Modelling the spatial distribution of beta diversity in Australian subtropical rainforest

Investigation of the spatial distribution of biodiversity among communities or across habitats (beta diversity) is often hampered by a scarcity of biological survey data. This is particularly the case in communities of high floristic diversity, such as the subtropical rainforests of eastern Australia. In contrast, there is excellent spatial coverage of environmental data for this region, such as geology, elevation and climate data. Generalized dissimilarity modelling was used in this study to combine biological survey data and environmental data grids for the investigation and prediction of floristic turnover among vegetation communities at a regional scale. Generalized dissimilarity modelling identified four environmental predictors of floristic turnover in the study region, all of which are linked with moisture stress: radiation of the driest quarter, precipitation of the driest period of the year, slope and aspect. Ten land classes representing largely homogeneous floristics and environment were identified and mapped for the region, allowing significantly greater discrimination than currently available mapping for this region. With increases in evapotranspiration and moisture stress predicted as a result of climate change, these results may allow future floristic shifts to be assessed in relation to regional‐scale gradients in floristic turnover.     

Analysis of character divergence along environmental gradients and other covariates

Character displacement is typically identified by comparing phenotypic differences in sympatry and allopatry. Recently, however, Goldberg and Lande (2006) pointed out that when phenotypic characters vary along an environmental gradient, the standard approach may fail to identify sympatric character divergence. Here we present a general analytical procedure for identifying sympatric character divergence while accounting for phenotypic changes that covary with environmental variables. Our approach uses residual randomization from a generalized linear model, and allows the statistical comparison of sympatric phenotypic divergence to allopatric phenotypic divergence while accounting for phenotypic variation along a gradient. Through simulation we demonstrate that our approach correctly identifies patterns of sympatric character divergence when they are present, and does not identify such patterns when they are not. Our analytical approach complements and extends the suggestions of Goldberg and Lande (2006), by allowing a full statistical assessment of the varied patterns of character displacement along environmental gradients, or while accounting for other covariates and sources of variation.     

Elevational gradients in species abundance,assemblage structure and energy use of rainforest birds in the Australian Wet Tropics bioregion

Elevational patterns of species richness, local abundance and assemblage structure of rainforest birds of north‐eastern Australia were explored using data from extensive standardized surveys throughout the region. Eighty‐two species of birds were recorded with strong turnover in assemblage structure across the elevational gradient and high levels of regional endemism in the uplands. Both species richness and bird abundance exhibited a humped‐shaped pattern with elevation with the highest values being between 600 and 800 m elevation. While much of the variability in species richness could be explained by the species–area relationship, analyses of net primary productivity (NPP) and total daily energy consumption of the bird community (energy use) suggest that ecosystem energy flow or constraints may be a significant determinant of species richness. Species richness is positively correlated with local bird abundance which itself is closely related to total energy use of the bird community. We suggest the hypothesis that lower NPP limits bird abundance and energy use in the uplands (>500 m) and that low bird energy use and species richness in the lowlands is limited by a seasonal bottleneck in available primary productivity and/or a species pool previously truncated by an extinction filter imposed by the almost complete disappearance of rainforest in the lowlands during the glacial maxima. We suggest that some of the previously predicted impacts of global warming on biodiversity in the uplands may be partially ameliorated by increases in NPP because of increasing temperatures. However, these relationships are complex and require further data specifically in regard to direct estimates of primary productivity and detailed estimates of energy flow within the assemblage.     

Elevational turnover in the composition of leaf miners and their interactions with host plants in Australian subtropical rainforest

