A bird’s eye view: using circuit theory to study urban landscape connectivity for birds

Context Connectivity is fundamental to understanding how landscape form influences ecological function. However, uncertainties persist due to the difficulty and expense of gathering empirical data to drive or to validate connectivity models, especially in urban areas, where relationships are multifaceted and the habitat matrix cannot be considered to be binary. Objectives This research used circuit theory to model urban bird flows (i.e. ‘current’), and compared results to observed abundance. The aims were to explore the ability of this approach to predict wildlife flows and to test relationships between modelled connectivity and variation in abundance. Methods Circuitscape was used to model functional connectivity in Bedford, Luton/Dunstable, and Milton Keynes, UK, for great tits (Parus major) and blue tits (Cyanistes caeruleus), drawing parameters from published studies of woodland bird flows in urban environments. Model performance was then tested against observed abundance data. Results Modelled current showed a weak yet positive agreement with combined abundance for P. major and C. caeruleus. Weaker correlations were found for other woodland species, suggesting the approach may be expandable if re-parameterised. Conclusions Trees provide suitable habitat for urban woodland bird species, but their location in large, contiguous patches and corridors along barriers also facilitates connectivity networks throughout the urban matrix. Urban connectivity studies are well-served by the advantages of circuit theory approaches, and benefit from the empirical study of wildlife flows in these landscapes to parameterise this type of modelling more explicitly. Such results can prove informative and beneficial in designing urban green space and new developments

Estimating the potential biodiversity impact of redeveloping small urban spaces: the Natural History Museum’s grounds

The file attached is the Published/publisher’s pdf version of the article.Copyright 2017 Phillips et al. Distributed under Creative Commons CC-BY 4.

Urban Biodiversity and Landscape Ecology: Patterns, Processes and Planning

Effective planning for biodiversity in cities and towns is increasingly important as urban areas and their human populations grow, both to achieve conservation goals and because ecological communities support services on which humans depend. Landscape ecology provides important frameworks for understanding and conserving urban biodiversity both within cities and considering whole cities in their regional context, and has played an important role in the development of a substantial and expanding body of knowledge about urban landscapes and communities. Characteristics of the whole city including size, overall amount of green space, age and regional context are important considerations for understanding and planning for biotic assemblages at the scale of entire cities, but have received relatively little research attention. Studies of biodiversity within cities are more abundant and show that longstanding principles regarding how patch size, configuration and composition influence biodiversity apply to urban areas as they do in other habitats. However, the fine spatial scales at which urban areas are fragmented and the altered temporal dynamics compared to non-urban areas indicate a need to apply hierarchical multi-scalar landscape ecology models to urban environments. Transferring results from landscape-scale urban biodiversity research into planning remains challenging, not least because of the requirements for urban green space to provide multiple functions. An increasing array of tools is available to meet this challenge and increasingly requires ecologists to work with planners to address biodiversity challenges. Biodiversity conservation and enhancement is just one strand in urban planning, but is increasingly important in a rapidly urbanising world

Novel Hepatitis E Virus Genotype in Norway Rats, Germany

Human hepatitis E virus infections may be caused by zoonotic transmission of virus genotypes 3 and 4. To determine whether rodents are a reservoir, we analyzed the complete nucleotide sequence of a hepatitis E–like virus from 2 Norway rats in Germany. The sequence suggests a separate genotype for this hepatotropic virus

Ground beetle (Coleoptera: Carabidae) communities on green roofs in Switzerland : synthesis and perspectives

Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch)Green roofs have recently gained recognition for their potential contribution to urban ecosystems by providing, among other services, habitat for plants and animals, and stepping stones for mobile organisms, thereby enhancing permeability among habitat patches across densely built cities. In Switzerland, investigations over the past 20 years on more than one hundred distinct green roofs across six cities have provided an unprecedented dataset on ground beetles, albeit with information that is scattered across unpublished reports and local databases. We present here for the first time a synthesis of the state of knowledge of ground beetle communities from green roofs in Switzerland. We describe 91 ground beetles species (19,428 individuals) and highlight patterns of species occurrence and composition across green roofs and cities. Most of the roofs host ground beetle communities dominated by five common mobile species with quite diversified ecological requirements. In addition, we observed nine species (10% of all species collected) that are conservation concerns in Switzerland and Central Europe as well as numerous stenotopic species (from grasslands and pioneer vegetation). This indicates that, besides sustaining local populations of common species, green roofs can also offer suitable ecological conditions of high conservation interest. We suggest both improving the design of green roofs (composition and configuration of vegetation, as well as soil depth and substrate composition) to increase their ecological value for species with the most different ecological needs, and to integrate green roofs into urban planning to make them more efficient as biodiversity supports

