decreased with minimum temperatures, increased with rainfall, and showed a peak at PAR of ~ 400 μmol/m²s⁻¹. There was considerable variation in monthly seed and leaf production not explained by climatic factors, and there was some evidence for a mediating effect of daylength. Thus, the impact of future climate change on this forest will depend on how climate change interacts with other factors such as daylength, biotic, and/or evolutionary constraints. Our results nonetheless provide insight into how climate change may affect different species in unique ways with potential consequences for shifts in species distributions and community composition.     

Can hybridization cause local extinction: a case for demographic swamping of the Australian native Senecio pinnatifolius by the invasive Senecio madagascariensis?

Hybridization between native and invasive species can have several outcomes, including enhanced weediness in hybrid progeny, evolution of new hybrid lineages and decline of hybridizing species. Whether there is a decline of hybridizing species largely depends on the relative frequencies of parental taxa and the viability of hybrid progeny. Here, the individual- and population-level consequences of hybridization between the Australian native Senecio pinnatifolius and the exotic Senecio madagascariensis were investigated with amplified fragment length polymorphism (AFLP) markers, and this information was used to estimate the annual loss of viable seeds to hybridization. A high frequency (range 8.3-75.6%) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations. A hybridization advantage was observed for S. madagascariensis, where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Calculations indicated that S. pinnatifolius would produce less viable seed than S. madagascariensis, if hybridization was frequency dependent and S. madagascariensis reached a frequency of between 10 and 60%. For this native-exotic species pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. As a result of asymmetric hybridization, S. pinnatifolius would appear to be under threat if S. madagascariensis increases numerically in areas of contact.     

How does climate change cause extinction?

Anthropogenic climate change is predicted to be a major cause of species extinctions in the next 100 years. But what will actually cause these extinctions? For example, will it be limited physiological tolerance to high temperatures, changing biotic interactions or other factors? Here, we systematically review the proximate causes of climate-change related extinctions and their empirical support. We find 136 case studies of climatic impacts that are potentially relevant to this topic. However, only seven identified proximate causes of demonstrated local extinctions due to anthropogenic climate change. Among these seven studies, the proximate causes vary widely. Surprisingly, none show a straightforward relationship between local extinction and limited tolerances to high temperature. Instead, many studies implicate species interactions as an important proximate cause, especially decreases in food availability. We find very similar patterns in studies showing decreases in abundance associated with climate change, and in those studies showing impacts of climatic oscillations. Collectively, these results highlight our disturbingly limited knowledge of this crucial issue but also support the idea that changing species interactions are an important cause of documented population declines and extinctions related to climate change. Finally, we briefly outline general research strategies for identifying these proximate causes in future studies.     

The mid-Holocene extinction of silver fir (Abies alba) in the Southern Alps: a consequence of forest fires? Palaeobotanical records and forest simulations

Pollen records suggest that Abies alba played a dominating role in both the montane and lowland forests at the border of the Southern Alps between ca. 8500 and 5700 years ago. Two major declines in fir, at about 7300–7000 cal b.p. and at ca. 6000 cal b.p., followed by the local extinction of the species are characteristic of the area below ca. 1000 m a.s.l. In order to test the impact of fire on the population dynamics of silver fir, a dynamic model (DisCForm) with a fire module was applied to simulate the early- and mid-Holocene forest development. Simulation outputs based on different fire scenarios were compared with the pollen record from Lago di Annone (226 m a.s.l.). The marked Abies decreases shown in the pollen record can be simulated with very intensive fire scenarios, but they do not result in an extinction of silver fir in the model. Low charcoal influx values related to the Abies declines in the palaeobotanical record suggest that fire was not the only reason for the extinction of silver fir. Human impact, as well as Holocene climatic changes leading to temporary moisture deficits and reduced adaptability due to low genetic variation may have had a significant impact on the Abies forests.     

First human-caused extinction of a cetacean species?

