Bird communities across different levels of human settlement: A comparative analysis from two northern Amazonian ecoregions

Urban ecosystems are increasingly dominating landscapes globally, so it is critical to understand the effects of human settlements on biodiversity. Bird communities are effective indicators because they are impacted by the size and expansion of human settlements, exemplified by changes in their habitat use, breeding and foraging behaviours, as well as patterns of richness and abundance. Existing studies on bird community responses to human settlements have mainly focused on single ecoregions and large cities, leaving a gap in comparative research on how differently sized human settlements affect bird communities across various ecoregions. To address this gap, we examine species richness, bird abundances and community composition in human settlements, which exhibit variable sizes, populations, landscape configurations, and overall intensity of settlement in two tropical ecoregions in Guyana, Amazonia: forest and savannah. In each ecoregion we explored how different groupings of urban tolerance in birds responded to human settlements of differing population size and building densities. Overall, we found significant differences in bird communities across the varying levels of human settlement intensity in both ecoregions, with greater differences in bird community composition in the forest ecoregion than the savannah region. In both ecoregions, species richness and abundance were highest at the medium level of settlement of human settlement. Our findings suggest that bird tolerance to human settlements varies based on ecoregion and site-level factors. In the savannah, built features may be benefitting birds from all urban tolerance levels, but they have a negative impact on less urban-tolerant species in the forest ecoregion. Our comparative analysis reveals for the first time that the impact of human settlements on avian communities in northern Amazonia varies among ecoregions, indicating that species evolved to live in a savannah may be more tolerant to human settlements than those more evolved to a forest system.

Bird diversity and psychological wellbeing: A comparison of green and coastal blue space in a neotropical city

Accelerating rates of urbanisation are contributing to biodiversity declines worldwide. However, urban green (e.g. parks) and blue spaces (e.g. coast) provide important habitat for species. Emerging evidence also shows that green and blue spaces can benefit human psychological wellbeing, although few studies originate from the Global South and it is unclear whether more biodiverse spaces offer greater wellbeing gains. We examine how bird diversity (abundance, species richness, Shannon diversity, and community composition) in green and coastal blue space in Georgetown, Guyana, is associated with people's wellbeing (positive and negative affect, anxiety) in situ, using point counts and questionnaires. Bird community composition differed between green and coastal sites, and diversity was significantly higher in green sites. Positive affect and anxiety did not differ between green and coastal sites, but negative affect was higher in coastal sites. Mixed-effect models showed no associations between biodiversity and wellbeing, implying other features are contributing to people's positive wellbeing. Despite no association between biodiversity and wellbeing, both green and coastal blue sites are important for wellbeing and supporting different bird communities. City planning authorities and public health professionals should ensure these social and environmental needs are met in developing cities in the Global South.

Quantifying and addressing the prevalence and bias of study designs in the environmental and social sciences

Building trust in science and evidence-based decision-making depends heavily on the credibility of studies and their findings. Researchers employ many different study designs that vary in their risk of bias to evaluate the true effect of interventions or impacts. Here, we empirically quantify, on a large scale, the prevalence of different study designs and the magnitude of bias in their estimates. Randomised designs and controlled observational designs with pre-intervention sampling were used by just 23% of intervention studies in biodiversity conservation, and 36% of intervention studies in social science. We demonstrate, through pairwise within-study comparisons across 49 environmental datasets, that these types of designs usually give less biased estimates than simpler observational designs. We propose a model-based approach to combine study estimates that may suffer from different levels of study design bias, discuss the implications for evidence synthesis, and how to facilitate the use of more credible study designs.

Quantifying the impacts of defaunation on natural forest regeneration in a global meta-analysis

Intact forests provide diverse and irreplaceable ecosystem services that are critical to human well-being, such as carbon storage to mitigate climate change. However, the ecosystem functions that underpin these services are highly dependent on the woody vegetation-animal interactions occurring within forests. While vertebrate defaunation is of growing policy concern, the effects of vertebrate loss on natural forest regeneration have yet to be quantified globally. Here we conduct a meta-analysis to assess the direction and magnitude of defaunation impacts on forests. We demonstrate that real-world defaunation caused by hunting and habitat fragmentation leads to reduced forest regeneration, although manipulation experiments provide contrasting findings. The extirpation of primates and birds cause the greatest declines in forest regeneration, emphasising their key role in maintaining carbon stores, and the need for national and international climate change and conservation strategies to protect forests from defaunation fronts as well as deforestation fronts.

