The species and functional composition of bird communities in regenerating tropical forests

The widespread threat of species extinctions caused by the destruction and degradation of tropical primary forest (PF) could potentially be mitigated by the expansion of regenerating secondary forest (SF). However, the conservation value of SF remains controversial, and is dependent on many site- and landscape-scale factors, such as habitat age and isolation. The aim of this thesis was to assess the role that SF can play in conserving forest bird communities in central Panama. We study a chronosequence of SF aged 20 – 120-years-old, with sites either isolated from or connected to extensive PF. Our results suggest that SF supports high levels of avian species diversity, and similar community composition to PF. Whilst forest age plays a small role in determining compositional similarity to PF, connectivity to extensive PF was the main determinant of community composition. However, despite high species richness and complex community composition, some specialist PF bird species were consistently absent from SF, and isolated PF. The functional diversity of bird communities did not vary substantially across the forest age and isolation gradient, although we did find some inter-guild differences; with distinct responses in communities of avian insectivores and frugivores. Isolation caused shifts in the trophic traits of insectivores, but resulted in alterations in the dispersal traits of frugivores. The response of bird and tree community composition to forest age and isolation was similar, although isolation had a stronger impact on bird communities. Bird diversity and composition tracked changes in forest structure over succession. When examining the role of birds in seed-dispersal networks, we found bird gape width was the key predictor of seed size consumed. Large-gaped birds consume a wider variety of seed-sizes than small-gaped birds, and small-seeded trees attract a greater number of bird species than large-seeded trees. These results imply high levels of redundancy among small-gaped avian frugivores and small-seeded plant species, but low levels of redundancy among large-seeded plant species and their avian dispersers. This suggests that large-seeded plants may be most at risk of dispersal failure following any change in avian frugivore assemblages. Together, these results suggest that SF can play a key role in sustaining most tropical biodiversity, and in maintaining ecosystem services. Our findings emphasise the importance of integrating SF into conservation strategies to support and buffer tropical PF habitats

City life makes females fussy : sex differences in habitat use of temperate bats in urban areas

Urbanization is a major driver of the global loss of biodiversity; to mitigate its adverse effects, it is essential to understand what drives species' patterns of habitat use within the urban matrix. While many animal species are known to exhibit sex differences in habitat use, adaptability to the urban landscape is commonly examined at the species level, without consideration of intraspecific differences. The high energetic demands of pregnancy and lactation in female mammals can lead to sexual differences in habitat use, but little is known of how this might affect their response to urbanization. We predicted that female Pipistrellus pygmaeus would show greater selectivity of forging locations within urban woodland in comparison to males at both a local and landscape scale. In line with these predictions, we found there was a lower probability of finding females within woodlands which were poorly connected, highly cluttered, with a higher edge : interior ratio and fewer mature trees. By contrast, habitat quality and the composition of the surrounding landscape were less of a limiting factor in determining male distributions. These results indicate strong sexual differences in the habitat use of fragmented urban woodland, and this has important implications for our understanding of the adaptability of bats and mammals more generally to urbanization.Publisher PDFPeer reviewe

