Social network analysis and valid Markov chain Monte Carlo tests of null models

Analyses of animal social networks derived from group-based associations often rely on randomisation methods developed in ecology (Manly, Ecology 76:1109–1115, 1995) and made available to the animal behaviour community through implementation of a pair-wise swapping algorithm by Bejder et al. (Anim Behav 56:719–725, 1998). We report a correctable flaw in this method and point the reader to a wider literature on the subject of null models in the ecology literature. We illustrate the importance of correcting the method using a toy network and use it to make a preliminary analysis of a network of associations among eagle rays.

Genetic structure of rhinoceros auklets,Cerorhinca monocerata,breeding in British Columbia,Alaska, and Japan

Data from eight microsatellite markers screened in 246 rhinoceros auklets (Cerorhinca monocerata) from across the North Pacific revealed multiple genetic groups. The east (North America) to west (Japan) split was clearly evident in all analyses. Within the eastern Pacific, a minimum of three genetic groups are present. Surprisingly, rhinoceros auklets from Triangle Island, British Columbia, were genetically isolated from other nearby populations, including the breeding colony on Pine Island (~100 km to the east). A fourth genetic cluster (Chowiet Is) was detected using principal coordinate’s analysis; however, sample sizes were limited. Patterns of differentiation correspond to nonbreeding distributions with the eastern and western Pacific birds spending time off the west coast of North America and Japan, respectively, and may represent historical isolation in separate refugia during the Pleistocene glaciations. The patterns of genetic structure result from a combination of historical and contemporary factors influencing dispersal of rhinoceros auklets.     

Pleistocene diversification of the Pomacentrus coelestis species complex (Pisces: Pomacentridae): historical biogeography and species boundaries

Pleistocene eustatic changes in sea level are often invoked to explain genetic divergence among marine organisms. However, molecular phylogenies have revealed relatively few examples of speciation events dating to the Pleistocene. We present a species-level hypothesis of the timing of evolution for the Pomacentrus coelestis species complex (Pomacentridae), based on the nuclear S7 intron and the mitochondrial Cytb gene, and reconstruct ancestral range distributions across the timetree. Ancestral range reconstruction suggests the complex originated in the Coral Triangle and East Indian Ocean, with subsequent range expansion outward from this region. We suggest that land barriers to dispersal (e.g., Indo-Pacific barrier) may be responsible for the divergence between Indian (P. alleni, P. similis, P. caeruleopunctatus, and P. caeruleus) and Pacific (P. micronesicus, P. auriventris, and P. coelestis) species groups, and subsequent isolation by Pleistocene sea-level fluctuations in certain areas of the Coral Triangle (glacial refugia) may play an important role in the diversification of this species complex. Additionally, our analyses show cryptic lineages within P. micronesicus and highlight the need for comprehensive sampling within and among species to reveal recent speciation events.     

Preliminary assessment of surface soil lead concentrations in Melbourne,Australia

Urban soils in many cities have been found to be contaminated with lead from past usage of leaded petrol, deteriorating lead-based exterior paints and industrial sources. Currently, the spatial distribution of soil lead concentrations in the Melbourne metropolitan area is unknown. The objective of this study was to perform a preliminary assessment of the spatial distributions of the surface soil lead (Pb) concentrations in the Melbourne metropolitan area, Australia. Fifty-eight surface soil samples were collected at a depth of 0–2 cm along three linear transects oriented across the Melbourne metropolitan area. Surface soil samples were also collected at a higher density in five Melbourne suburbs. Soil cores (0–50 cm) were collected in four locations, soil transects were collected at intervals with distance away from the roadway (0–50 m) in two inner city parks, and one control soil sample was collected in a rural setting. The median soil Pb concentration of the soil transect samples was 173 mg/kg (range 32–710 mg/kg), and the median soil Pb concentration of the five suburbs was 69 mg/kg (range 9–1750 mg/kg). The suburb of Footscray had the highest soil Pb concentration with a median soil Pb concentration of 192 mg/kg (range 40–1750 mg/kg). Soil Pb concentrations were generally higher nearest the centre of the Melbourne metropolitan area and in the west of Melbourne and lower in the outer suburbs to the east and north of the city centre. Soil Pb concentrations decreased with distance from roadways in the two transects taken from urban parks, and soil lead decreased with depth in the four soil cores. The soil Pb concentrations in the Melbourne metropolitan area appear to be lower than soil lead concentrations observed in inner city areas of Sydney New South Wales (NSW) and Newcastle NSW. The spatial extent of the soil Pb hazard remains undefined in portions of the Melbourne metropolitan area.     