The defaunation of vertebrates may disrupt forest functioning through the loss of plant-animal interactions, but impacts on forests remain unquantified. Here the authors show that seed dispersal is a key interaction and defaunation of primates and birds negatively impacts forest regeneration.

The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

Reconciling timber extraction with biodiversity conservation in tropical forests using reduced-impact logging

Over 20% of the world's tropical forests have been selectively logged, and large expanses are allocated for future timber extraction. Reduced‐impact logging (RIL) is being promoted as best practice forestry that increases sustainability and lowers CO₂ emissions from logging, by reducing collateral damage associated with timber extraction. RIL is also expected to minimize the impacts of selective logging on biodiversity, although this is yet to be thoroughly tested.

We undertake the most comprehensive study to date to investigate the biodiversity impacts of RIL across multiple taxonomic groups. We quantified birds, bats and large mammal assemblage structures, using a before‐after control‐impact (BACI) design across 20 sample sites over a 5‐year period. Faunal surveys utilized point counts, mist nets and line transects and yielded >250 species. We examined assemblage responses to logging, as well as partitions of feeding guild and strata (understorey vs. canopy), and then tested for relationships with logging intensity to assess the primary determinants of community composition.

Community analysis revealed little effect of RIL on overall assemblages, as structure and composition were similar before and after logging, and between logging and control sites. Variation in bird assemblages was explained by natural rates of change over time, and not logging intensity. However, when partitioned by feeding guild and strata, the frugivorous and canopy bird ensembles changed as a result of RIL, although the latter was also associated with change over time. Bats exhibited variable changes post‐logging that were not related to logging, whereas large mammals showed no change at all.

Indicator species analysis and correlations with logging intensities revealed that some species exhibited idiosyncratic responses to RIL, whilst abundance change of most others was associated with time.

Synthesis and applications. Our study demonstrates the relatively benign effect of reduced‐impact logging (RIL) on birds, bats and large mammals in a neotropical forest context, and therefore, we propose that forest managers should improve timber extraction techniques more widely. If RIL is extensively adopted, forestry concessions could represent sizeable and important additions to the global conservation estate – over 4 million km².

Our study demonstrates the relatively benign effect of reduced‐impact logging (RIL) on birds, bats and large mammals in a neotropical forest context, and therefore, we propose that forest managers should improve timber extraction techniques more widely. If RIL is extensively adopted, forestry concessions could represent sizeable and important additions to the global conservation estate – over 4 million km².

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

Aberrant expression of G(1)/S regulators is a frequent event in sporadic pituitary adenomas

Components of the pRb/p16/cyclin D1/CDK4 pathway are frequent targets in numerous tumour types, including those of pituitary origin. However, previous studies of pituitary tumours have examined individual components of this pathway. Therefore, to determine their overall contribution we have simultaneously examined the immunohistochemical status of pRb, p16 and cyclin D1 and analysed the CDK4 gene for a characterized activating mutation. Of the total pituitary tumour cohort (29 clinically non-functioning adenomas and 16 somatotrophinomas) abnormal expression of either pRb, p16 or cyclin D1 was observed in 36 of 45 (80%) tumours and was significantly (P = 0.005) associated with non-functioning tumours (27/29; 93%) compared with somatotrophinomas (9/16, 56%). Loss of either pRb or p16 expression was mutually exclusive in 23 of 45 (51%) tumours, whilst concomitant loss of pRb and p16 expression was observed in five tumours. Cyclin D1 overexpression was observed in 22 of 45 (49%) tumours, however, there was no significant association between overexpression of cyclin D1 and the expression status of either pRb or p16. In addition, no activating mutations within codon 24 of the CDK4 gene were detected. This study provides evidence for the first time that components of the pRb/p16/cyclin D1/CDK4 pathway, either alone or in combination, are frequently deregulated in human pituitary tumours, suggesting that this pathway may be a useful target in drug or gene therapeutic approaches.