The Yangtze River dolphin or baiji (Lipotes vexillifer), an obligate freshwater odontocete known only from the middle-lower Yangtze River system and neighbouring Qiantang River in eastern China, has long been recognized as one of the world's rarest and most threatened mammal species. The status of the baiji has not been investigated since the late 1990s, when the surviving population was estimated to be as low as 13 individuals. An intensive six-week multi-vessel visual and acoustic survey carried out in November-December 2006, covering the entire historical range of the baiji in the main Yangtze channel, failed to find any evidence that the species survives. We are forced to conclude that the baiji is now likely to be extinct, probably due to unsustainable by-catch in local fisheries. This represents the first global extinction of a large vertebrate for over 50 years, only the fourth disappearance of an entire mammal family since AD 1500, and the first cetacean species to be driven to extinction by human activity. Immediate and extreme measures may be necessary to prevent the extinction of other endangered cetaceans, including the sympatric Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis).     

Does forest fragmentation cause an increase in forest temperature?

Forest fragmentation is considered by many to be a primary cause of the current biodiversity crisis. The underlying mechanisms are poorly known, but a potentially important one is associated with altered thermal conditions within the remaining forest patches, especially at forest edges. Yet, large uncertainty remains about the effect of fragmentation on forest temperature, as it is unclear whether temperature decreases from forest edge to forest interior, and whether this local gradient scales up to an effect of fragmentation (landscape attribute) on temperature. We calculated the effect size (correlation coefficient) of distance from forest edge on air temperature, and tested for differences among forest types surrounded by different matrices using meta-analysis techniques. We found a negative edge-interior temperature gradient, but correlation coefficients were highly variable, and significant only for temperate and tropical forests surrounded by a highly contrasting open matrix. Nevertheless, it is unclear if these local-scale changes in temperature can be scaled up to an effect of fragmentation on temperature. Although it may be valid when considering “fragmentation” as forest loss only, the landscape-scale inference is not so clear when we consider the second aspect of fragmentation, where a given amount of forest is divided into a large number of small patches (fragmentation per se). Therefore, care is needed when assuming that fragmentation changes forest temperature, as thermal changes at forest edges depend on forest type and matrix composition, and it is still uncertain if this local gradient can be scaled up to the landscape.     

Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold‐adapted birds

Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high‐latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate‐driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold‐adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long‐term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back‐casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum.     

Will forest conservation areas protect functionally important diversity of fungi and lichens over time?

Incorporating functional values in biodiversity monitoring systems could add novel perspectives of the status of biodiversity in conservation areas. Stable frequencies of large foliose nitrogen-fixing cyanolichens likely have positive effects on the nitrogen budget of forests and provide food, material and shelter for invertebrates, gastropods and birds. Stable volumes of deadwood and frequencies of associated fungi provide an important supporting function for ecosystem services such as nutrient cycling, carbon storage and soil formation. Based on regional monitoring data from boreal old-growth forest nature reserves and key habitats, we tested for changes in the frequency of various functionally important substrates and species over time. We detected significant reductions in the frequency of indicator cyanolichens occurring on deciduous trees already after 10 years in key habitats, despite non-significant changes in their host substrates. Frequencies of indicator pendulous lichens Alectoria sarmentosa and Bryoria nadvornikiana had also decreased in key habitats, despite overall stable volumes of large conifer host trees. Lichen reductions were more pronounced in the smaller key habitats compared to the larger formally protected nature reserves, likely due to degrading fragmentation and isolation effects. In contrast to these lichens, the average frequencies of old-growth forest indicator fungi decaying coniferous deadwood and common fungi on deciduous trees (Fomes fomentarius) and coniferous trees (Fomitopsis pinicola) remained unchanged. The studied cyanolichens and fruiting fungi generally had similar extinction rates over 10 years, whilst only cyanolichens had substantially lower colonization rates. Amid a severely fragmented landscape, conservation areas seem to struggle in preserving some of the basic old-growth forest values.     

Alien grass disrupts reproduction and post-settlement recruitment of co-occurring native vegetation: a mechanism for diversity decline in invaded forest?

