Landscape -scale predictors of persistence of an urban stock dove Columba oenas population

While a few species may thrive in urban areas, urban expansion is a major driver of biodiversity loss. Columbids such as feral Rock Doves (Columba livia domestica) and Common Woodpigeon (Columba palumbus) have adapted extremely well to the urban environment in Europe and beyond, but the Stock Dove (Columba oenas), a bird of farmland and woodland edge in the UK and of national conservation concern, is encountered infrequently in urban areas. Here we explore the multi-scale landscape associations of the little-studied Stock Dove within the urban matrix of Greater Manchester, UK, in order to identify its habitat requirements. We built a pilot model from historical citizen science records to identify potentially occupied sites within the city, and then surveyed these sites for Stock Dove during Spring 2019. We combined the survey results with citizen science records from the same period and described the habitat and landscape characteristics of sites occupied by Stock Dove using four variables at different scales plus twelve unscaled variables. We used a three-stage random forest approach to identify a subset of these variables for interpretation and a subset for prediction for the presence of Stock Dove within these sites. Key variables for predicting Stock Dove presence were their relative abundance in the landscape immediately beyond the core urban area, the greenness (NDVI) of the environment around sites, and the canopy cover of individual trees over 20 m high within sites. Stock Doves tended to be associated with habitats with more surface water during the non-breeding season than the breeding season. Our results highlight the importance of large trees within urban greenspace for this cavity-nesting species, softer boundaries around urban sites for Stock Doves and stock dove presence in nearby areas. While Stock Dove share many traits with species that are successful in the urban environment, they remain relatively poor urban adapters

Detecting and reducing heterogeneity of error in acoustic classification

Passive acoustic monitoring can be an effective method for monitoring species, allowing the assembly of large audio datasets, removing logistical constraints in data collection and reducing anthropogenic monitoring disturbances. However, the analysis of large acoustic datasets is challenging and fully automated machine learning processes are rarely developed or implemented in ecological field studies. One of the greatest uncertainties hindering the development of these methods is spatial generalisability—can an algorithm trained on data from one place be used elsewhere? We demonstrate that heterogeneity of error across space is a problem that could go undetected using common classification accuracy metrics. Second, we develop a method to assess the extent of heterogeneity of error in a random forest classification model for six Amazonian bird species. Finally, we propose two complementary ways to reduce heterogeneity of error, by (i) accounting for it in the thresholding process and (ii) using a secondary classifier that uses contextual data. We found that using a thresholding approach that accounted for heterogeneity of precision error reduced the coefficient of variation of the precision score from a mean of 0.61 ± 0.17 (SD) to 0.41 ± 0.25 in comparison to the initial classification with threshold selection based on F-score. The use of a secondary, contextual classification with thresholding selection accounting for heterogeneity of precision reduced it further still, to 0.16 ± 0.13, and was significantly lower than the initial classification in all but one species. Mean average precision scores increased, from 0.66 ± 0.4 for the initial classification, to 0.95 ± 0.19, a significant improvement for all species. We recommend assessing—and if necessary correcting for—heterogeneity of precision error when using automated classification on acoustic data to quantify species presence as a function of an environmental, spatial or temporal predictor variable

Avian diversity and function across the world's most populous cities

Understanding the composition of urban wildlife communities is crucial to promote biodiversity, ecosystem function and links between nature and people. Using crowdsourced data from over five million eBird checklists, we examined the influence of urban characteristics on avian richness and function at 8443 sites within and across 137 global cities. Under half of the species from regional pools were recorded in cities, and we found a significant phylogenetic signal for urban tolerance. Site-level avian richness was positively influenced by the extent of open forest, cultivation and wetlands and avian functional diversity by wetlands. Functional diversity co-declined with richness, but groups including granivores and aquatic birds occurred even at species-poor sites. Cities in arid areas held a higher percentage of regional species richness. Our results indicate commonalities in the influence of habitat on richness and function, as well as lower niche availability, and phylogenetic diversity across the world's cities