Analysis of cyclin D1 (CCND1) allelic imbalance and overexpression in sporadic human pituitary tumors

Cyclin D1 plays an important role in the regulation of cell progression through G1 of the cell cycle and has been demonstrated to have oncogenic properties. Using RFLP-PCR, an A/G polymorphism within the cyclin D1 (CCND1) gene was analyzed in 151 sporadic human pituitary tumors, of which 60 were informative at this locus. Further analysis showed that in 15 of 60 (25%) tumors, there was evidence of allelic imbalance, which is indicative of gene amplification. Allelic imbalance was observed more frequently in invasive tumors (11 of 29 tumors; 38%) than in their noninvasive counterparts (4 of 31 tumors; 13%; P = 0.02). Forty-six of the tumors informative for the polymorphism were available for immunohistochemical analysis. Cyclin D1 expression (nuclear and/or cytoplasmic) was detected in 25 of 46 (54%) tumors. Of these cases, expression of nuclear cyclin D1 was detected in 9 of 46 (20%) tumors, whereas 16 of 46 (35%) tumors showed cyclin D1 staining exclusively confined to the cytoplasm. Neither nuclear staining nor cytoplasmic staining was observed in any of the normal pituitaries or in the negative control. Expression of cyclin D1 was observed in significantly more nonfunctional tumors (18 of 27 tumors; 67%) than in somatotrophinomas (7 of 19 tumors; 37%; P = 0.046). Nuclear cyclin D1 expression was observed more frequently in nonfunctional tumors (8 of 27 tumors; 30%) than in somatotrophinomas (1 of 19 tumors; 5%; P = 0.04). There was no correlation between cyclin D1 expression and tumor grade or between allelic imbalance of CCND1 and cyclin D1 expression. We conclude that amplification of CCND1 occurs in pituitary tumors and that the overexpression of cyclin D1 may be an early event in tumorigenesis. Cyclin D1 overexpression occurring in the absence of CCND1 allelic imbalance suggests that additional mechanisms responsible for deregulated cyclin D1 expression are involved in human pituitary tumorigenesis.

Hypermethylation of the p16/CDKN2A/MTSI gene and loss of protein expression is associated with nonfunctional pituitary adenomas but not somatotrophinomas

The cyclin-dependent kinase inhibitor 2A/multiple tumor suppressor gene 1 (CDKN2A/MTS//p16) plays an important role in the control of progression from G to S-phase of the cell cycle through the inhibition of CDK4-mediated RBI phosphorylation. In this study we investigated 46 nonfunctional pituitary tumors and 21 somatotrophinomas for aberrant methylation of the CpG island contained within the CDKN2A gene as an alternative mechanism of gene silencing. We demonstrate methylation in 32/46 (70%) of nonfunctioning tumors, in contrast to 2/21 (9.5%) somatotrophinomas and 0/15 histologically normal postmortem pituitaries. Methylation in noninvasive and invasive nonfunctional tumors was approximately equal at 15/20 (75%) and 17/26 (65%), respectively. Immunohistochemical analysis showed an absence of CDKN2A protein in 25/32 (78%) methylated nonfunctioning tumors, demonstrating a highly significant overall correlation (P = 0.00007) between hypermethylation of the gene and absence of the p 16 protein. The association between hypermethylation and absence of CDKN2A protein remained when the cohort of nonfunctional tumors was further subdivided into noninvasive 12/15 (80%; P = 0.004) and invasive 13/17 (76%; P = 0.01), suggesting this to be an early event in pituitary tumorigenesis. In contrast, a single invasive methylated somatotrophinoma failed to express the CDKN2A protein. These data show that hypermethylation of the CpG island within exon 1, but not exon 2, of the CDKN2A gene is frequently associated with loss of protein expression in nonfunctional pituitary tumors, but not somatotrophinomas, suggesting different tumorigenic pathways.