Invasive plants significantly threaten native plant biodiversity, yet the mechanisms by which they drive species losses and maintain their own dominance are poorly known. We examined the effects of alien grass invasion (Stenotaphrum secundatum) on (1) abundance and frequency of occurrence, (2) reproductive effort (flowering) and output (fruit production) and (3) soil seed banks for three focal native plants that are characteristic of endangered coastal forest of south-eastern Australia. First, we sampled and compared the foliage cover abundance and frequency (proportion of sites occupied) of the focal natives across invaded and non-invaded (reference) sites (n = 20). We then intensively sampled reproductive effort and output (range of 5–9 sites per species), and density of propagules within the soil (using a standard glasshouse ‘emergence’ method; n = 26) for each species. Invasion was associated with reduced population sizes of all species within the standing vegetation but did not affect population frequency (i.e. proportion of sites where each species was present). Reproductive effort and output were about 75 % lower at invaded than native sites for all species. However, invasion had no effect on propagule densities of the focal natives within the seed bank, despite the substantial reduction in their reproduction. This indicates that the ultimate driver of population declines across invaded landscapes is post-settlement recruitment limitation from the seed bank (e.g. low rates of germination and seedling survival) rather than a reduction in the arrival and storage of propagules at invaded sites. Removal of Stenotaphrum alone might thus be sufficient to stimulate the recovery of native populations from the seed bank.     

MicroRNA and brain tumors: a cause and a cure?

Malignant brain tumors, including high-grade gliomas, are among the most lethal of all cancers. Despite considerable advances, including multi-modal treatments with surgery, radiotherapy, and chemotherapy, the overall prognosis remains dismal for patients diagnosed with these tumors. With the discovery of RNA interference (RNAi) for target-specific gene silencing via small interfering RNA (siRNA), a novel method to target malignant gliomas has been exposed, an endeavor that is aggressively being carried out in numerous laboratories. However, practical difficulties in tissue- or organ-specific targeting of therapeutic quantities of siRNA still preclude its applicability in a clinical setting. MicroRNA (miRNA), an endogenously expressed form of siRNA, not only presents an alternate method to induce RNAi in a given diseased tissue or organ, but also exposes a unique set of diagnostic markers that can be used to identify, and then differentiate between tumor grades. Thus, miRNA can be considered the cells' answer to siRNA. Discovered over a decade ago, miRNA is fast becoming recognized as crucial in regulating gene expression in cancers. Therein lies the therapeutic potential of miRNA, as it may now be possible to induce or inhibit RNAi in a given diseased cell population by controlling the cells' miRNA expression profile. This review outlines the potential of miRNA as a therapeutic strategy against high-grade gliomas, and also the technological hurdles that need to be addressed before this promising technique can be administered in a clinical setting.     

Is telomere erosion a mechanism of species extinction?

According to the fossil record, 99.9% of all species that have ever lived on Earth have disappeared. However, only about 4% died out during the five mass extinction events, whereas it seems that the majority of species vanished without any signs of significant earthbound or extraterrestrial physical threats. Clearly, biological extinction mechanisms are by far the most important, but they are subject to serious limitations concerning the worldwide disappearance of species. In view of that, species-inherent mechanisms, which could lead to the worldwide destabilization of a population, might be worth reconsideration. Telomeres, the protective caps of chromosome ends, and the enzyme telomerase have been well preserved in plants and animals during evolution. In the absence of telomerase activity, telomeric DNA has been shown to shorten every time a cell divides. The concept of a mitotic clock based on the gradual erosion of telomeres is now generally accepted and has been confirmed in numerous plants and animals. Chromosomal rearrangements are the hallmarks of two completely different biological phenomena, cancer and speciation. In premalignant cells, gradual telomere erosion beyond a critical threshold is a well-known inducer of chromosomal instability. The species clock hypothesis, as presented here, is based on the idea of a tiny loss of mean telomere length per generation. This mechanism would not rapidly endanger the survival of a particular species. Yet, after many thousands of generations, critically short telomeres could lead to the weakening and even the extinction of old species and would simultaneously create the unstable chromosomal environment that might result in the origination of new species.     

Weak or strong invaders? A comparison of impact between the native and invaded ranges of mammals and birds alien to Europe

Aim Species introduced to an area outside of their native range are often thought to have higher impact in this new area. We examined whether this is really the case in mammals and birds and to what extent. In particular, we explored how impacts of alien species vary in relationship to invader identity and type of impact. Location Global. Methods We conducted a thorough review of the literature to compare the impact of alien European mammals and birds in their native and invaded ranges. Based on a series of environmental and economic impact scores, we ordered species along a continuum from weak invaders, which have lower impact in the invaded range, to strong invaders, which have higher impact in the invaded range. Results We found that nearly 80% of the mammals are strong invaders, but only half of the birds. Members of these two classes also affect their communities in different ways; birds more often have an impact via hybridization, whereas mammals have stronger impacts via herbivory, transmission of diseases to wildlife and their effects on agriculture, livestock and forestry. Main conclusions Generally, mammals and birds have different impacts when invading new regions. Although there are some bird species that are strong invaders, these remain the exception among birds, whereas most mammals increase their impact in the invaded range. This study provides a deeper insight into patterns of impact in the invaded range.     