Leaf miners are specialist herbivorous insects that are potentially vulnerable to environmental change because of their dependency on particular host plants. Little, however, is known about how climate affects the distribution of leaf miner communities and their interactions with host plants. Elevational gradients are useful tools for understanding how ecological communities respond to local clines in climate. Given that plant communities are known to undergo elevational turnover in response to changes in climatic conditions, we expect that leaf miner species will also change with elevation. We repeatedly hand collected leaf miners along three elevational gradients in subtropical rainforest in eastern Australia. Individual leaf miners were counted and identified to species, and their host plants were recorded. We tested if leaf miner species richness and the number of unique interactions among leaf miner and host plant species were affected by elevation. We also tested if the composition of leaf miner species and the composition of interactions between leaf miners and host plants showed a relationship with elevation. The rarefied number of unique leaf miner–host plant interactions significantly decreased with elevation, with a slight peak at approx. 700 m a.s.l., while neither rarefied or observed species richness (species density) of leaf miners nor observed numbers of unique interactions (interaction density) were significantly affected by elevation. The composition of leaf miner species and the composition of leaf miner–host plant interactions (occurrence of pairwise interactions) were significantly related to elevation. Elevational turnover in leaf miner species composition indicated that different species varied in their response to changes in biotic and/or abiotic conditions imposed by increasing elevation. Through our analyses, we identified four leaf miner species that may be locally vulnerable to climate change, as a result of their restricted elevational distribution and level of host specificity.     

A weak upward elevational shift in the distributions of breeding birds in the Italian Alps

Aim To test whether bird assemblages are shifting upwards in their elevational distribution in synchrony with current climate warming and/or habitat changes. Location A gradient of elevation in the Italian Alps (Alta Valsessera, Piedmont). Methods We used data from two recent atlas surveys performed on a 1 × 1 km grid at an 11‐year interval (1992–94 and 2003–05). We modelled the elevational gradient of avifaunal composition, using a sample‐based approach, in an effort to detect evidence for an upward elevational shift of bird zonation. Changes in species richness were controlled for. The results from this analysis were compared with those obtained using a species‐based approach. Changes in climate and landscape between the two surveys were assessed using local meteorological data and Corine Land Cover maps, respectively. Results We detected small avifaunal changes between the two surveys: (1) mean elevations increased for the majority of species, but the average change was not significantly different from zero; (2) the species richness increased, but this was mainly due to an increase in sampling effort; and (3) a change in species composition was detected, which was at the limit of significance and corresponded on average to a 29‐m upward elevational shift in the distribution of the avifauna. The shift was the same for open land and forest bird communities. During the same period, the mean temperature increased by c. 1 °C in the area, and a slight trend towards vegetation closure by woody plants was detected. Main conclusions The use of fine‐scale breeding bird atlases in mountainous regions, together with ordination methods, provides a sensitive tool to test and measure elevational shifts in species ranges, but the results have to be interpreted carefully. In our case, the observed elevational shift in the distributions of the avifauna cannot unambiguously be attributed to climate warming. This shift is smaller than expected from the regional increase in temperature, which raises the question of how closely bird distributions match climate change.     

Alternative responses to rare selection events are differentially vulnerable to changes in the frequency,scope, and intensity of environmental extremes

Extreme weather events are becoming more frequent, severe, and/or widespread as a consequence of anthropogenic climate change. While the economic and ecological implications of these changes have received considerable attention, the role of evolutionary processes in determining organismal responses to these critical challenges is currently unknown. Here we develop a novel theoretical framework that explores how alternative pathways for adaptation to rare selection events can influence population‐level vulnerabilities to future changes in the frequency, scope, and intensity of environmental extremes. We begin by showing that different life histories and trait expression profiles can shift the balance between additive and multiplicative properties of fitness accumulation, favoring different evolutionary responses to identical environmental phenomena. We then demonstrate that these different adaptive outcomes lead to predictable differences in population‐level vulnerabilities to rapid increases in the frequency, intensity, or scope of extreme weather events. Specifically, we show that when the primary mode of fitness accumulation is additive, evolution favors ignoring environmental extremes and lineages become highly vulnerable to extinction if the frequency or scope of extreme weather events suddenly increases. Conversely, when fitness accumulates primarily multiplicatively, evolution favors bet‐hedging phenotypes that cope well with historical extremes and are instead vulnerable to sudden increases in extreme event intensity. Our findings address a critical gap in our understanding of the potential consequences of rare selection events and provide a relatively simple rubric for assessing the vulnerabilities of any population of interest to changes in a wide variety of extreme environmental phenomena.     