Multi‐decadal land use impacts across the vast range of an iconic threatened species

Abstract Aim To explore spatiotemporal changes in Hyacinth Macaw Anodorhynchus hyacinthinus distribution and the impacts of land use change over 25 years, across its vast range in central/eastern South America. Location Brazil, Bolivia and Paraguay, South America, covering almost 3 million km2. Methods We use a novel, multi-temporal species distribution model, to combine both year-specific occurrence records and land use/cover data in a single model that is subsequently projected over a land cover time series. We investigate changes in geographic range over 25 years and potential drivers of range extent at multiple spatial scales (10 and 30 km) and time-lags (current and 10 years previously). We also assess protected area coverage and impacts from degazettement within the remaining range and highlight priority areas to search for undiscovered populations. Results The modelled range of the species increased by 75,000 km2 to over 500,000 km2 between 1995 and 2019, during which period agriculture and pasture increased by 600,000 km2 within the species' extent of occurrence. Habitat suitability was influenced most strongly by distribution of palms, forest cover and changes in pasture over 10 years and usually by predictors measured at larger spatial scales. Just 8% of the macaw's modelled range falls within protected areas, and more than 20,500 km2 of protected areas overlapping with the range have been degazetted in the last 40 years. We highlight key areas to search for undiscovered populations in under-sampled and remote areas, especially led by community citizen science initiatives involving indigenous groups and protected area staff. Main conclusions Novel modelling methods, combining multi-temporal occurrence records and land cover data, appropriate for small sample sizes per year, have revealed habitat dynamics and changes to the range of this threatened species over 25 years. The method may have wide applicability for a range of species, including elusive and poorly studied species

Acoustic indices perform better when applied at ecologically meaningful time and frequency scales

Acoustic indices are increasingly employed in the analysis of soundscapes to ascertain biodiversity value. However, conflicting results and lack of consensus on best practices for their usage has hindered their application in conservation and land‐use management contexts. Here we propose that the sensitivity of acoustic indices to ecological change and fidelity of acoustic indices to ecological communities are negatively impacted by signal masking. Signal masking can occur when acoustic responses of taxa sensitive to the effect of interest are masked by less sensitive acoustic groups, or target taxa sonification is masked by non‐target noise. We argue that by calculating acoustic indices at ecologically appropriate time and frequency bins, masking effects can be reduced and the efficacy of indices increased. We test this on a large acoustic dataset collected in Eastern Amazonia spanning a disturbance gradient of undisturbed, logged, burned, logged‐and‐burned, and secondary forests. We calculated values for two acoustic indices: the Acoustic Complexity Index and the Bioacoustic Index, across the entire frequency spectrum (0‐22.1 kHz), and four narrower subsets of the frequency spectrum; at dawn, day, dusk and night. We show that signal masking has a large impact on the sensitivity of acoustic indices to forest disturbance classes. Calculating acoustic indices at a range of narrower time‐frequency bins substantially increases the classification accuracy of forest classes by random forest models. Furthermore, signal masking led to misleading correlations, including spurious inverse correlations, between biodiversity indicator metrics and acoustic index values compared to correlations derived from manual sampling of the audio data. Consequently, we recommend that acoustic indices are calculated either at a range of time and frequency bins, or at a single narrow bin, predetermined by a priori ecological understanding of the soundscape

Heterogeneity of tree diversity and carbon stocks in Amazonian oil palm landscapes