Do mobbing calls affect the perception of predation risk by forest birds?

We report the results of two field experiments assessing whether exposure to mobbing calls, which usually indicates the presence of a predator, elicits changes in risk perception as measured by the willingness of forest birds to enter or cross gaps in forest cover. In the first experiment, we tested the prediction that wintering black-capped chickadees,Poecile atricapilla , will travel less in open areas to seek food from a feeder during a simulated mobbing event than they will under control conditions. The number of visits to feeders decreased at increasing distances from forest edges (0-10 m) when mobbing calls were played. Mobbing calls increased the overall rate of visits to feeders, but lowered the rate of visits to feeders located at 10 m from forest edges. By contrast, when a stuffed merlin, Falco columbarius, was placed near the feeder, chickadees rarely visited the feeder, regardless of the distance to forest edge. In the second experiment, we tested the prediction that breeding male red-eyed vireos, Vireo olivaceus, would be less attracted to the song of a nearby red-eyed vireo after a playback of a mobbing event than after a ‘neutral’ sound stimulus, especially if they had to cross an open area. Vireos were as willing to enter or cross gaps in forest cover following exposure to mobbing calls, although they responded more frequently to conspecific song under forest cover than across gaps. Our results suggest that forest birds under cover assess the risk of a mobbing situation largely on the basis of the distance to the cause of mobbing. It follows that a trade-off between risk and reward may not occur with mobbing birds, unless mobbing occurs far outside forest cover and/or at very close range (<5 m) to a predator. Copyright 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.     

Are fragments islands? Landscape context and density-area relationships in boreal forest birds

We investigated the role of matrix type as a determinant of change in bird densities with forest patch area (patch area effect) in two different Fennoscandian landscape types: mature forest fragments surrounded by cut-over or regenerating forest and true forested islands surrounded by water. Since the matrix of forested archipelagoes offers no resources to and impedes movement of forest birds, we predict that patch area effects on bird densities should be stronger on forested islands than in forest patches fragmented by forestry. We compiled correlation estimates of the bird density-patch area relationship from the literature and analyzed the data using meta-analysis. Combined correlation coefficients were significantly positive on islands but were not significantly different from 0 in fragments. Within-species comparisons also showed that correlations were consistently more positive on islands than in fragments. On islands but not in fragments, the densities of forest specialist species were more sensitive to area than were the densities of forest generalists, suggesting that specialists are more sensitive to changes in matrix quality. Migration status was only weakly associated with bird responses to island or fragment area. Thus, forest fragments do not function as true islands. We interpret this as the result of compensatory effects of the surrounding matrix in terms of availability of resources and enhanced connectivity (matrix quality hypothesis). A purely patch-centered approach seems an unrealistic framework to analyze population processes occurring in complex landscapes. The characteristics of the habitat matrix should therefore be explicitly incorporated into the assessment of species' responses to habitat fragmentation.     

Do birds of a feather disperse plants together?

1. Dispersal of propagules by waterbirds is thought to be important for wetland plants because of the abundance of birds and their frequent movements among aquatic habitats. Differences in bird characteristics (size, movement, feeding ecology) were expected to lead to different outcomes for plant dispersal. 2. We investigated heterogeneity in plant dispersal by ducks (Anas superciliosa, Anas gracilis, Anas castanea). We calculated the probability of transport of viable seeds by germinating propagules retrieved from feathers and feet (epizoochory) and the contents of the oesophagus, gizzard and lower gut (endozoochory). 3. The abundance and richness of seeds carried internally and externally did not differ among sympatric bird species. We used estimates from the literature of movements of Anas species to approximate dispersal kernels for the transport of plant propagules. 4. Heterogeneity in the abundance and movement ecology of disperser species will result in differing patterns and degrees of connectivity for wetland plant metacommunities. Sedentary waterfowl are likely to have an important role in replenishing propagules and connecting aquatic metacommunities over small distances. Nomadic waterfowl may facilitate long‐distance dispersal. We discuss the implications of differences between duck species in movement patterns for connectivity of aquatic plant metacommunities across landscapes.