AVONET: morphological, ecological and geographical data for all birds

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.Additional co-authors: Samuel E. I. Jones, Claire Vincent, Anna G. Phillips, Nicola M. Marples, Flavia A. Montaño-Centellas, Victor Leandro-Silva, Santiago Claramunt, Bianca Darski, Benjamin G. Freeman, Tom P. Bregman, Christopher R. Cooney, Emma C. Hughes, Elliot J. R. Capp, Zoë K. Varley, Nicholas R. Friedman, Heiko Korntheuer, Andrea Corrales-Vargas, Christopher H. Trisos, Brian C. Weeks, Dagmar M. Hanz, Till Töpfer, Gustavo A. Bravo, Vladimír Remeš, Larissa Nowak, Lincoln S. Carneiro, Amilkar J. Moncada R., Beata Matysioková, Daniel T. Baldassarre, Alejandra Martínez-Salinas, Jared D. Wolfe, Philip M. Chapman, Benjamin G. Daly, Marjorie C. Sorensen, Alexander Neu, Michael A. Ford, Luis Fabio Silveira, David J. Kelly, Nathaniel N. D. Annorbah, Henry S. Pollock, Ada M. Grabowska-Zhang, Jay P. McEntee, Juan Carlos T. Gonzalez, Camila G. Meneses, Marcia C. Muñoz, Luke L. Powell, Gabriel A. Jamie, Thomas J. Matthews, Oscar Johnson, Guilherme R. R. Brito, Kristof Zyskowski, Ross Crates, Michael G. Harvey, Maura Jurado Zevallos, Peter A. Hosner, James M. Maley, F. Gary Stiles, Hevana S. Lima, Kaiya L. Provost, Moses Chibesa, Mmatjie Mashao, Jeffrey T. Howard, Edson Mlamba, Marcus A. H. Chua, Bicheng Li, M. Isabel Gómez, Natalia C. García, Martin Päckert, Jérôme Fuchs, Jarome R. Ali, Elizabeth P. Derryberry, Monica L. Carlson, Rolly C. Urriza, Kristin E. Brzeski, Dewi M. Prawiradilaga, Matt J. Rayner, Eliot T. Miller, Rauri C. K. Bowie, René-Marie Lafontaine, R. Paul Scofield, Yingqiang Lou, Lankani Somarathna, Denis Lepage, Marshall Illif, Eike Lena Neuschulz, Mathias Templin, D. Matthias Dehling, Jacob C. Cooper, Olivier S. G. Pauwels, Kangkuso Analuddin, Jon Fjeldså, Nathalie Seddon, Paul R. Sweet, Fabrice A. J. DeClerck, Luciano N. Naka, Jeffrey D. Brawn, Alexandre Aleixo, Katrin Böhning-Gaese, Carsten Rahbek, Susanne A. Fritz, Gavin H. Thomas, Matthias Schleunin

Differential responses to woodland character and landscape context by cryptic bats in urban environments

© 2015 Lintott et al. Urbanisation is one of the most dramatic forms of land use change which relatively few species can adapt to. Determining how and why species respond differently to urban habitats is important in predicting future biodiversity loss as urban areas rapidly expand. Understanding how morphological or behavioural traits can influence species adaptability to the built environment may enable us to improve the effectiveness of conservation efforts. Although many bat species are able to exploit human resources, bat species richness generally declines with increasing urbanisation and there is considerable variation in the responses of different bat species to urbanisation. Here, we use acoustic recordings from two cryptic, and largely sympatric European bat species to assess differential responses in their use of fragmented urban woodland and the surrounding urban matrix. There was a high probability of P. pygmaeus activity relative to P. pipistrellus in woodlands with low clutter and understory cover which were surrounded by low levels of built environment. Additionally, the probability of recording P. pygmaeus relative to P. pipistrellus was considerably higher in urban woodland interior or edge habitat in contrast to urban grey or non-wooded green space. These results show differential habitat use occurring between two morphologically similar species; whilst the underlying mechanism for this partitioning is unknown it may be driven by competition avoidance over foraging resources. Their differing response to urbanisation indicates the difficulties involved when attempting to assess how adaptable a species is to urbanisation for conservation purposes

AVONET: morphological, ecological and geographical data for all birds

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species‐level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16–20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Background: The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes. Methods: This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status. Findings: Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low. Interpretation: This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant. Funding: Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research

Stratificazioni difatti e di culture nella vicenda di S. Angelo in Formis in Misteri e presenze. La civiltà di S. Angelo in Formis

Predicted species extinctions caused by the destruction and degradation of tropical primary forest may be at least partially mitigated by the expansion of regenerating secondary forest. However, the conservation value of secondary forest remains controversial, and potentially underestimated, since most previous studies have focused on young, single-aged, or isolated stands. Here we use point count surveys to compare tropical forest bird communities in 20–120-yr-old secondary forest and primary forest stands in central Panama, with varying connectivity between secondary forest sites and extensive primary forest. We found that species richness and other metrics of ecological diversity, as well as the combined population density of all birds, reached a peak in younger (20-yr-old) secondary forests, and appeared to decline in older secondary forest stands. This counter-intuitive result can be explained by the greater connectivity between younger secondary forests and extensive primary forests at our study site, compared with older secondary forests that are either (1) more isolated, or (2) connected to primary forests that are themselves small and isolated. Our results suggest that connectivity with extensive primary forest is a more important determinant of avian species richness and community structure than forest age, and highlight the vital contribution secondary forests can make in conserving tropical bird diversity, so long as extensive primary habitats are adjacent and spatially connected