Assessing the vulnerability of an assemblage of subtropical rainforest vertebrate species to climate change in south‐east Queensland

Global climate change is a threat to ecosystems that are rich in biodiversity and endemism, such as the World Heritage‐listed subtropical rainforests of central eastern Australia. Possible effects of climate change on the biota of tropical rainforests have been studied, but subtropical rainforests have received less attention. We analysed published data for an assemblage of 38 subtropical rainforest vertebrate species in four taxonomic groups to evaluate their relative vulnerability to climate change. Focusing on endemic and/or threatened species, we considered two aspects of vulnerability: (i) resistance, defined by indicators of rarity (geographical range, habitat specificity and local abundance); and (ii) resilience, defined by indicators of a species potential to recover (reproductive output, dispersal potential and climatic niche). Our analysis indicated that frogs are most vulnerable to climate change, followed by reptiles, birds, then mammals. Many species in our assemblage are regionally endemic montane rainforest specialists with high vulnerability. Monitoring of taxa in regenerating rainforest showed that many species with high resilience traits also persisted in disturbed habitat, suggesting that they have capacity to recolonize habitats after disturbance, that is climate change‐induced events. These results will allow us to prioritize adaptation strategies for species most at risk. We conclude that to safeguard the most vulnerable amphibian, reptile and bird species against climate change, climatically stable habitats (cool refugia) that are currently without protection status need to be identified, restored and incorporated in the current reserve system. Our study provides evidence that montane subtropical rainforest deserves highest protection status as habitat for vulnerable taxa.     

Driving factors of a vegetation shift from Scots pine to pubescent oak in dry Alpine forests

An increasing number of studies have reported on forest declines and vegetation shifts triggered by drought. In the Swiss Rhone valley (Valais), one of the driest inner‐Alpine regions, the species composition in low elevation forests is changing: The sub‐boreal Scots pine (Pinus sylvestris L.) dominating the dry forests is showing high mortality rates. Concurrently the sub‐Mediterranean pubescent oak (Quercus pubescens Willd.) has locally increased in abundance. However, it remains unclear whether this local change in species composition is part of a larger‐scale vegetation shift. To study variability in mortality and regeneration in these dry forests we analysed data from the Swiss national forest inventory (NFI) on a regular grid between 1983 and 2003, and combined it with annual mortality data from a monitoring site. Pine mortality was found to be highest at low elevation (below 1000 m a.s.l.). Annual variation in pine mortality was correlated with a drought index computed for the summer months prior to observed tree death. A generalized linear mixed‐effects model indicated for the NFI data increased pine mortality on dryer sites with high stand competition, particularly for small‐diameter trees. Pine regeneration was low in comparison to its occurrence in the overstorey, whereas oak regeneration was comparably abundant. Although both species regenerated well at dry sites, pine regeneration was favoured at cooler sites at higher altitude and oak regeneration was more frequent at warmer sites, indicating a higher adaptation potential of oaks under future warming. Our results thus suggest that an extended shift in species composition is actually occurring in the pine forests in the Valais. The main driving factors are found to be climatic variability, particularly drought, and variability in stand structure and topography. Thus, pine forests at low elevations are developing into oak forests with unknown consequences for these ecosystems and their goods and services.     

Winners and losers: How the elevational range of breeding birds on Alps has varied over the past four decades due to climate and habitat changes

Climate warming and habitat transformation are widely recognized as worrying threatening factors. Understanding the individual contribution of these two factors to the change of species distribution could be very important in order to effectively counteract the species range contraction, especially in mountains, where alpine species are strongly limited in finding new areas to be colonized at higher elevations. We proposed a method to disentangle the effects of the two drivers of range change for breeding birds in Italian Alps, in the case of co‐occurring climate warming and shrub and forest encroachment. For each species, from 1982 to 2017, we related the estimated yearly elevational distribution of birds to the correspondent overall average of the daily minimum temperatures during the breeding season and the estimated amount of shrubs and forest cover. Using a hierarchical partitioning approach, we assessed the net contribution (i.e., without the shared effect) of each driver. Both temperature and shrub and forest cover showed a positive trend along the time series and resulted the most likely causes of the significant elevational displacement for 21 of the 29 investigated birds. While shrub and forest cover was found to be an important driver of the expansion of forest bird range toward higher elevations, the effect of temperature on favouring the colonization of previously climatically unsuitable forests at higher elevations was not negligible. Shrub and forest expansion resulted the main driver of the range contraction for edge and open habitat species, which suffered a distribution shrinkage at their lower elevational boundary. In light of climate warming, these results highlighted how the net range loss for edge and open habitat species, caused by shrub and forest encroachment consequent to land abandonment, should be counteracted by implementing proper conservation management strategies and promoting sustainable economic activities in rangeland areas.     