Mapping cumulative impacts of mining on sediment retention ecosystem service in an Australian mining region

Mining development can potentially lead to cumulative impacts on ecosystems and their services across a range of scales. Site-specific environmental impact assessments are commonly assessed for mining projects; however, large-scale cumulative impacts of multiple mines that aggregate and interact in resources regions have had little attention in the literature and there are few examples where regional-scale mining impacts have been assessed on ecosystem services. The objective of this study is to quantify regional-scale cumulative impacts of mining on sediment retention ecosystem services. We apply the sediment delivery ratio model of Integrated Valuation of Ecosystem Services and Trade-offs to calculate and map the sediment retention and export using a synthetic catchment model and a real case study under different mining scenarios in an Australian mining region. Two impact indices were created to quantify the cumulative impacts associated with a single mine and the interactions between multiple mines. The indices clarified the magnitude of impacts and the positive/negative impacts associated with regional-scale sediment retention and export. We found cumulative impacts associated with multiple mines’ interaction occurred but the influence of these interactions was relatively weak. This research demonstrated the potential for utilising ecosystem services modelling for the quantitative assessment of the cumulative impacts. Such research provide decision-makers and planners with a tool for sustainable regional and landscape planning that balances the needs of mining and the provision of ecosystem services.     

Urban growth and landscape connectivity threats assessment at Saguaro National Park,Arizona, USA

Urban and exurban expansion results in habitat and biodiversity loss globally. We hypothesize that a coupled-model approach could connect urban planning for future cities with landscape ecology to consider wildland habitat connectivity. Our work combines urban growth simulations with models of wildlife corridors to examine how species will be impacted by development to test this hypothesis. We leverage a land use change model (SLEUTH) with structural and functional landscape-connectivity modeling techniques to ascertain the spatial extent and locations of connectivity related threats to a national park in southern Arizona, USA, and describe how protected areas might be impacted by urban expansion. Results of projected growth significantly altered structural connectivity (80%) when compared to current (baseline) corridor conditions. Moreover, projected growth impacted functional connectivity differently amongst species, indicating resilience of some species and near-complete displacement of others. We propose that implementing a geospatial-design-based model will allow for a better understanding of the impacts management decisions have on wildlife populations. The application provides the potential to understand both human and environmental impacts of land-system dynamics, critical for long-term sustainability.     

Threshold amounts of organic carbon needed to initiate reductive dechlorination in groundwater systems

Aquifer sediment and groundwater chemistry data from 15 Department of Defense facilities located throughout the United States were collected and analyzed with the goal of estimating the amount of natural organic carbon needed to initiate reductive dechlorination in groundwater systems. Aquifer sediments were analyzed for hydroxylamine and NaOH‐extractable organic carbon, yielding a probable underestimate of potentially bioavailable organic carbon (PBOC). Aquifer sediments were also analyzed for total organic carbon (TOC) using an elemental combustion analyzer, yielding a probable overestimate of bioavailable carbon. Concentrations of PBOC correlated linearly with TOC with a slope near one. However, concentrations of PBOC were consistently five to ten times lower than TOC. When mean concentrations of dissolved oxygen observed at each site were plotted versus PBOC, it showed that anoxic conditions were initiated at approximately 200 mg/kg of PBOC. Similarly, the accumulation of reductive dechlorination daughter products relative to parent compounds increased at a PBOC concentration of approximately 200 mg/kg. Concentrations of total hydrolysable amino acids (THAA) in sediments also increased at approximately 200 mg/kg, and bioassays showed that sediment CO₂ production correlated positively with THAA. The results of this study provide an estimate for threshold amounts of bioavailable carbon present in aquifer sediments (approximately 200 mg/kg of PBOC; approximately 1,000 to 2,000 mg/kg of TOC) needed to support reductive dechlorination in groundwater systems. © 2012 Wiley Periodicals, Inc.     

Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems

Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) through anthropogenic activities. Although the effects of increased N inputs on plant communities have been reasonably well studied, few comparable studies have examined impacts on whole soil bacterial communities, though they play critical roles in ecosystem functioning. We sampled soils from two long-term ecological research (LTER) experimental N gradients, both of which have been amended with NH4NO3; a grassland at Cedar Creek (27 years of N additions) and an agricultural field at Kellogg Biological Station (8 years of N additions). By examining shifts in bacterial communities across these contrasting ecosystem types, we could test competing hypotheses about the direct and indirect factors that might drive bacterial responses to elevated N inputs. Bacterial community structure was highly responsive to N additions. We observed predictable and consistent changes in the structure of the bacterial communities across both ecosystem types. Our results suggest that bacterial communities across these gradients are more structured by N and/or soil carbon availability than by shifts in the plant community or soil pH associated with the elevated nitrogen inputs. In contrast to the pronounced shifts in bacterial community composition and in direct contrast to the patterns often observed in plant communities, increases in N availability did not have consistent effects on the richness and diversity of soil bacterial communities.     

Wintering areas of adult Atlantic puffins Fratercula arctica from a North Sea colony as revealed by geolocation technology

Most seabirds die outside the breeding season, but understanding the key factors involved is hampered by limited knowledge of nonbreeding distributions. We used miniature geolocating loggers to examine the movements between breeding seasons of Atlantic puffins Fratercula arctica from a major North Sea colony where numbers have declined in recent years, apparently due to increased overwinter mortality. The most intensively used region was the northwestern North Sea but most puffins also made excursions into the east Atlantic in the early winter. Ringing recoveries previously indicated that adults from British east coast colonies remained within the North Sea and hence were spatially segregated from those breeding on the west throughout the year. Updated analyses of ringing recoveries support results from geolocators suggesting that usage of Atlantic waters is a recent phenomenon. We propose that the increased adult mortality is related to changes in distribution during the nonbreeding period and reflects worsening conditions in the North Sea.