Chromosome 13q deletion mapping in pituitary tumors: infrequent loss of the retinoblastoma susceptibility gene (RB1) locus despite loss of RB1 protein product in somatotrophinomas

Two recent studies have described allelic loss of an RB1 intragenic marker on chromosome 13q in aggressive and metastatic pituitary tumors that did not correlate with loss of pRB. The second report also showed that losses were more frequently associated with a more centromeric marker. Because both of these studies suggest the presence of another or other tumor suppressor genes (TSGs) on 13q, we carried out an allelotype analysis encompassing known and recently described TSG loci on 13q, together with immunohistochemical analysis of pRB. We analyzed 82 nonfunctional tumors and 53 somatotrophinomas subdivided into invasive and noninvasive cohorts. A significantly higher frequency of loss, at one or more of 13 markers, was evident in the invasive nonfunctional tumors (54%, 26 of 48) than in their noninvasive counterparts (29%, 10 of 34). An approximately equal frequency of loss was apparent in invasive (28%, 5 of 18) and noninvasive (31%, 11 of 35) somatotrophinomas at one or more markers. In those tumors harboring deletion, loss at two or more markers was more frequent in invasive nonfunctional tumors 65% (17 of 26) compared with 36% (4 of 11) of their noninvasive counterparts. In somatotrophinomas, 40% (2 of 5) of invasive tumors as compared with 64% (7 of 11) of noninvasive tumors had evidence of two or more deletions. In tumors showing loss at two or more loci, the majority showed large deletions; however, loss of the RB1 intragenic marker D13S153 was infrequent. In most cases, loss at individual markers was more frequent in invasive tumors than their noninvasive counterparts. A marker 3 cM telomeric to RB1 (D13S1319) showed the highest frequency of deletion in both invasive cohorts (29% of somatotrophinomas and 24% of nonfunctional tumors). Immunohistochemical analysis of pRB showed frequent loss in somatotrophinomas (27%, 9 of 33) in comparison with 4% (2 of 53) of non-functional tumors. Although loss of pRB did not correlate with loss of an intragenic marker or tumor grade, it was significantly associated with the somatotrophinoma subtype (P = 0.002). These data suggest that chromosome 13q is a frequent target for allelic deletion in pituitary tumors and point to another or other TSG loci in these regions.

Chromosome 9p deletions in invasive and noninvasive nonfunctional pituitary adenomas: the deleted region involves markers outside of the MTS1 and MTS2 genes

We have screened 57 cases of primary, nonfunctional, pituitary adenomas for loss of heterozygosity of markers on chromosome 9p. Using a panel of 11 microsatellite markers, we found hemizygous deletion with at least one of the markers in 18 tumors (31.5%). The frequency of loss was similar in both noninvasive (8 of 26; 31%) and invasive tumors (10 of 31; 32%), suggesting that loss on this chromosome might be an early event in pituitary tumorigenesis. Two discrete areas of loss were punctuated by a region of retention of heterozygosity between the markers D9S171 and IFNA, indicative of homozygous deletion. However, multiplex PCR analysis (MTS1 and MTS2) and the presence of a 3' untranslated region polymorphism in MTS1 suggested that neither of these tumor suppressor genes was homozygously deleted. In 6 of the 18 tumors showing LOH, sufficient DNA was also available for Southern blot analysis and, in all cases, showed retention of MTS1. Cell mixing experiments of tumor cell DNA homozygously deleted for MTS1 with DNA in which neither copy of the gene was deleted only gave rise to a signal at contamination levels greater than 30% and could discriminate homozygous and hemizygous loss. These studies support the recent findings that mechanisms other than hemi- and homozygous deletion are most likely responsible for the loss of MTS1 gene product in pituitary tumors (M. Woloschak et al., Cancer Res., 56: 2493-2486, 1996.). These data show that losses on either side of 9p21-22, both or either of which may be deleted, are involved in pituitary tumorigenesis and provide evidence for distinct suppressor gene loci, in addition to MTS1, on chromosome 9p.