Comparison of statistical models to analyse the genetic effect on within-litter variance in pigs

Genetics affects not only the weight of piglets at birth but also the variability of birth weight within litter. Previous studies on this topic assigned the sample standard deviation of piglet birth weights within litter as an observation to the sow. However, the contribution of the difference in mean birth weight per sex on the within-litter variance has been neglected so far. This work deals with the genetic effect on within-litter variance when different statistical models with different distributional assumptions are used and considers the sex effect and appropriate weights per trait. Traits were formed from the pooled sample variance of male and female birth weights within litter. A linear model approach was fitted to the logarithmized within-litter variance and the sample standard deviation. A generalized linear model with gamma-distributed residuals and log-link function was applied to the untransformed sample variance. Models were compared by analysing data from 9439 litters from Landrace and Large White of a commercial breeding programme. The estimates of heritability for different traits ranged from 7% to 11%. Although the generalized linear mixed model is preferred from a mathematical view, the rank correlations between breeding values of the linear mixed models and the generalized linear mixed model were relatively high, i.e. 94% to 98%. By residual diagnostics, a linear mixed model using the weighted and pooled within-litter standard deviation was identified as most suitable.     

Modelling seasonal changes in the distribution of Common Quail Coturnix coturnix in farmland landscapes using remote sensing

Species’ distribution models are widely used in landscape ecology but usually lack explicit information about species’ responses to ecosystem dynamics, leading to uncertainty when applied to the prediction of seasonal change in distributions. In this study, we aimed to build a species’ distribution model for the Common Quail Coturnix coturnix, a farmland species that shows changes in its distribution in response to seasonal changes in habitat suitability. During the course of three breeding seasons we collected temporal replicates of presence–absence data in 13 sampling locations in four countries (Morocco, Portugal, Spain and France). We used generalized linear mixed models to relate the species’ presence or absence to environmental variables and to the normalized difference vegetation index at each sampling location through the seasons, the latter variable being an indicator of within‐ and between‐season habitat changes. The preferred model showed that occurrence was highly dependent on habitat changes associated with crop seasonality, as measured by the normalized difference vegetation index. Common Quail selected areas with dense vegetation and warm climate and tracked spatial changes in these two parameters. The model allows accurate mapping of within‐ and between‐season distribution changes. Such changes are related to habitat variations caused mainly by drought and agricultural practices. Our results demonstrate that seasonal changes in farmland ecosystems can be incorporated into a simple distribution model, and our approach could be applied to other species to predict the effects of agricultural changes on the distribution of birds inhabiting farmland landscapes.     

Modelling both dominance and species distribution provides a more complete picture of changes to mangrove ecosystems under climate change

Dominant species influence the composition and abundance of other species present in ecosystems. However, forecasts of distributional change under future climates have predominantly focused on changes in species distribution and ignored possible changes in spatial and temporal patterns of dominance. We develop forecasts of spatial changes for the distribution of species dominance, defined in terms of basal area, and for species occurrence, in response to sea level rise for three tree taxa within an extensive mangrove ecosystem in northern Australia. Three new metrics are provided, indicating the area expected to be suitable under future conditions (E_occupied), the instability of suitable area (E_instability) and the overlap between the current and future spatial distribution (E_overlap). The current dominance and occurrence were modelled in relation to a set of environmental variables using boosted regression tree (BRT) models, under two scenarios of seedling establishment: unrestricted and highly restricted. While forecasts of spatial change were qualitatively similar for species occurrence and dominance, the models of species dominance exhibited higher metrics of model fit and predictive performance, and the spatial pattern of future dominance was less similar to the current pattern than was the case for the distributions of species occurrence. This highlights the possibility of greater changes in the spatial patterning of mangrove tree species dominance under future sea level rise. Under the restricted seedling establishment scenario, the area occupied by or dominated by a species declined between 42.1% and 93.8%, while for unrestricted seedling establishment, the area suitable for dominance or occurrence of each species varied from a decline of 68.4% to an expansion of 99.5%. As changes in the spatial patterning of dominance are likely to cause a cascade of effects throughout the ecosystem, forecasting spatial changes in dominance provides new and complementary information in addition to that provided by forecasts of species occurrence.     