ABSTRACT Background: Quantitative effects of large-scale oil palm expansion in the Neotropics on biodiversity and carbon stocks are still poorly documented. Aims: We evaluated differences in tree species composition and richness, and above-ground carbon stocks among dominant land cover types in Pará state, Brazil. Methods: We quantified tree species composition and richness and above-ground carbon stock in stands in remnant primary rain forest, young secondary forest, oil palm plantation and pastures. Results: We sampled 5,696 trees with a DBH≥2 cm, of 413 species in 68 families, of which 381 species were recorded in primary forest fragments. We found significant differences in species richness and carbon stock among the four land cover classes. Carbon stocks in remnant primary forest were typically over 190 Mg ha −1 , while those in other land cover types were typically less than 60 Mg ha −1 . Conclusion: Oil palm plantations have a species-poor tree community given active manage- ment; old plantations have a standing carbon stock which is comparable to that of secondary forest and far greater than that of pastures. Private forest reserves within oil palm company holdings play an important role in preserving primary forest tree diversity in human-modified landscapes in Amazonia

Single-molecule transcript counting of stem-cell markers in the mouse intestine

available in PMC 2012 July 1.Determining the molecular identities of adult stem cells requires technologies for sensitive transcript detection in tissues. In mouse intestinal crypts, lineage-tracing studies indicated that different genes uniquely mark spatially distinct stem-cell populations, residing either at crypt bases or at position +4, but a detailed analysis of their spatial co-expression has not been feasible. Here we apply three-colour single-molecule fluorescent in situ hybridization to study a comprehensive panel of intestinal stem-cell markers during homeostasis, ageing and regeneration. We find that the expression of all markers overlaps at crypt-base cells. This co-expression includes Lgr5, Bmi1 and mTert, genes previously suggested to mark distinct stem cells. Strikingly, Dcamkl1 tuft cells, distributed throughout the crypt axis, co-express Lgr5 and other stem-cell markers that are otherwise confined to crypt bases. We also detect significant changes in the expression of some of the markers following irradiation, indicating their potential role in the regeneration process. Our approach can enable the sensitive detection of putative stem cells in other tissues and in tumours, guiding complementary functional studies to evaluate their stem-cell properties.National Institutes of Health (U.S.) (U54CA143874)National Cancer Institute (U.S.) (Physical Sciences Oncology Center at MIT (U54CA143874))National Institutes of Health (U.S.) (NIH Pioneer award (1DP1OD003936))National Cancer Institute (U.S.) (Cancer Center Support (core) grant P30-CA14051)European Molecular Biology Organization (postdoctoral fellowship)Human Frontier Science Program (Strasbourg, France)Machiah FoundationHoward Hughes Medical Institute (Gilliam fellowship

Management dilemma; a woman with cystic fibrosis and severe lung disease presenting with colonic carcinoma: a case report

Introduction There are increasing reports of bowel cancer in cystic fibrosis, suggesting a possible causal link. Individuals with cystic fibrosis who have advanced lung disease present a high operative risk, limiting curative treatment options in early bowel malignancy. Case presentation We describe a 41-year-old Caucasian woman with cystic fibrosis and severe lung disease who had been considered for lung transplantation, who presented with rectal bleeding and was found to have a Stage I adenocarcinoma of the sigmoid colon. After considerable discussion as to the operative risks, she underwent a laparoscopic resection and remains relatively well 1 year postoperatively with no recurrence. Conclusion We discuss the complexity of the management decisions for cystic fibrosis patients with severe lung disease and early stage colonic malignancy, particularly in the context of potential need for lung transplantation. The case demonstrates that cystic fibrosis patients with very severe lung function impairment may undergo laparoscopic abdominal surgical interventions without compromising postoperative airway clearance

A discretized integral hydrodynamics

Using an interpolant form for the gradient of a function of position, we write an integral version of the conservation equations for a fluid. In the appropriate limit, these become the usual conservation laws of mass, momentum and energy. We also discuss the special cases of the Navier-Stokes equations for viscous flow and the Fourier law for thermal conduction in the presence of hydrodynamic fluctuations. By means of a discretization procedure, we show how these equations can give rise to the so-called "particle dynamics" of Smoothed Particle Hydrodynamics and Dissipative Particle Dynamics.Comment: 10 pages, RevTex, submitted to Phys. Rev.