When have we looked hard enough? A novel method for setting minimum survey effort protocols for flora surveys

There is now a substantial body of literature documenting the detectability of plants and animals under standard survey conditions. Despite the evidence that many flora and fauna species have detection probabilities of less than one, it is still the default assumption of most environmental impact assessment processes that if a species is present, it will be detected. Here we briefly review a number of existing studies that have estimated the survey effort necessary to detect animal species, based on what is known about their detection rates in standard surveys. We then propose a novel method, based on failure‐time analysis, for quantifying the detectability of and determining appropriate survey effort for plant species during flora surveys. We provide computer code for implementing the method in the Bayesian freeware WinBUGS. Methods for estimating detectability can be used to inform minimum survey requirements and have important applications in environmental impact assessment and monitoring.     

The impact of epistatic selection on the genomic traces of selection

The rapid accumulation of genomic data has led to an explosion of studies searching for signals of past selection left within DNA sequences. Yet the majority of theoretical studies investigating the traces of selection have assumed a simple form of selection, without interactions among selectively fixed sites. Fitness interactions—‘epistasis’—are commonplace, however, and take on a myriad of forms ( Whitlock et al. 1995 ; Segrèet al. 2005 ; Phillips 2008 ). It is thus important to determine how such epistasis would influence selective sweeps. On p. 5018 of this issue, Takahasi (2009) explores the effect of epistasis on genetic variation neighbouring two sites that interact in determining fitness, finding that such epistasis has a dramatic impact on the genetic variability in regions surrounding the interacting sites.     

Gene expression profiling: opening the black box of plant ecosystem responses to global change

The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Because the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical, and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and nonmodel species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.     

An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea)

DNA sequences are currently used to propose primary hypotheses of species delimitation, especially when morphological variability is difficult to assess. In an integrative taxonomy framework, these hypotheses are then compared with other characters, such as morphology or geography, to produce robust species delimitations. For this purpose, the cytochrome oxidase subunit I (COI) gene has been sequenced for almost 50 specimens of the genus Benthomangelia , a deep-sea marine gastropod genus, collected in the South-West Pacific. Five genetic groups, displaying low and high genetic distances respectively within and between groups, were defined. COI hypotheses were compared with both the results obtained with the independent nuclear 28S gene and with an elliptic Fourier analysis of the shape of the last whorl of the shell. 28S gene analysis confirmed the same well-supported groups as COI, and elliptic Fourier analysis identified several morphological characters that vary similarly to genetic variability.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 696–708.     

Trophic level asynchrony in rates of phenological change for marine,freshwater and terrestrial environments

Recent changes in the seasonal timing (phenology) of familiar biological events have been one of the most conspicuous signs of climate change. However, the lack of a standardized approach to analysing change has hampered assessment of consistency in such changes among different taxa and trophic levels and across freshwater, terrestrial and marine environments. We present a standardized assessment of 25 532 rates of phenological change for 726 UK terrestrial, freshwater and marine taxa. The majority of spring and summer events have advanced, and more rapidly than previously documented. Such consistency is indicative of shared large scale drivers. Furthermore, average rates of change have accelerated in a way that is consistent with observed warming trends. Less coherent patterns in some groups of organisms point to the agency of more local scale processes and multiple drivers. For the first time we show a broad scale signal of differential phenological change among trophic levels; across environments advances in timing were slowest for secondary consumers, thus heightening the potential risk of temporal mismatch in key trophic interactions. If current patterns and rates of phenological change are indicative of future trends, future climate warming may exacerbate trophic mismatching, further disrupting the functioning, persistence and resilience of many ecosystems and having a major impact on ecosystem services.     

Differential responses of UK upland plants to nitrogen deposition

Native upland species, Nardus stricta , Eriophorum vaginatum , Erica cinerea and Vaccinium vitis-idaea were given 3 or 60 kg N ha⁻¹ yr⁻¹, over 2 yr, applied as a mist (NH₄NO₃). The high N treatment increased above-ground biomass in all four species, but only significantly in E. cinerea , E. vaginatum and N. stricta . Biomass increases in E. vaginatum and N. stricta resulted from enhanced tiller production rather than shoot elongation. Root growth increased in N. stricta , so that root:shoot ratio in this species was unchanged by N. Root growth in E. vaginatum , E. cinerea and V. vitis-idaea did not respond to N and their root:shoot ratios decreased. Tissue N concentrations increased in both shoots and roots of all species in response to N. The accumulated foliar N did not increase the proportion of N allocated to Rubisco and the photosynthetic capacities of N. stricta , E. vaginatum and V. vitis-idaea were unchanged. Thus growth responses to N were due to altered allocation rather than increased rate of photosynthesis per unit leaf area. The high N treatment increased flower production significantly in E. cinerea but not in the other species. Although in this experiment dwarf shrubs were more responsive than graminoids to N, in the field at current N inputs the enhanced tillering of the graminoids may be more competitively advantageous, especially where gaps develop in the canopy. Thus increasing N deposition may lead to increased grassiness of upland heath, and in particular, a spread of N. stricta .     

Albedo estimates for land surface models and support for a new paradigm based on foliage nitrogen concentration

Vegetation albedo is a critical component of the Earth's climate system, yet efforts to evaluate and improve albedo parameterizations in climate models have lagged relative to other aspects of model development. Here, we calculated growing season albedos for deciduous and evergreen forests, crops, and grasslands based on over 40 site‐years of data from the AmeriFlux network and compared them with estimates presently used in the land surface formulations of a variety of climate models. Generally, the albedo estimates used in land surface models agreed well with this data compilation. However, a variety of models using fixed seasonal estimates of albedo overestimated the growing season albedo of northerly evergreen trees. In contrast, climate models that rely on a common two‐stream albedo submodel provided accurate predictions of boreal needle‐leaf evergreen albedo but overestimated grassland albedos. Inverse analysis showed that parameters of the two‐stream model were highly correlated. Consistent with recent observations based on remotely sensed albedo, the AmeriFlux dataset demonstrated a tight linear relationship between canopy albedo and foliage nitrogen concentration (for forest vegetation: albedo=0.01+0.071%N, r²=0.91; forests, grassland, and maize: albedo=0.02+0.067%N, r²=0.80). However, this relationship saturated at the higher nitrogen concentrations displayed by soybean foliage. We developed similar relationships between a foliar parameter used in the two‐stream albedo model and foliage nitrogen concentration. These nitrogen‐based relationships can serve as the basis for a new approach to land surface albedo modeling that simplifies albedo estimation while providing a link to other important ecosystem processes.