A matter of timing: changes in the first date of arrival and last date of departure of Australian migratory birds

Although there is substantial evidence that Northern Hemisphere species have responded to climatic change over the last few decades, there is little documented evidence that Southern Hemisphere species have responded in the same way. Here, we report that Australian migratory birds have undergone changes in the first arrival date (FAD) and last date of departure (LDD) of a similar magnitude as species from the Northern Hemisphere. We compiled data on arrival and departure of migratory birds in south‐east Australia since 1960 from the published literature, Bird Observer Reports, and personal observations from bird watchers. Data on the FAD for 24 species and the LDD for 12 species were analyzed. Sixteen species were short‐ to middle‐distance species arriving at their breeding grounds, seven were long‐distance migrants arriving at their nonbreeding grounds, and one was a middle‐distance migrant also arriving at its nonbreeding ground. For 12 species, we gathered data from more than one location, enabling us to assess the consistency of intraspecific trends at different locations. Regressions of climate variables against year show that across south‐east Australia average annual maximum and minimum temperatures have increased by 0.17°C and 0.13°C decade^?1 since 1960, respectively. Over this period there has been an average advance in arrival of 3.5 days decade^?1; 16 of the 45 time‐series (representing 12 of the 24 species studied) showed a significant trend toward earlier arrival, while only one time‐series showed a significant delay. Conversely, there has been an average delay in departure of 5.1 days decade^?1; four of the 21 departure time‐series (four species) showed a significant trend toward later departure, while one species showed a significant trend toward earlier departure. However, differences emerge between the arrival and departure of short‐ to middle‐distance species visiting south‐east Australia to breed compared with long‐distance species that spend their nonbreeding period here. On average, short‐ to middle‐distance migrants have arrived at their breeding grounds 3.1 days decade^?1 earlier and delayed departure by 8.1 days decade^?1, thus extending the time spent in their breeding grounds by ～11 days decade^?1. The average advance in arrival at the nonbreeding grounds of long‐distance migrants is 6.8 days decade^?1. These species, however, have also advanced departure by an average of 6.9 days decade^?1. Hence, the length of stay has not changed but rather, the timing of events has advanced. The patterns of change in FAD and LDD of Australian migratory birds are of a similar magnitude to changes undergone by Northern Hemisphere species, and add further evidence that the modest warming experienced over the past few decades has already had significant biological impacts on a global scale.     

Challenging claims in the study of migratory birds and climate change

Recent shifts in phenology in response to climate change are well established but often poorly understood. Many animals integrate climate change across a spatially and temporally dispersed annual life cycle, and effects are modulated by ecological interactions, evolutionary change and endogenous control mechanisms. Here we assess and discuss key statements emerging from the rapidly developing study of changing spring phenology in migratory birds. These well‐studied organisms have been instrumental for understanding climate‐change effects, but research is developing rapidly and there is a need to attack the big issues rather than risking affirmative science. Although we agree poorly on the support for most claims, agreement regarding the knowledge basis enables consensus regarding broad patterns and likely causes. Empirical data needed for disentangling mechanisms are still scarce, and consequences at a population level and on community composition remain unclear. With increasing knowledge, the overall support (‘consensus view’) for a claim increased and between‐researcher variability in support (‘expert opinions') decreased, indicating the importance of assessing and communicating the knowledge basis. A proper integration across biological disciplines seems essential for the field's transition from affirming patterns to understanding mechanisms and making robust predictions regarding future consequences of shifting phenologies.