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

BACKGROUND: The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. RESULTS: Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. CONCLUSION: ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results

Ecological connectivity in the three-dimensional urban green volume using waveform airborne lidar

This is the final version. Available on open access from Nature Research via the DOI in this record.The movements of organisms and the resultant flows of ecosystem services are strongly shaped by landscape connectivity. Studies of urban ecosystems have relied on two-dimensional (2D) measures of greenspace structure to calculate connectivity. It is now possible to explore three-dimensional (3D) connectivity in urban vegetation using waveform lidar technology that measures the full 3D structure of the canopy. Making use of this technology, here we evaluate urban greenspace 3D connectivity, taking into account the full vertical stratification of the vegetation. Using three towns in southern England, UK, all with varying greenspace structures, we describe and compare the structural and functional connectivity using both traditional 2D greenspace models and waveform lidar-generated vegetation strata (namely, grass, shrubs and trees). Measures of connectivity derived from 3D greenspace are lower than those derived from 2D models, as the latter assumes that all vertical vegetation strata are connected, which is rarely true. Fragmented landscapes that have more complex 3D vegetation showed greater functional connectivity and we found highest 2D to 3D functional connectivity biases for short dispersal capacities of organisms (6 m to 16 m). These findings are particularly pertinent in urban systems where the distribution of greenspace is critical for delivery of ecosystem services.This work was funded under the NERC Biodiversity and Ecosystem Services Sustainability (BESS) thematic programme for the ‘Fragments Functions and Flows in Urban Ecosystems’ project (Reference: NE/J015237/1; http://bess-urban.group.shef.ac.uk/). The waveform ALS data were acquired by the NERC Airborne Research and Survey Facility (ARSF) and the team from the ARSF Data Analysis Node at Plymouth Marine Laboratory is acknowledged for undertaking initial ALS processing

The role of the urban landscape on species with contrasting dispersal ability: insights from greening plans for Barcelona

With the expansion of urban areas, promoting urban biodiversity is now a priority. Many municipalities are implementing greening strategies to improve and increase green space within city boundaries. The effectiveness of these strategies, while rarely assessed, likely depends on the landscape and on relevant species intrinsic traits such as dispersal ability. Using a spatially explicit individual-based model, we evaluated the effect of the urban landscape on the projected distribution of three butterfly species with contrasting dispersal abilities, and assessed the effectiveness of the Barcelona greening strategy as a case study. Species distribution (in terms of patch occupancy) and effectiveness (in terms of population size and number of occupied gardens) were analysed using generalised linear models. The percentage of (semi) natural source area around each urban green space (garden hereafter) was the most important variable for the distribution of all three types of species, followed by the percentage of neighbouring gardens and by the garden carrying capacity, although the effect of neighbouring gardens was negative in the early phase of colonisation. The planned Barcelona greening strategy increased the number of gardens occupied by high and medium, but not by low dispersive species. Increasing the carrying capacity of the gardens improved colonisation for all three species types. While the best strategies can be context dependent, our results indicated that increasing garden area might be more effective in the long term but it can be overridden by garden capacity in the short term, especially if there are constraints to increasing garden area

Challenging the European southern refugium hypothesis: species-specific structures vs. general patterns of genetic diversity and differentiation among small mammals

Aim: In this study, we conduct a quantitative meta-analysis to investigate broad patterns of genetic variation throughout large geographic regions in order to elucidate concordant geographical patterns across species and identify common historical processes to better inform the ‘cryptic refugia’ vs. the traditional ‘southern refugia’ hypothesis debate. Location: Europe Time period: Late Pleistocene to present day. Major taxa studied: small mammals (Rodentia, Eulipotyphla) Methods: A meta-analysis was performed on large scale patterns of genetic diversity for 19 species from 59 papers. For each species, haplotype and nucleotide diversity were calculated using the mitochondrial D-loop and compared to the species range. Results: No consistent patterns were observed between mtDNA diversity indices (nucleotide and haplotype diversity) and any of the indicators of distribution examined (latitude and longitude (max, min, centre, range)). The patterns of genetic diversity observed in all the 19 species studied appear to be species-specific. Main conclusion: In contrast to the traditional southern refugial hypotheses, we found no evidence for a consistent south-north post-glacial expansion. Instead individual species appear to respond to climate oscillations in niche-specific ways. This individual nature of each species’ phylogeographical history indicates a complex web of postglacial recolonisation dynamics across Europe